From 96e7dd70e9c279b0e8dd01d5bf52fc6255e54b13 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 24 Dec 2024 17:09:54 -0800 Subject: [PATCH] GRDI update --- web/templates/grdi/schema.json | 14513 ++++++++++++++------------ web/templates/grdi/schema.yaml | 1813 ++-- web/templates/grdi/schema_enums.tsv | 39 +- web/templates/grdi/schema_slots.tsv | 1623 +-- 4 files changed, 10035 insertions(+), 7953 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index 914feff4..c46a8e03 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -338,17 +338,14 @@ "title": "sample_collected_by menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]": { - "text": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" - }, - "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]": { - "text": "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]" - }, "Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]": { "text": "Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]" }, - "Health Canada (HC) [GENEPIO:0100554]": { - "text": "Health Canada (HC) [GENEPIO:0100554]" + "BCCDC Public Health Laboratory [GENEPIO:0102053]": { + "text": "BCCDC Public Health Laboratory [GENEPIO:0102053]" + }, + "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]": { + "text": "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]" }, "Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]": { "text": "Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]" @@ -356,6 +353,21 @@ "Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]": { "text": "Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]" }, + "Health Canada (HC) [GENEPIO:0100554]": { + "text": "Health Canada (HC) [GENEPIO:0100554]" + }, + "Laboratoire de santé publique du Québec (LSPQ) [GENEPIO:0102056]": { + "text": "Laboratoire de santé publique du Québec (LSPQ) [GENEPIO:0102056]" + }, + "Manitoba Cadham Provincial Laboratory [GENEPIO:0102054]": { + "text": "Manitoba Cadham Provincial Laboratory [GENEPIO:0102054]" + }, + "New Brunswick - Vitalité Health Network [GENEPIO:0102055]": { + "text": "New Brunswick - Vitalité Health Network [GENEPIO:0102055]" + }, + "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]": { + "text": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + }, "University of Manitoba (UM) [GENEPIO:0004434]": { "text": "University of Manitoba (UM) [GENEPIO:0004434]" } @@ -6036,6 +6048,12 @@ "NCBI_ANTIBIOGRAM:nalidixic%20acid" ] }, + "neomycin": { + "text": "neomycin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:neomycin" + ] + }, "nitrofurantoin": { "text": "nitrofurantoin", "exact_mappings": [ @@ -6060,6 +6078,12 @@ "NCBI_ANTIBIOGRAM:oxytetracycline" ] }, + "penicillin": { + "text": "penicillin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:penicillin" + ] + }, "piperacillin": { "text": "piperacillin", "exact_mappings": [ @@ -8882,6 +8906,37 @@ } ] }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "GRDI" + ], + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, "sequencing_project_name": { "name": "sequencing_project_name", "description": "The name of the project/initiative/program for which sequencing was performed.", @@ -20152,10 +20207,10 @@ ], "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_resistance_phenotype": { - "name": "nitrofurantoin_resistance_phenotype", + "neomycin_resistance_phenotype": { + "name": "neomycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "nitrofurantoin_resistance_phenotype", + "title": "neomycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -20165,9 +20220,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:resistance_phenotype" - ], "domain_of": [ "GRDI" ], @@ -20181,10 +20233,10 @@ } ] }, - "nitrofurantoin_measurement": { - "name": "nitrofurantoin_measurement", - "description": "The measured value of nitrofurantoin resistance.", - "title": "nitrofurantoin_measurement", + "neomycin_measurement": { + "name": "neomycin_measurement", + "description": "The measured value of neomycin resistance.", + "title": "neomycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -20194,9 +20246,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement" - ], "domain_of": [ "GRDI" ], @@ -20210,10 +20259,10 @@ } ] }, - "nitrofurantoin_measurement_units": { - "name": "nitrofurantoin_measurement_units", + "neomycin_measurement_units": { + "name": "neomycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "nitrofurantoin_measurement_units", + "title": "neomycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -20223,9 +20272,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_units" - ], "domain_of": [ "GRDI" ], @@ -20239,10 +20285,10 @@ } ] }, - "nitrofurantoin_measurement_sign": { - "name": "nitrofurantoin_measurement_sign", + "neomycin_measurement_sign": { + "name": "neomycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "nitrofurantoin_measurement_sign", + "title": "neomycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -20252,9 +20298,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_sign" - ], "domain_of": [ "GRDI" ], @@ -20268,10 +20311,10 @@ } ] }, - "nitrofurantoin_laboratory_typing_method": { - "name": "nitrofurantoin_laboratory_typing_method", + "neomycin_laboratory_typing_method": { + "name": "neomycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "nitrofurantoin_laboratory_typing_method", + "title": "neomycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -20281,9 +20324,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_method" - ], "domain_of": [ "GRDI" ], @@ -20296,10 +20336,10 @@ } ] }, - "nitrofurantoin_laboratory_typing_platform": { - "name": "nitrofurantoin_laboratory_typing_platform", + "neomycin_laboratory_typing_platform": { + "name": "neomycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "nitrofurantoin_laboratory_typing_platform", + "title": "neomycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -20309,9 +20349,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_platform" - ], "domain_of": [ "GRDI" ], @@ -20324,10 +20361,10 @@ } ] }, - "nitrofurantoin_laboratory_typing_platform_version": { - "name": "nitrofurantoin_laboratory_typing_platform_version", + "neomycin_laboratory_typing_platform_version": { + "name": "neomycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "nitrofurantoin_laboratory_typing_platform_version", + "title": "neomycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -20342,10 +20379,10 @@ ], "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_vendor_name": { - "name": "nitrofurantoin_vendor_name", + "neomycin_vendor_name": { + "name": "neomycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "nitrofurantoin_vendor_name", + "title": "neomycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -20355,9 +20392,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:vendor" - ], "domain_of": [ "GRDI" ], @@ -20370,10 +20404,10 @@ } ] }, - "nitrofurantoin_testing_standard": { - "name": "nitrofurantoin_testing_standard", + "neomycin_testing_standard": { + "name": "neomycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "nitrofurantoin_testing_standard", + "title": "neomycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -20383,9 +20417,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:testing_standard" - ], "domain_of": [ "GRDI" ], @@ -20399,10 +20430,10 @@ } ] }, - "nitrofurantoin_testing_standard_version": { - "name": "nitrofurantoin_testing_standard_version", + "neomycin_testing_standard_version": { + "name": "neomycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "nitrofurantoin_testing_standard_version", + "title": "neomycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -20417,10 +20448,10 @@ ], "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_testing_standard_details": { - "name": "nitrofurantoin_testing_standard_details", + "neomycin_testing_standard_details": { + "name": "neomycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "nitrofurantoin_testing_standard_details", + "title": "neomycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -20438,10 +20469,10 @@ ], "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_susceptible_breakpoint": { - "name": "nitrofurantoin_susceptible_breakpoint", + "neomycin_susceptible_breakpoint": { + "name": "neomycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "nitrofurantoin_susceptible_breakpoint", + "title": "neomycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -20456,10 +20487,10 @@ ], "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_intermediate_breakpoint": { - "name": "nitrofurantoin_intermediate_breakpoint", + "neomycin_intermediate_breakpoint": { + "name": "neomycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "nitrofurantoin_intermediate_breakpoint", + "title": "neomycin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -20471,10 +20502,10 @@ ], "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_resistant_breakpoint": { - "name": "nitrofurantoin_resistant_breakpoint", + "neomycin_resistant_breakpoint": { + "name": "neomycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "nitrofurantoin_resistant_breakpoint", + "title": "neomycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -20489,10 +20520,10 @@ ], "range": "WhitespaceMinimizedString" }, - "norfloxacin_resistance_phenotype": { - "name": "norfloxacin_resistance_phenotype", + "nitrofurantoin_resistance_phenotype": { + "name": "nitrofurantoin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "norfloxacin_resistance_phenotype", + "title": "nitrofurantoin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -20518,10 +20549,10 @@ } ] }, - "norfloxacin_measurement": { - "name": "norfloxacin_measurement", - "description": "The measured value of norfloxacin resistance.", - "title": "norfloxacin_measurement", + "nitrofurantoin_measurement": { + "name": "nitrofurantoin_measurement", + "description": "The measured value of nitrofurantoin resistance.", + "title": "nitrofurantoin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -20547,10 +20578,10 @@ } ] }, - "norfloxacin_measurement_units": { - "name": "norfloxacin_measurement_units", + "nitrofurantoin_measurement_units": { + "name": "nitrofurantoin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "norfloxacin_measurement_units", + "title": "nitrofurantoin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -20576,10 +20607,10 @@ } ] }, - "norfloxacin_measurement_sign": { - "name": "norfloxacin_measurement_sign", + "nitrofurantoin_measurement_sign": { + "name": "nitrofurantoin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "norfloxacin_measurement_sign", + "title": "nitrofurantoin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -20605,10 +20636,10 @@ } ] }, - "norfloxacin_laboratory_typing_method": { - "name": "norfloxacin_laboratory_typing_method", + "nitrofurantoin_laboratory_typing_method": { + "name": "nitrofurantoin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "norfloxacin_laboratory_typing_method", + "title": "nitrofurantoin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -20633,10 +20664,10 @@ } ] }, - "norfloxacin_laboratory_typing_platform": { - "name": "norfloxacin_laboratory_typing_platform", + "nitrofurantoin_laboratory_typing_platform": { + "name": "nitrofurantoin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "norfloxacin_laboratory_typing_platform", + "title": "nitrofurantoin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -20661,10 +20692,10 @@ } ] }, - "norfloxacin_laboratory_typing_platform_version": { - "name": "norfloxacin_laboratory_typing_platform_version", + "nitrofurantoin_laboratory_typing_platform_version": { + "name": "nitrofurantoin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "norfloxacin_laboratory_typing_platform_version", + "title": "nitrofurantoin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -20679,10 +20710,10 @@ ], "range": "WhitespaceMinimizedString" }, - "norfloxacin_vendor_name": { - "name": "norfloxacin_vendor_name", + "nitrofurantoin_vendor_name": { + "name": "nitrofurantoin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "norfloxacin_vendor_name", + "title": "nitrofurantoin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -20707,10 +20738,10 @@ } ] }, - "norfloxacin_testing_standard": { - "name": "norfloxacin_testing_standard", + "nitrofurantoin_testing_standard": { + "name": "nitrofurantoin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "norfloxacin_testing_standard", + "title": "nitrofurantoin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -20736,10 +20767,10 @@ } ] }, - "norfloxacin_testing_standard_version": { - "name": "norfloxacin_testing_standard_version", + "nitrofurantoin_testing_standard_version": { + "name": "nitrofurantoin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "norfloxacin_testing_standard_version", + "title": "nitrofurantoin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -20754,10 +20785,10 @@ ], "range": "WhitespaceMinimizedString" }, - "norfloxacin_testing_standard_details": { - "name": "norfloxacin_testing_standard_details", + "nitrofurantoin_testing_standard_details": { + "name": "nitrofurantoin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "norfloxacin_testing_standard_details", + "title": "nitrofurantoin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -20775,10 +20806,10 @@ ], "range": "WhitespaceMinimizedString" }, - "norfloxacin_susceptible_breakpoint": { - "name": "norfloxacin_susceptible_breakpoint", + "nitrofurantoin_susceptible_breakpoint": { + "name": "nitrofurantoin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "norfloxacin_susceptible_breakpoint", + "title": "nitrofurantoin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -20793,10 +20824,10 @@ ], "range": "WhitespaceMinimizedString" }, - "norfloxacin_intermediate_breakpoint": { - "name": "norfloxacin_intermediate_breakpoint", + "nitrofurantoin_intermediate_breakpoint": { + "name": "nitrofurantoin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "norfloxacin_intermediate_breakpoint", + "title": "nitrofurantoin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -20808,10 +20839,10 @@ ], "range": "WhitespaceMinimizedString" }, - "norfloxacin_resistant_breakpoint": { - "name": "norfloxacin_resistant_breakpoint", + "nitrofurantoin_resistant_breakpoint": { + "name": "nitrofurantoin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "norfloxacin_resistant_breakpoint", + "title": "nitrofurantoin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -20826,10 +20857,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxolinicacid_resistance_phenotype": { - "name": "oxolinicacid_resistance_phenotype", + "norfloxacin_resistance_phenotype": { + "name": "norfloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "oxolinic-acid_resistance_phenotype", + "title": "norfloxacin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -20855,10 +20886,10 @@ } ] }, - "oxolinicacid_measurement": { - "name": "oxolinicacid_measurement", - "description": "The measured value of oxolinic-acid resistance.", - "title": "oxolinic-acid_measurement", + "norfloxacin_measurement": { + "name": "norfloxacin_measurement", + "description": "The measured value of norfloxacin resistance.", + "title": "norfloxacin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -20884,10 +20915,10 @@ } ] }, - "oxolinicacid_measurement_units": { - "name": "oxolinicacid_measurement_units", + "norfloxacin_measurement_units": { + "name": "norfloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "oxolinic-acid_measurement_units", + "title": "norfloxacin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -20913,10 +20944,10 @@ } ] }, - "oxolinicacid_measurement_sign": { - "name": "oxolinicacid_measurement_sign", + "norfloxacin_measurement_sign": { + "name": "norfloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "oxolinic-acid_measurement_sign", + "title": "norfloxacin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -20942,10 +20973,10 @@ } ] }, - "oxolinicacid_laboratory_typing_method": { - "name": "oxolinicacid_laboratory_typing_method", + "norfloxacin_laboratory_typing_method": { + "name": "norfloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "oxolinic-acid_laboratory_typing_method", + "title": "norfloxacin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -20970,10 +21001,10 @@ } ] }, - "oxolinicacid_laboratory_typing_platform": { - "name": "oxolinicacid_laboratory_typing_platform", + "norfloxacin_laboratory_typing_platform": { + "name": "norfloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "oxolinic-acid_laboratory_typing_platform", + "title": "norfloxacin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -20998,10 +21029,10 @@ } ] }, - "oxolinicacid_laboratory_typing_platform_version": { - "name": "oxolinicacid_laboratory_typing_platform_version", + "norfloxacin_laboratory_typing_platform_version": { + "name": "norfloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "oxolinic-acid_laboratory_typing_platform_version", + "title": "norfloxacin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -21016,10 +21047,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxolinicacid_vendor_name": { - "name": "oxolinicacid_vendor_name", + "norfloxacin_vendor_name": { + "name": "norfloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "oxolinic-acid_vendor_name", + "title": "norfloxacin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -21044,10 +21075,10 @@ } ] }, - "oxolinicacid_testing_standard": { - "name": "oxolinicacid_testing_standard", + "norfloxacin_testing_standard": { + "name": "norfloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "oxolinic-acid_testing_standard", + "title": "norfloxacin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -21073,10 +21104,10 @@ } ] }, - "oxolinicacid_testing_standard_version": { - "name": "oxolinicacid_testing_standard_version", + "norfloxacin_testing_standard_version": { + "name": "norfloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "oxolinic-acid_testing_standard_version", + "title": "norfloxacin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -21091,10 +21122,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxolinicacid_testing_standard_details": { - "name": "oxolinicacid_testing_standard_details", + "norfloxacin_testing_standard_details": { + "name": "norfloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "oxolinic-acid_testing_standard_details", + "title": "norfloxacin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -21112,10 +21143,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxolinicacid_susceptible_breakpoint": { - "name": "oxolinicacid_susceptible_breakpoint", + "norfloxacin_susceptible_breakpoint": { + "name": "norfloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "oxolinic-acid_susceptible_breakpoint", + "title": "norfloxacin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -21130,10 +21161,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxolinicacid_intermediate_breakpoint": { - "name": "oxolinicacid_intermediate_breakpoint", + "norfloxacin_intermediate_breakpoint": { + "name": "norfloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "oxolinic-acid_intermediate_breakpoint", + "title": "norfloxacin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -21145,10 +21176,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxolinicacid_resistant_breakpoint": { - "name": "oxolinicacid_resistant_breakpoint", + "norfloxacin_resistant_breakpoint": { + "name": "norfloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "oxolinic-acid_resistant_breakpoint", + "title": "norfloxacin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -21163,10 +21194,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxytetracycline_resistance_phenotype": { - "name": "oxytetracycline_resistance_phenotype", + "oxolinicacid_resistance_phenotype": { + "name": "oxolinicacid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "oxytetracycline_resistance_phenotype", + "title": "oxolinic-acid_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -21192,10 +21223,10 @@ } ] }, - "oxytetracycline_measurement": { - "name": "oxytetracycline_measurement", - "description": "The measured value of oxytetracycline resistance.", - "title": "oxytetracycline_measurement", + "oxolinicacid_measurement": { + "name": "oxolinicacid_measurement", + "description": "The measured value of oxolinic-acid resistance.", + "title": "oxolinic-acid_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -21221,10 +21252,10 @@ } ] }, - "oxytetracycline_measurement_units": { - "name": "oxytetracycline_measurement_units", + "oxolinicacid_measurement_units": { + "name": "oxolinicacid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "oxytetracycline_measurement_units", + "title": "oxolinic-acid_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -21250,10 +21281,10 @@ } ] }, - "oxytetracycline_measurement_sign": { - "name": "oxytetracycline_measurement_sign", + "oxolinicacid_measurement_sign": { + "name": "oxolinicacid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "oxytetracycline_measurement_sign", + "title": "oxolinic-acid_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -21279,10 +21310,10 @@ } ] }, - "oxytetracycline_laboratory_typing_method": { - "name": "oxytetracycline_laboratory_typing_method", + "oxolinicacid_laboratory_typing_method": { + "name": "oxolinicacid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "oxytetracycline_laboratory_typing_method", + "title": "oxolinic-acid_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -21307,10 +21338,10 @@ } ] }, - "oxytetracycline_laboratory_typing_platform": { - "name": "oxytetracycline_laboratory_typing_platform", + "oxolinicacid_laboratory_typing_platform": { + "name": "oxolinicacid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "oxytetracycline_laboratory_typing_platform", + "title": "oxolinic-acid_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -21335,10 +21366,10 @@ } ] }, - "oxytetracycline_laboratory_typing_platform_version": { - "name": "oxytetracycline_laboratory_typing_platform_version", + "oxolinicacid_laboratory_typing_platform_version": { + "name": "oxolinicacid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "oxytetracycline_laboratory_typing_platform_version", + "title": "oxolinic-acid_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -21353,10 +21384,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxytetracycline_vendor_name": { - "name": "oxytetracycline_vendor_name", + "oxolinicacid_vendor_name": { + "name": "oxolinicacid_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "oxytetracycline_vendor_name", + "title": "oxolinic-acid_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -21381,10 +21412,10 @@ } ] }, - "oxytetracycline_testing_standard": { - "name": "oxytetracycline_testing_standard", + "oxolinicacid_testing_standard": { + "name": "oxolinicacid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "oxytetracycline_testing_standard", + "title": "oxolinic-acid_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -21410,10 +21441,10 @@ } ] }, - "oxytetracycline_testing_standard_version": { - "name": "oxytetracycline_testing_standard_version", + "oxolinicacid_testing_standard_version": { + "name": "oxolinicacid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "oxytetracycline_testing_standard_version", + "title": "oxolinic-acid_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -21428,10 +21459,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxytetracycline_testing_standard_details": { - "name": "oxytetracycline_testing_standard_details", + "oxolinicacid_testing_standard_details": { + "name": "oxolinicacid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "oxytetracycline_testing_standard_details", + "title": "oxolinic-acid_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -21449,10 +21480,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxytetracycline_susceptible_breakpoint": { - "name": "oxytetracycline_susceptible_breakpoint", + "oxolinicacid_susceptible_breakpoint": { + "name": "oxolinicacid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "oxytetracycline_susceptible_breakpoint", + "title": "oxolinic-acid_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -21467,10 +21498,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxytetracycline_intermediate_breakpoint": { - "name": "oxytetracycline_intermediate_breakpoint", + "oxolinicacid_intermediate_breakpoint": { + "name": "oxolinicacid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "oxytetracycline_intermediate_breakpoint", + "title": "oxolinic-acid_intermediate_breakpoint", "examples": [ { "value": "16" @@ -21482,10 +21513,10 @@ ], "range": "WhitespaceMinimizedString" }, - "oxytetracycline_resistant_breakpoint": { - "name": "oxytetracycline_resistant_breakpoint", + "oxolinicacid_resistant_breakpoint": { + "name": "oxolinicacid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "oxytetracycline_resistant_breakpoint", + "title": "oxolinic-acid_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -21500,10 +21531,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillin_resistance_phenotype": { - "name": "piperacillin_resistance_phenotype", + "oxytetracycline_resistance_phenotype": { + "name": "oxytetracycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "piperacillin_resistance_phenotype", + "title": "oxytetracycline_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -21529,10 +21560,10 @@ } ] }, - "piperacillin_measurement": { - "name": "piperacillin_measurement", - "description": "The measured value of piperacillin resistance.", - "title": "piperacillin_measurement", + "oxytetracycline_measurement": { + "name": "oxytetracycline_measurement", + "description": "The measured value of oxytetracycline resistance.", + "title": "oxytetracycline_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -21558,10 +21589,10 @@ } ] }, - "piperacillin_measurement_units": { - "name": "piperacillin_measurement_units", + "oxytetracycline_measurement_units": { + "name": "oxytetracycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "piperacillin_measurement_units", + "title": "oxytetracycline_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -21587,10 +21618,10 @@ } ] }, - "piperacillin_measurement_sign": { - "name": "piperacillin_measurement_sign", + "oxytetracycline_measurement_sign": { + "name": "oxytetracycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "piperacillin_measurement_sign", + "title": "oxytetracycline_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -21616,10 +21647,10 @@ } ] }, - "piperacillin_laboratory_typing_method": { - "name": "piperacillin_laboratory_typing_method", + "oxytetracycline_laboratory_typing_method": { + "name": "oxytetracycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "piperacillin_laboratory_typing_method", + "title": "oxytetracycline_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -21644,10 +21675,10 @@ } ] }, - "piperacillin_laboratory_typing_platform": { - "name": "piperacillin_laboratory_typing_platform", + "oxytetracycline_laboratory_typing_platform": { + "name": "oxytetracycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "piperacillin_laboratory_typing_platform", + "title": "oxytetracycline_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -21672,10 +21703,10 @@ } ] }, - "piperacillin_laboratory_typing_platform_version": { - "name": "piperacillin_laboratory_typing_platform_version", + "oxytetracycline_laboratory_typing_platform_version": { + "name": "oxytetracycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "piperacillin_laboratory_typing_platform_version", + "title": "oxytetracycline_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -21690,10 +21721,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillin_vendor_name": { - "name": "piperacillin_vendor_name", + "oxytetracycline_vendor_name": { + "name": "oxytetracycline_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "piperacillin_vendor_name", + "title": "oxytetracycline_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -21718,10 +21749,10 @@ } ] }, - "piperacillin_testing_standard": { - "name": "piperacillin_testing_standard", + "oxytetracycline_testing_standard": { + "name": "oxytetracycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "piperacillin_testing_standard", + "title": "oxytetracycline_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -21747,10 +21778,10 @@ } ] }, - "piperacillin_testing_standard_version": { - "name": "piperacillin_testing_standard_version", + "oxytetracycline_testing_standard_version": { + "name": "oxytetracycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "piperacillin_testing_standard_version", + "title": "oxytetracycline_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -21765,10 +21796,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillin_testing_standard_details": { - "name": "piperacillin_testing_standard_details", + "oxytetracycline_testing_standard_details": { + "name": "oxytetracycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "piperacillin_testing_standard_details", + "title": "oxytetracycline_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -21786,10 +21817,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillin_susceptible_breakpoint": { - "name": "piperacillin_susceptible_breakpoint", + "oxytetracycline_susceptible_breakpoint": { + "name": "oxytetracycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "piperacillin_susceptible_breakpoint", + "title": "oxytetracycline_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -21804,10 +21835,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillin_intermediate_breakpoint": { - "name": "piperacillin_intermediate_breakpoint", + "oxytetracycline_intermediate_breakpoint": { + "name": "oxytetracycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "piperacillin_intermediate_breakpoint", + "title": "oxytetracycline_intermediate_breakpoint", "examples": [ { "value": "16" @@ -21819,10 +21850,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillin_resistant_breakpoint": { - "name": "piperacillin_resistant_breakpoint", + "oxytetracycline_resistant_breakpoint": { + "name": "oxytetracycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "piperacillin_resistant_breakpoint", + "title": "oxytetracycline_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -21837,10 +21868,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillintazobactam_resistance_phenotype": { - "name": "piperacillintazobactam_resistance_phenotype", + "penicillin_resistance_phenotype": { + "name": "penicillin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "piperacillin-tazobactam_resistance_phenotype", + "title": "penicillin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -21850,9 +21881,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:resistance_phenotype" - ], "domain_of": [ "GRDI" ], @@ -21866,10 +21894,10 @@ } ] }, - "piperacillintazobactam_measurement": { - "name": "piperacillintazobactam_measurement", - "description": "The measured value of piperacillin-tazobactam resistance.", - "title": "piperacillin-tazobactam_measurement", + "penicillin_measurement": { + "name": "penicillin_measurement", + "description": "The measured value of penicillin resistance.", + "title": "penicillin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -21879,9 +21907,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement" - ], "domain_of": [ "GRDI" ], @@ -21895,10 +21920,10 @@ } ] }, - "piperacillintazobactam_measurement_units": { - "name": "piperacillintazobactam_measurement_units", + "penicillin_measurement_units": { + "name": "penicillin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "piperacillin-tazobactam_measurement_units", + "title": "penicillin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -21908,9 +21933,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_units" - ], "domain_of": [ "GRDI" ], @@ -21924,10 +21946,10 @@ } ] }, - "piperacillintazobactam_measurement_sign": { - "name": "piperacillintazobactam_measurement_sign", + "penicillin_measurement_sign": { + "name": "penicillin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "piperacillin-tazobactam_measurement_sign", + "title": "penicillin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -21937,9 +21959,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_sign" - ], "domain_of": [ "GRDI" ], @@ -21953,10 +21972,10 @@ } ] }, - "piperacillintazobactam_laboratory_typing_method": { - "name": "piperacillintazobactam_laboratory_typing_method", + "penicillin_laboratory_typing_method": { + "name": "penicillin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "piperacillin-tazobactam_laboratory_typing_method", + "title": "penicillin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -21966,9 +21985,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_method" - ], "domain_of": [ "GRDI" ], @@ -21981,10 +21997,10 @@ } ] }, - "piperacillintazobactam_laboratory_typing_platform": { - "name": "piperacillintazobactam_laboratory_typing_platform", + "penicillin_laboratory_typing_platform": { + "name": "penicillin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "piperacillin-tazobactam_laboratory_typing_platform", + "title": "penicillin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -21994,9 +22010,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_platform" - ], "domain_of": [ "GRDI" ], @@ -22009,10 +22022,10 @@ } ] }, - "piperacillintazobactam_laboratory_typing_platform_version": { - "name": "piperacillintazobactam_laboratory_typing_platform_version", + "penicillin_laboratory_typing_platform_version": { + "name": "penicillin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "piperacillin-tazobactam_laboratory_typing_platform_version", + "title": "penicillin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -22027,10 +22040,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillintazobactam_vendor_name": { - "name": "piperacillintazobactam_vendor_name", + "penicillin_vendor_name": { + "name": "penicillin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "piperacillin-tazobactam_vendor_name", + "title": "penicillin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -22040,9 +22053,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:vendor" - ], "domain_of": [ "GRDI" ], @@ -22055,10 +22065,10 @@ } ] }, - "piperacillintazobactam_testing_standard": { - "name": "piperacillintazobactam_testing_standard", + "penicillin_testing_standard": { + "name": "penicillin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "piperacillin-tazobactam_testing_standard", + "title": "penicillin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -22068,9 +22078,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:testing_standard" - ], "domain_of": [ "GRDI" ], @@ -22084,10 +22091,10 @@ } ] }, - "piperacillintazobactam_testing_standard_version": { - "name": "piperacillintazobactam_testing_standard_version", + "penicillin_testing_standard_version": { + "name": "penicillin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "piperacillin-tazobactam_testing_standard_version", + "title": "penicillin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -22102,10 +22109,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillintazobactam_testing_standard_details": { - "name": "piperacillintazobactam_testing_standard_details", + "penicillin_testing_standard_details": { + "name": "penicillin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "piperacillin-tazobactam_testing_standard_details", + "title": "penicillin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -22123,10 +22130,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillintazobactam_susceptible_breakpoint": { - "name": "piperacillintazobactam_susceptible_breakpoint", + "penicillin_susceptible_breakpoint": { + "name": "penicillin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "piperacillin-tazobactam_susceptible_breakpoint", + "title": "penicillin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -22141,10 +22148,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillintazobactam_intermediate_breakpoint": { - "name": "piperacillintazobactam_intermediate_breakpoint", + "penicillin_intermediate_breakpoint": { + "name": "penicillin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "piperacillin-tazobactam_intermediate_breakpoint", + "title": "penicillin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -22156,10 +22163,10 @@ ], "range": "WhitespaceMinimizedString" }, - "piperacillintazobactam_resistant_breakpoint": { - "name": "piperacillintazobactam_resistant_breakpoint", + "penicillin_resistant_breakpoint": { + "name": "penicillin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "piperacillin-tazobactam_resistant_breakpoint", + "title": "penicillin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -22174,10 +22181,10 @@ ], "range": "WhitespaceMinimizedString" }, - "polymyxinb_resistance_phenotype": { - "name": "polymyxinb_resistance_phenotype", + "piperacillin_resistance_phenotype": { + "name": "piperacillin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "polymyxin-b_resistance_phenotype", + "title": "piperacillin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -22203,10 +22210,10 @@ } ] }, - "polymyxinb_measurement": { - "name": "polymyxinb_measurement", - "description": "The measured value of polymyxin B resistance.", - "title": "polymyxin-b_measurement", + "piperacillin_measurement": { + "name": "piperacillin_measurement", + "description": "The measured value of piperacillin resistance.", + "title": "piperacillin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -22232,10 +22239,10 @@ } ] }, - "polymyxinb_measurement_units": { - "name": "polymyxinb_measurement_units", + "piperacillin_measurement_units": { + "name": "piperacillin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "polymyxin-b_measurement_units", + "title": "piperacillin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -22261,10 +22268,10 @@ } ] }, - "polymyxinb_measurement_sign": { - "name": "polymyxinb_measurement_sign", + "piperacillin_measurement_sign": { + "name": "piperacillin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "polymyxin-b_measurement_sign", + "title": "piperacillin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -22290,10 +22297,10 @@ } ] }, - "polymyxinb_laboratory_typing_method": { - "name": "polymyxinb_laboratory_typing_method", + "piperacillin_laboratory_typing_method": { + "name": "piperacillin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "polymyxin-b_laboratory_typing_method", + "title": "piperacillin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -22318,10 +22325,10 @@ } ] }, - "polymyxinb_laboratory_typing_platform": { - "name": "polymyxinb_laboratory_typing_platform", + "piperacillin_laboratory_typing_platform": { + "name": "piperacillin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "polymyxin-b_laboratory_typing_platform", + "title": "piperacillin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -22346,10 +22353,10 @@ } ] }, - "polymyxinb_laboratory_typing_platform_version": { - "name": "polymyxinb_laboratory_typing_platform_version", + "piperacillin_laboratory_typing_platform_version": { + "name": "piperacillin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "polymyxin-b_laboratory_typing_platform_version", + "title": "piperacillin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -22364,10 +22371,10 @@ ], "range": "WhitespaceMinimizedString" }, - "polymyxinb_vendor_name": { - "name": "polymyxinb_vendor_name", + "piperacillin_vendor_name": { + "name": "piperacillin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "polymyxin-b_vendor_name", + "title": "piperacillin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -22392,10 +22399,10 @@ } ] }, - "polymyxinb_testing_standard": { - "name": "polymyxinb_testing_standard", + "piperacillin_testing_standard": { + "name": "piperacillin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "polymyxin-b_testing_standard", + "title": "piperacillin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -22421,10 +22428,10 @@ } ] }, - "polymyxinb_testing_standard_version": { - "name": "polymyxinb_testing_standard_version", + "piperacillin_testing_standard_version": { + "name": "piperacillin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "polymyxin-b_testing_standard_version", + "title": "piperacillin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -22439,10 +22446,10 @@ ], "range": "WhitespaceMinimizedString" }, - "polymyxinb_testing_standard_details": { - "name": "polymyxinb_testing_standard_details", + "piperacillin_testing_standard_details": { + "name": "piperacillin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "polymyxin-b_testing_standard_details", + "title": "piperacillin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -22460,10 +22467,10 @@ ], "range": "WhitespaceMinimizedString" }, - "polymyxinb_susceptible_breakpoint": { - "name": "polymyxinb_susceptible_breakpoint", + "piperacillin_susceptible_breakpoint": { + "name": "piperacillin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "polymyxin-b_susceptible_breakpoint", + "title": "piperacillin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -22478,10 +22485,10 @@ ], "range": "WhitespaceMinimizedString" }, - "polymyxinb_intermediate_breakpoint": { - "name": "polymyxinb_intermediate_breakpoint", + "piperacillin_intermediate_breakpoint": { + "name": "piperacillin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "polymyxin-b_intermediate_breakpoint", + "title": "piperacillin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -22493,10 +22500,10 @@ ], "range": "WhitespaceMinimizedString" }, - "polymyxinb_resistant_breakpoint": { - "name": "polymyxinb_resistant_breakpoint", + "piperacillin_resistant_breakpoint": { + "name": "piperacillin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "polymyxin-b_resistant_breakpoint", + "title": "piperacillin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -22511,10 +22518,10 @@ ], "range": "WhitespaceMinimizedString" }, - "quinupristindalfopristin_resistance_phenotype": { - "name": "quinupristindalfopristin_resistance_phenotype", + "piperacillintazobactam_resistance_phenotype": { + "name": "piperacillintazobactam_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "quinupristin-dalfopristin_resistance_phenotype", + "title": "piperacillin-tazobactam_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -22540,10 +22547,10 @@ } ] }, - "quinupristindalfopristin_measurement": { - "name": "quinupristindalfopristin_measurement", - "description": "The measured value of quinupristin-dalfopristin resistance.", - "title": "quinupristin-dalfopristin_measurement", + "piperacillintazobactam_measurement": { + "name": "piperacillintazobactam_measurement", + "description": "The measured value of piperacillin-tazobactam resistance.", + "title": "piperacillin-tazobactam_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -22569,10 +22576,10 @@ } ] }, - "quinupristindalfopristin_measurement_units": { - "name": "quinupristindalfopristin_measurement_units", + "piperacillintazobactam_measurement_units": { + "name": "piperacillintazobactam_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "quinupristin-dalfopristin_measurement_units", + "title": "piperacillin-tazobactam_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -22598,10 +22605,10 @@ } ] }, - "quinupristindalfopristin_measurement_sign": { - "name": "quinupristindalfopristin_measurement_sign", + "piperacillintazobactam_measurement_sign": { + "name": "piperacillintazobactam_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "quinupristin-dalfopristin_measurement_sign", + "title": "piperacillin-tazobactam_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -22627,10 +22634,10 @@ } ] }, - "quinupristindalfopristin_laboratory_typing_method": { - "name": "quinupristindalfopristin_laboratory_typing_method", + "piperacillintazobactam_laboratory_typing_method": { + "name": "piperacillintazobactam_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "quinupristin-dalfopristin_laboratory_typing_method", + "title": "piperacillin-tazobactam_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -22655,10 +22662,10 @@ } ] }, - "quinupristindalfopristin_laboratory_typing_platform": { - "name": "quinupristindalfopristin_laboratory_typing_platform", + "piperacillintazobactam_laboratory_typing_platform": { + "name": "piperacillintazobactam_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "quinupristin-dalfopristin_laboratory_typing_platform", + "title": "piperacillin-tazobactam_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -22683,10 +22690,10 @@ } ] }, - "quinupristindalfopristin_laboratory_typing_platform_version": { - "name": "quinupristindalfopristin_laboratory_typing_platform_version", + "piperacillintazobactam_laboratory_typing_platform_version": { + "name": "piperacillintazobactam_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "quinupristin-dalfopristin_laboratory_typing_platform_version", + "title": "piperacillin-tazobactam_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -22701,10 +22708,10 @@ ], "range": "WhitespaceMinimizedString" }, - "quinupristindalfopristin_vendor_name": { - "name": "quinupristindalfopristin_vendor_name", + "piperacillintazobactam_vendor_name": { + "name": "piperacillintazobactam_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "quinupristin-dalfopristin_vendor_name", + "title": "piperacillin-tazobactam_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -22729,10 +22736,10 @@ } ] }, - "quinupristindalfopristin_testing_standard": { - "name": "quinupristindalfopristin_testing_standard", + "piperacillintazobactam_testing_standard": { + "name": "piperacillintazobactam_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "quinupristin-dalfopristin_testing_standard", + "title": "piperacillin-tazobactam_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -22758,10 +22765,10 @@ } ] }, - "quinupristindalfopristin_testing_standard_version": { - "name": "quinupristindalfopristin_testing_standard_version", + "piperacillintazobactam_testing_standard_version": { + "name": "piperacillintazobactam_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "quinupristin-dalfopristin_testing_standard_version", + "title": "piperacillin-tazobactam_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -22776,10 +22783,10 @@ ], "range": "WhitespaceMinimizedString" }, - "quinupristindalfopristin_testing_standard_details": { - "name": "quinupristindalfopristin_testing_standard_details", + "piperacillintazobactam_testing_standard_details": { + "name": "piperacillintazobactam_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "quinupristin-dalfopristin_testing_standard_details", + "title": "piperacillin-tazobactam_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -22797,10 +22804,10 @@ ], "range": "WhitespaceMinimizedString" }, - "quinupristindalfopristin_susceptible_breakpoint": { - "name": "quinupristindalfopristin_susceptible_breakpoint", + "piperacillintazobactam_susceptible_breakpoint": { + "name": "piperacillintazobactam_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "quinupristin-dalfopristin_susceptible_breakpoint", + "title": "piperacillin-tazobactam_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -22815,10 +22822,10 @@ ], "range": "WhitespaceMinimizedString" }, - "quinupristindalfopristin_intermediate_breakpoint": { - "name": "quinupristindalfopristin_intermediate_breakpoint", + "piperacillintazobactam_intermediate_breakpoint": { + "name": "piperacillintazobactam_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "quinupristin-dalfopristin_intermediate_breakpoint", + "title": "piperacillin-tazobactam_intermediate_breakpoint", "examples": [ { "value": "16" @@ -22830,10 +22837,10 @@ ], "range": "WhitespaceMinimizedString" }, - "quinupristindalfopristin_resistant_breakpoint": { - "name": "quinupristindalfopristin_resistant_breakpoint", + "piperacillintazobactam_resistant_breakpoint": { + "name": "piperacillintazobactam_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "quinupristin-dalfopristin_resistant_breakpoint", + "title": "piperacillin-tazobactam_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -22848,10 +22855,10 @@ ], "range": "WhitespaceMinimizedString" }, - "streptomycin_resistance_phenotype": { - "name": "streptomycin_resistance_phenotype", + "polymyxinb_resistance_phenotype": { + "name": "polymyxinb_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "streptomycin_resistance_phenotype", + "title": "polymyxin-b_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -22877,10 +22884,10 @@ } ] }, - "streptomycin_measurement": { - "name": "streptomycin_measurement", - "description": "The measured value of streptomycin resistance.", - "title": "streptomycin_measurement", + "polymyxinb_measurement": { + "name": "polymyxinb_measurement", + "description": "The measured value of polymyxin B resistance.", + "title": "polymyxin-b_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -22906,10 +22913,10 @@ } ] }, - "streptomycin_measurement_units": { - "name": "streptomycin_measurement_units", + "polymyxinb_measurement_units": { + "name": "polymyxinb_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "streptomycin_measurement_units", + "title": "polymyxin-b_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -22935,10 +22942,10 @@ } ] }, - "streptomycin_measurement_sign": { - "name": "streptomycin_measurement_sign", + "polymyxinb_measurement_sign": { + "name": "polymyxinb_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "streptomycin_measurement_sign", + "title": "polymyxin-b_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -22964,10 +22971,10 @@ } ] }, - "streptomycin_laboratory_typing_method": { - "name": "streptomycin_laboratory_typing_method", + "polymyxinb_laboratory_typing_method": { + "name": "polymyxinb_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "streptomycin_laboratory_typing_method", + "title": "polymyxin-b_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -22992,10 +22999,10 @@ } ] }, - "streptomycin_laboratory_typing_platform": { - "name": "streptomycin_laboratory_typing_platform", + "polymyxinb_laboratory_typing_platform": { + "name": "polymyxinb_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "streptomycin_laboratory_typing_platform", + "title": "polymyxin-b_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -23020,10 +23027,10 @@ } ] }, - "streptomycin_laboratory_typing_platform_version": { - "name": "streptomycin_laboratory_typing_platform_version", + "polymyxinb_laboratory_typing_platform_version": { + "name": "polymyxinb_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "streptomycin_laboratory_typing_platform_version", + "title": "polymyxin-b_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -23038,10 +23045,10 @@ ], "range": "WhitespaceMinimizedString" }, - "streptomycin_vendor_name": { - "name": "streptomycin_vendor_name", + "polymyxinb_vendor_name": { + "name": "polymyxinb_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "streptomycin_vendor_name", + "title": "polymyxin-b_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -23066,10 +23073,10 @@ } ] }, - "streptomycin_testing_standard": { - "name": "streptomycin_testing_standard", + "polymyxinb_testing_standard": { + "name": "polymyxinb_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "streptomycin_testing_standard", + "title": "polymyxin-b_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -23095,10 +23102,10 @@ } ] }, - "streptomycin_testing_standard_version": { - "name": "streptomycin_testing_standard_version", + "polymyxinb_testing_standard_version": { + "name": "polymyxinb_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "streptomycin_testing_standard_version", + "title": "polymyxin-b_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -23113,10 +23120,10 @@ ], "range": "WhitespaceMinimizedString" }, - "streptomycin_testing_standard_details": { - "name": "streptomycin_testing_standard_details", + "polymyxinb_testing_standard_details": { + "name": "polymyxinb_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "streptomycin_testing_standard_details", + "title": "polymyxin-b_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -23134,10 +23141,10 @@ ], "range": "WhitespaceMinimizedString" }, - "streptomycin_susceptible_breakpoint": { - "name": "streptomycin_susceptible_breakpoint", + "polymyxinb_susceptible_breakpoint": { + "name": "polymyxinb_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "streptomycin_susceptible_breakpoint", + "title": "polymyxin-b_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -23152,10 +23159,10 @@ ], "range": "WhitespaceMinimizedString" }, - "streptomycin_intermediate_breakpoint": { - "name": "streptomycin_intermediate_breakpoint", + "polymyxinb_intermediate_breakpoint": { + "name": "polymyxinb_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "streptomycin_intermediate_breakpoint", + "title": "polymyxin-b_intermediate_breakpoint", "examples": [ { "value": "16" @@ -23167,10 +23174,10 @@ ], "range": "WhitespaceMinimizedString" }, - "streptomycin_resistant_breakpoint": { - "name": "streptomycin_resistant_breakpoint", + "polymyxinb_resistant_breakpoint": { + "name": "polymyxinb_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "streptomycin_resistant_breakpoint", + "title": "polymyxin-b_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -23185,10 +23192,10 @@ ], "range": "WhitespaceMinimizedString" }, - "sulfisoxazole_resistance_phenotype": { - "name": "sulfisoxazole_resistance_phenotype", + "quinupristindalfopristin_resistance_phenotype": { + "name": "quinupristindalfopristin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "sulfisoxazole_resistance_phenotype", + "title": "quinupristin-dalfopristin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -23214,10 +23221,10 @@ } ] }, - "sulfisoxazole_measurement": { - "name": "sulfisoxazole_measurement", - "description": "The measured value of sulfisoxazole resistance.", - "title": "sulfisoxazole_measurement", + "quinupristindalfopristin_measurement": { + "name": "quinupristindalfopristin_measurement", + "description": "The measured value of quinupristin-dalfopristin resistance.", + "title": "quinupristin-dalfopristin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -23243,10 +23250,10 @@ } ] }, - "sulfisoxazole_measurement_units": { - "name": "sulfisoxazole_measurement_units", + "quinupristindalfopristin_measurement_units": { + "name": "quinupristindalfopristin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "sulfisoxazole_measurement_units", + "title": "quinupristin-dalfopristin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -23272,10 +23279,10 @@ } ] }, - "sulfisoxazole_measurement_sign": { - "name": "sulfisoxazole_measurement_sign", + "quinupristindalfopristin_measurement_sign": { + "name": "quinupristindalfopristin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "sulfisoxazole_measurement_sign", + "title": "quinupristin-dalfopristin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -23301,10 +23308,10 @@ } ] }, - "sulfisoxazole_laboratory_typing_method": { - "name": "sulfisoxazole_laboratory_typing_method", + "quinupristindalfopristin_laboratory_typing_method": { + "name": "quinupristindalfopristin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "sulfisoxazole_laboratory_typing_method", + "title": "quinupristin-dalfopristin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -23329,10 +23336,10 @@ } ] }, - "sulfisoxazole_laboratory_typing_platform": { - "name": "sulfisoxazole_laboratory_typing_platform", + "quinupristindalfopristin_laboratory_typing_platform": { + "name": "quinupristindalfopristin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "sulfisoxazole_laboratory_typing_platform", + "title": "quinupristin-dalfopristin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -23357,10 +23364,10 @@ } ] }, - "sulfisoxazole_laboratory_typing_platform_version": { - "name": "sulfisoxazole_laboratory_typing_platform_version", + "quinupristindalfopristin_laboratory_typing_platform_version": { + "name": "quinupristindalfopristin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "sulfisoxazole_laboratory_typing_platform_version", + "title": "quinupristin-dalfopristin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -23375,10 +23382,10 @@ ], "range": "WhitespaceMinimizedString" }, - "sulfisoxazole_vendor_name": { - "name": "sulfisoxazole_vendor_name", + "quinupristindalfopristin_vendor_name": { + "name": "quinupristindalfopristin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "sulfisoxazole_vendor_name", + "title": "quinupristin-dalfopristin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -23403,10 +23410,10 @@ } ] }, - "sulfisoxazole_testing_standard": { - "name": "sulfisoxazole_testing_standard", + "quinupristindalfopristin_testing_standard": { + "name": "quinupristindalfopristin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "sulfisoxazole_testing_standard", + "title": "quinupristin-dalfopristin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -23432,10 +23439,10 @@ } ] }, - "sulfisoxazole_testing_standard_version": { - "name": "sulfisoxazole_testing_standard_version", + "quinupristindalfopristin_testing_standard_version": { + "name": "quinupristindalfopristin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "sulfisoxazole_testing_standard_version", + "title": "quinupristin-dalfopristin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -23450,10 +23457,10 @@ ], "range": "WhitespaceMinimizedString" }, - "sulfisoxazole_testing_standard_details": { - "name": "sulfisoxazole_testing_standard_details", + "quinupristindalfopristin_testing_standard_details": { + "name": "quinupristindalfopristin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "sulfisoxazole_testing_standard_details", + "title": "quinupristin-dalfopristin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -23471,10 +23478,10 @@ ], "range": "WhitespaceMinimizedString" }, - "sulfisoxazole_susceptible_breakpoint": { - "name": "sulfisoxazole_susceptible_breakpoint", + "quinupristindalfopristin_susceptible_breakpoint": { + "name": "quinupristindalfopristin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "sulfisoxazole_susceptible_breakpoint", + "title": "quinupristin-dalfopristin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -23489,10 +23496,10 @@ ], "range": "WhitespaceMinimizedString" }, - "sulfisoxazole_intermediate_breakpoint": { - "name": "sulfisoxazole_intermediate_breakpoint", + "quinupristindalfopristin_intermediate_breakpoint": { + "name": "quinupristindalfopristin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "sulfisoxazole_intermediate_breakpoint", + "title": "quinupristin-dalfopristin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -23504,10 +23511,10 @@ ], "range": "WhitespaceMinimizedString" }, - "sulfisoxazole_resistant_breakpoint": { - "name": "sulfisoxazole_resistant_breakpoint", + "quinupristindalfopristin_resistant_breakpoint": { + "name": "quinupristindalfopristin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "sulfisoxazole_resistant_breakpoint", + "title": "quinupristin-dalfopristin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -23522,10 +23529,10 @@ ], "range": "WhitespaceMinimizedString" }, - "telithromycin_resistance_phenotype": { - "name": "telithromycin_resistance_phenotype", + "streptomycin_resistance_phenotype": { + "name": "streptomycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "telithromycin_resistance_phenotype", + "title": "streptomycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -23551,10 +23558,10 @@ } ] }, - "telithromycin_measurement": { - "name": "telithromycin_measurement", - "description": "The measured value of telithromycin resistance.", - "title": "telithromycin_measurement", + "streptomycin_measurement": { + "name": "streptomycin_measurement", + "description": "The measured value of streptomycin resistance.", + "title": "streptomycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -23580,10 +23587,10 @@ } ] }, - "telithromycin_measurement_units": { - "name": "telithromycin_measurement_units", + "streptomycin_measurement_units": { + "name": "streptomycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "telithromycin_measurement_units", + "title": "streptomycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -23609,10 +23616,10 @@ } ] }, - "telithromycin_measurement_sign": { - "name": "telithromycin_measurement_sign", + "streptomycin_measurement_sign": { + "name": "streptomycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "telithromycin_measurement_sign", + "title": "streptomycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -23638,10 +23645,10 @@ } ] }, - "telithromycin_laboratory_typing_method": { - "name": "telithromycin_laboratory_typing_method", + "streptomycin_laboratory_typing_method": { + "name": "streptomycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "telithromycin_laboratory_typing_method", + "title": "streptomycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -23666,10 +23673,10 @@ } ] }, - "telithromycin_laboratory_typing_platform": { - "name": "telithromycin_laboratory_typing_platform", + "streptomycin_laboratory_typing_platform": { + "name": "streptomycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "telithromycin_laboratory_typing_platform", + "title": "streptomycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -23694,10 +23701,10 @@ } ] }, - "telithromycin_laboratory_typing_platform_version": { - "name": "telithromycin_laboratory_typing_platform_version", + "streptomycin_laboratory_typing_platform_version": { + "name": "streptomycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "telithromycin_laboratory_typing_platform_version", + "title": "streptomycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -23712,10 +23719,10 @@ ], "range": "WhitespaceMinimizedString" }, - "telithromycin_vendor_name": { - "name": "telithromycin_vendor_name", + "streptomycin_vendor_name": { + "name": "streptomycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "telithromycin_vendor_name", + "title": "streptomycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -23740,10 +23747,10 @@ } ] }, - "telithromycin_testing_standard": { - "name": "telithromycin_testing_standard", + "streptomycin_testing_standard": { + "name": "streptomycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "telithromycin_testing_standard", + "title": "streptomycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -23769,10 +23776,10 @@ } ] }, - "telithromycin_testing_standard_version": { - "name": "telithromycin_testing_standard_version", + "streptomycin_testing_standard_version": { + "name": "streptomycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "telithromycin_testing_standard_version", + "title": "streptomycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -23787,10 +23794,10 @@ ], "range": "WhitespaceMinimizedString" }, - "telithromycin_testing_standard_details": { - "name": "telithromycin_testing_standard_details", + "streptomycin_testing_standard_details": { + "name": "streptomycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "telithromycin_testing_standard_details", + "title": "streptomycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -23808,10 +23815,10 @@ ], "range": "WhitespaceMinimizedString" }, - "telithromycin_susceptible_breakpoint": { - "name": "telithromycin_susceptible_breakpoint", + "streptomycin_susceptible_breakpoint": { + "name": "streptomycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "telithromycin_susceptible_breakpoint", + "title": "streptomycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -23826,10 +23833,10 @@ ], "range": "WhitespaceMinimizedString" }, - "telithromycin_intermediate_breakpoint": { - "name": "telithromycin_intermediate_breakpoint", + "streptomycin_intermediate_breakpoint": { + "name": "streptomycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "telithromycin_intermediate_breakpoint", + "title": "streptomycin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -23841,10 +23848,10 @@ ], "range": "WhitespaceMinimizedString" }, - "telithromycin_resistant_breakpoint": { - "name": "telithromycin_resistant_breakpoint", + "streptomycin_resistant_breakpoint": { + "name": "streptomycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "telithromycin_resistant_breakpoint", + "title": "streptomycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -23859,10 +23866,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tetracycline_resistance_phenotype": { - "name": "tetracycline_resistance_phenotype", + "sulfisoxazole_resistance_phenotype": { + "name": "sulfisoxazole_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "tetracycline_resistance_phenotype", + "title": "sulfisoxazole_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -23888,10 +23895,10 @@ } ] }, - "tetracycline_measurement": { - "name": "tetracycline_measurement", - "description": "The measured value of tetracycline resistance.", - "title": "tetracycline_measurement", + "sulfisoxazole_measurement": { + "name": "sulfisoxazole_measurement", + "description": "The measured value of sulfisoxazole resistance.", + "title": "sulfisoxazole_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -23917,10 +23924,10 @@ } ] }, - "tetracycline_measurement_units": { - "name": "tetracycline_measurement_units", + "sulfisoxazole_measurement_units": { + "name": "sulfisoxazole_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "tetracycline_measurement_units", + "title": "sulfisoxazole_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -23946,10 +23953,10 @@ } ] }, - "tetracycline_measurement_sign": { - "name": "tetracycline_measurement_sign", + "sulfisoxazole_measurement_sign": { + "name": "sulfisoxazole_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "tetracycline_measurement_sign", + "title": "sulfisoxazole_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -23975,10 +23982,10 @@ } ] }, - "tetracycline_laboratory_typing_method": { - "name": "tetracycline_laboratory_typing_method", + "sulfisoxazole_laboratory_typing_method": { + "name": "sulfisoxazole_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "tetracycline_laboratory_typing_method", + "title": "sulfisoxazole_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -24003,10 +24010,10 @@ } ] }, - "tetracycline_laboratory_typing_platform": { - "name": "tetracycline_laboratory_typing_platform", + "sulfisoxazole_laboratory_typing_platform": { + "name": "sulfisoxazole_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "tetracycline_laboratory_typing_platform", + "title": "sulfisoxazole_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -24031,10 +24038,10 @@ } ] }, - "tetracycline_laboratory_typing_platform_version": { - "name": "tetracycline_laboratory_typing_platform_version", + "sulfisoxazole_laboratory_typing_platform_version": { + "name": "sulfisoxazole_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "tetracycline_laboratory_typing_platform_version", + "title": "sulfisoxazole_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -24049,10 +24056,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tetracycline_vendor_name": { - "name": "tetracycline_vendor_name", + "sulfisoxazole_vendor_name": { + "name": "sulfisoxazole_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "tetracycline_vendor_name", + "title": "sulfisoxazole_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -24077,10 +24084,10 @@ } ] }, - "tetracycline_testing_standard": { - "name": "tetracycline_testing_standard", + "sulfisoxazole_testing_standard": { + "name": "sulfisoxazole_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "tetracycline_testing_standard", + "title": "sulfisoxazole_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -24106,10 +24113,10 @@ } ] }, - "tetracycline_testing_standard_version": { - "name": "tetracycline_testing_standard_version", + "sulfisoxazole_testing_standard_version": { + "name": "sulfisoxazole_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "tetracycline_testing_standard_version", + "title": "sulfisoxazole_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -24124,10 +24131,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tetracycline_testing_standard_details": { - "name": "tetracycline_testing_standard_details", + "sulfisoxazole_testing_standard_details": { + "name": "sulfisoxazole_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "tetracycline_testing_standard_details", + "title": "sulfisoxazole_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -24145,10 +24152,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tetracycline_susceptible_breakpoint": { - "name": "tetracycline_susceptible_breakpoint", + "sulfisoxazole_susceptible_breakpoint": { + "name": "sulfisoxazole_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "tetracycline_susceptible_breakpoint", + "title": "sulfisoxazole_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -24163,10 +24170,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tetracycline_intermediate_breakpoint": { - "name": "tetracycline_intermediate_breakpoint", + "sulfisoxazole_intermediate_breakpoint": { + "name": "sulfisoxazole_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "tetracycline_intermediate_breakpoint", + "title": "sulfisoxazole_intermediate_breakpoint", "examples": [ { "value": "16" @@ -24178,10 +24185,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tetracycline_resistant_breakpoint": { - "name": "tetracycline_resistant_breakpoint", + "sulfisoxazole_resistant_breakpoint": { + "name": "sulfisoxazole_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "tetracycline_resistant_breakpoint", + "title": "sulfisoxazole_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -24196,10 +24203,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tigecycline_resistance_phenotype": { - "name": "tigecycline_resistance_phenotype", + "telithromycin_resistance_phenotype": { + "name": "telithromycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "tigecycline_resistance_phenotype", + "title": "telithromycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -24225,10 +24232,10 @@ } ] }, - "tigecycline_measurement": { - "name": "tigecycline_measurement", - "description": "The measured value of tigecycline resistance.", - "title": "tigecycline_measurement", + "telithromycin_measurement": { + "name": "telithromycin_measurement", + "description": "The measured value of telithromycin resistance.", + "title": "telithromycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -24254,10 +24261,10 @@ } ] }, - "tigecycline_measurement_units": { - "name": "tigecycline_measurement_units", + "telithromycin_measurement_units": { + "name": "telithromycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "tigecycline_measurement_units", + "title": "telithromycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -24283,10 +24290,10 @@ } ] }, - "tigecycline_measurement_sign": { - "name": "tigecycline_measurement_sign", + "telithromycin_measurement_sign": { + "name": "telithromycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "tigecycline_measurement_sign", + "title": "telithromycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -24312,10 +24319,10 @@ } ] }, - "tigecycline_laboratory_typing_method": { - "name": "tigecycline_laboratory_typing_method", + "telithromycin_laboratory_typing_method": { + "name": "telithromycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "tigecycline_laboratory_typing_method", + "title": "telithromycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -24340,10 +24347,10 @@ } ] }, - "tigecycline_laboratory_typing_platform": { - "name": "tigecycline_laboratory_typing_platform", + "telithromycin_laboratory_typing_platform": { + "name": "telithromycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "tigecycline_laboratory_typing_platform", + "title": "telithromycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -24368,10 +24375,10 @@ } ] }, - "tigecycline_laboratory_typing_platform_version": { - "name": "tigecycline_laboratory_typing_platform_version", + "telithromycin_laboratory_typing_platform_version": { + "name": "telithromycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "tigecycline_laboratory_typing_platform_version", + "title": "telithromycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -24386,10 +24393,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tigecycline_vendor_name": { - "name": "tigecycline_vendor_name", + "telithromycin_vendor_name": { + "name": "telithromycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "tigecycline_vendor_name", + "title": "telithromycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -24414,10 +24421,10 @@ } ] }, - "tigecycline_testing_standard": { - "name": "tigecycline_testing_standard", + "telithromycin_testing_standard": { + "name": "telithromycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "tigecycline_testing_standard", + "title": "telithromycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -24443,10 +24450,10 @@ } ] }, - "tigecycline_testing_standard_version": { - "name": "tigecycline_testing_standard_version", + "telithromycin_testing_standard_version": { + "name": "telithromycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "tigecycline_testing_standard_version", + "title": "telithromycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -24461,10 +24468,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tigecycline_testing_standard_details": { - "name": "tigecycline_testing_standard_details", + "telithromycin_testing_standard_details": { + "name": "telithromycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "tigecycline_testing_standard_details", + "title": "telithromycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -24482,10 +24489,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tigecycline_susceptible_breakpoint": { - "name": "tigecycline_susceptible_breakpoint", + "telithromycin_susceptible_breakpoint": { + "name": "telithromycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "tigecycline_susceptible_breakpoint", + "title": "telithromycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -24500,10 +24507,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tigecycline_intermediate_breakpoint": { - "name": "tigecycline_intermediate_breakpoint", + "telithromycin_intermediate_breakpoint": { + "name": "telithromycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "tigecycline_intermediate_breakpoint", + "title": "telithromycin_intermediate_breakpoint", "examples": [ { "value": "16" @@ -24515,10 +24522,10 @@ ], "range": "WhitespaceMinimizedString" }, - "tigecycline_resistant_breakpoint": { - "name": "tigecycline_resistant_breakpoint", + "telithromycin_resistant_breakpoint": { + "name": "telithromycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "tigecycline_resistant_breakpoint", + "title": "telithromycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -24533,10 +24540,10 @@ ], "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_resistance_phenotype": { - "name": "trimethoprimsulfamethoxazole_resistance_phenotype", + "tetracycline_resistance_phenotype": { + "name": "tetracycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "trimethoprim-sulfamethoxazole_resistance_phenotype", + "title": "tetracycline_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -24562,10 +24569,10 @@ } ] }, - "trimethoprimsulfamethoxazole_measurement": { - "name": "trimethoprimsulfamethoxazole_measurement", - "description": "The measured value of trimethoprim-sulfamethoxazole resistance.", - "title": "trimethoprim-sulfamethoxazole_measurement", + "tetracycline_measurement": { + "name": "tetracycline_measurement", + "description": "The measured value of tetracycline resistance.", + "title": "tetracycline_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -24591,10 +24598,10 @@ } ] }, - "trimethoprimsulfamethoxazole_measurement_units": { - "name": "trimethoprimsulfamethoxazole_measurement_units", + "tetracycline_measurement_units": { + "name": "tetracycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "trimethoprim-sulfamethoxazole_measurement_units", + "title": "tetracycline_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -24620,10 +24627,10 @@ } ] }, - "trimethoprimsulfamethoxazole_measurement_sign": { - "name": "trimethoprimsulfamethoxazole_measurement_sign", + "tetracycline_measurement_sign": { + "name": "tetracycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "trimethoprim-sulfamethoxazole_measurement_sign", + "title": "tetracycline_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -24649,10 +24656,10 @@ } ] }, - "trimethoprimsulfamethoxazole_laboratory_typing_method": { - "name": "trimethoprimsulfamethoxazole_laboratory_typing_method", + "tetracycline_laboratory_typing_method": { + "name": "tetracycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "trimethoprim-sulfamethoxazole_laboratory_typing_method", + "title": "tetracycline_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -24677,10 +24684,10 @@ } ] }, - "trimethoprimsulfamethoxazole_laboratory_typing_platform": { - "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", + "tetracycline_laboratory_typing_platform": { + "name": "tetracycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform", + "title": "tetracycline_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -24705,10 +24712,10 @@ } ] }, - "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { - "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", + "tetracycline_laboratory_typing_platform_version": { + "name": "tetracycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version", + "title": "tetracycline_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -24723,10 +24730,10 @@ ], "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_vendor_name": { - "name": "trimethoprimsulfamethoxazole_vendor_name", + "tetracycline_vendor_name": { + "name": "tetracycline_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "trimethoprim-sulfamethoxazole_vendor_name", + "title": "tetracycline_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -24751,10 +24758,10 @@ } ] }, - "trimethoprimsulfamethoxazole_testing_standard": { - "name": "trimethoprimsulfamethoxazole_testing_standard", + "tetracycline_testing_standard": { + "name": "tetracycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "trimethoprim-sulfamethoxazole_testing_standard", + "title": "tetracycline_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -24780,10 +24787,10 @@ } ] }, - "trimethoprimsulfamethoxazole_testing_standard_version": { - "name": "trimethoprimsulfamethoxazole_testing_standard_version", + "tetracycline_testing_standard_version": { + "name": "tetracycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "trimethoprim-sulfamethoxazole_testing_standard_version", + "title": "tetracycline_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -24798,10 +24805,10 @@ ], "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_testing_standard_details": { - "name": "trimethoprimsulfamethoxazole_testing_standard_details", + "tetracycline_testing_standard_details": { + "name": "tetracycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "trimethoprim-sulfamethoxazole_testing_standard_details", + "title": "tetracycline_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -24819,10 +24826,10 @@ ], "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_susceptible_breakpoint": { - "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", + "tetracycline_susceptible_breakpoint": { + "name": "tetracycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "trimethoprim-sulfamethoxazole_susceptible_breakpoint", + "title": "tetracycline_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -24837,10 +24844,10 @@ ], "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_intermediate_breakpoint": { - "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", + "tetracycline_intermediate_breakpoint": { + "name": "tetracycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "trimethoprim-sulfamethoxazole_intermediate_breakpoint", + "title": "tetracycline_intermediate_breakpoint", "examples": [ { "value": "16" @@ -24852,10 +24859,10 @@ ], "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_resistant_breakpoint": { - "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", + "tetracycline_resistant_breakpoint": { + "name": "tetracycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "trimethoprim-sulfamethoxazole_resistant_breakpoint", + "title": "tetracycline_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -24870,136 +24877,810 @@ ], "range": "WhitespaceMinimizedString" }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", + "tigecycline_resistance_phenotype": { + "name": "tigecycline_resistance_phenotype", + "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", + "title": "tigecycline_resistance_phenotype", "comments": [ - "Include the first and last names of all individuals that should be attributed, separated by a comma." + "Select a phenotype from the pick list provided." ], "examples": [ { - "value": "Tejinder Singh, Fei Hu, Joe Blogs" + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001517", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:resistance_phenotype" + ], "domain_of": [ "GRDI" ], - "range": "WhitespaceMinimizedString", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialPhenotypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "dataharmonizer_provenance": { - "name": "dataharmonizer_provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", + "tigecycline_measurement": { + "name": "tigecycline_measurement", + "description": "The measured value of tigecycline resistance.", + "title": "tigecycline_measurement", "comments": [ - "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + "This field should only contain a number (either an integer or a number with decimals)." ], "examples": [ { - "value": "DataHarmonizer v1.4.3, GRDI v1.0.0" + "value": "4" } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001518", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement" + ], "domain_of": [ "GRDI" ], - "range": "Provenance" - } - }, - "classes": { - "dh_interface": { - "name": "dh_interface", - "description": "A DataHarmonizer interface", - "from_schema": "https://example.com/GRDI" + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "GRDI": { - "name": "GRDI", - "description": "Specification for GRDI virus biosample data gathering", + "tigecycline_measurement_units": { + "name": "tigecycline_measurement_units", + "description": "The units of the antimicrobial resistance measurement.", + "title": "tigecycline_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", - "is_a": "dh_interface", - "slot_usage": { - "sample_collector_sample_id": { - "name": "sample_collector_sample_id", - "rank": 1, - "slot_group": "Sample collection and processing" - }, - "alternative_sample_id": { - "name": "alternative_sample_id", - "rank": 2, - "slot_group": "Sample collection and processing" - }, - "sample_collected_by": { - "name": "sample_collected_by", - "rank": 3, - "slot_group": "Sample collection and processing" - }, - "sample_collected_by_laboratory_name": { - "name": "sample_collected_by_laboratory_name", - "rank": 4, - "slot_group": "Sample collection and processing" - }, - "sample_collection_project_name": { - "name": "sample_collection_project_name", - "rank": 5, - "slot_group": "Sample collection and processing" - }, - "sample_plan_name": { - "name": "sample_plan_name", - "rank": 6, - "slot_group": "Sample collection and processing" - }, - "sample_plan_id": { - "name": "sample_plan_id", - "rank": 7, - "slot_group": "Sample collection and processing" - }, - "sample_collector_contact_name": { - "name": "sample_collector_contact_name", - "rank": 8, - "slot_group": "Sample collection and processing" - }, - "sample_collector_contact_email": { - "name": "sample_collector_contact_email", - "rank": 9, - "slot_group": "Sample collection and processing" + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_units" + ], + "domain_of": [ + "GRDI" + ], + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementUnitsMenu" }, - "purpose_of_sampling": { - "name": "purpose_of_sampling", - "rank": 10, - "slot_group": "Sample collection and processing" + { + "range": "NullValueMenu" + } + ] + }, + "tigecycline_measurement_sign": { + "name": "tigecycline_measurement_sign", + "description": "The qualifier associated with the antimicrobial resistance measurement", + "title": "tigecycline_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_sign" + ], + "domain_of": [ + "GRDI" + ], + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementSignMenu" }, - "presampling_activity": { - "name": "presampling_activity", - "rank": 11, - "slot_group": "Sample collection and processing" + { + "range": "NullValueMenu" + } + ] + }, + "tigecycline_laboratory_typing_method": { + "name": "tigecycline_laboratory_typing_method", + "description": "The general method used for antimicrobial susceptibility testing.", + "title": "tigecycline_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, - "presampling_activity_details": { - "name": "presampling_activity_details", - "rank": 12, - "slot_group": "Sample collection and processing" + { + "range": "NullValueMenu" + } + ] + }, + "tigecycline_laboratory_typing_platform": { + "name": "tigecycline_laboratory_typing_platform", + "description": "The brand/platform used for antimicrobial susceptibility testing.", + "title": "tigecycline_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, - "experimental_protocol_field": { - "name": "experimental_protocol_field", - "rank": 13, - "slot_group": "Sample collection and processing" + { + "range": "NullValueMenu" + } + ] + }, + "tigecycline_laboratory_typing_platform_version": { + "name": "tigecycline_laboratory_typing_platform_version", + "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", + "title": "tigecycline_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "tigecycline_vendor_name": { + "name": "tigecycline_vendor_name", + "description": "The name of the vendor of the testing platform used.", + "title": "tigecycline_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "AntimicrobialVendorNameMenu" }, - "experimental_specimen_role_type": { - "name": "experimental_specimen_role_type", - "rank": 14, - "slot_group": "Sample collection and processing" + { + "range": "NullValueMenu" + } + ] + }, + "tigecycline_testing_standard": { + "name": "tigecycline_testing_standard", + "description": "The testing standard used for determination of resistance phenotype", + "title": "tigecycline_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:testing_standard" + ], + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialTestingStandardMenu" }, - "specimen_processing": { - "name": "specimen_processing", - "rank": 15, - "slot_group": "Sample collection and processing" + { + "range": "NullValueMenu" + } + ] + }, + "tigecycline_testing_standard_version": { + "name": "tigecycline_testing_standard_version", + "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", + "title": "tigecycline_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "tigecycline_testing_standard_details": { + "name": "tigecycline_testing_standard_details", + "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", + "title": "tigecycline_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" }, - "specimen_processing_details": { - "name": "specimen_processing_details", - "rank": 16, + { + "value": "2017." + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "tigecycline_susceptible_breakpoint": { + "name": "tigecycline_susceptible_breakpoint", + "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", + "title": "tigecycline_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "tigecycline_intermediate_breakpoint": { + "name": "tigecycline_intermediate_breakpoint", + "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", + "title": "tigecycline_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "tigecycline_resistant_breakpoint": { + "name": "tigecycline_resistant_breakpoint", + "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", + "title": "tigecycline_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "trimethoprimsulfamethoxazole_resistance_phenotype": { + "name": "trimethoprimsulfamethoxazole_resistance_phenotype", + "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", + "title": "trimethoprim-sulfamethoxazole_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:resistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialPhenotypeMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_measurement": { + "name": "trimethoprimsulfamethoxazole_measurement", + "description": "The measured value of trimethoprim-sulfamethoxazole resistance.", + "title": "trimethoprim-sulfamethoxazole_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement" + ], + "domain_of": [ + "GRDI" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_measurement_units": { + "name": "trimethoprimsulfamethoxazole_measurement_units", + "description": "The units of the antimicrobial resistance measurement.", + "title": "trimethoprim-sulfamethoxazole_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_units" + ], + "domain_of": [ + "GRDI" + ], + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_measurement_sign": { + "name": "trimethoprimsulfamethoxazole_measurement_sign", + "description": "The qualifier associated with the antimicrobial resistance measurement", + "title": "trimethoprim-sulfamethoxazole_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_sign" + ], + "domain_of": [ + "GRDI" + ], + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementSignMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_laboratory_typing_method": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_method", + "description": "The general method used for antimicrobial susceptibility testing.", + "title": "trimethoprim-sulfamethoxazole_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "AntimicrobialLaboratoryTypingMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_laboratory_typing_platform": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", + "description": "The brand/platform used for antimicrobial susceptibility testing.", + "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "AntimicrobialLaboratoryTypingPlatformMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", + "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", + "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "trimethoprimsulfamethoxazole_vendor_name": { + "name": "trimethoprimsulfamethoxazole_vendor_name", + "description": "The name of the vendor of the testing platform used.", + "title": "trimethoprim-sulfamethoxazole_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "AntimicrobialVendorNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_testing_standard": { + "name": "trimethoprimsulfamethoxazole_testing_standard", + "description": "The testing standard used for determination of resistance phenotype", + "title": "trimethoprim-sulfamethoxazole_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:testing_standard" + ], + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialTestingStandardMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimethoprimsulfamethoxazole_testing_standard_version": { + "name": "trimethoprimsulfamethoxazole_testing_standard_version", + "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", + "title": "trimethoprim-sulfamethoxazole_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "trimethoprimsulfamethoxazole_testing_standard_details": { + "name": "trimethoprimsulfamethoxazole_testing_standard_details", + "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", + "title": "trimethoprim-sulfamethoxazole_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "trimethoprimsulfamethoxazole_susceptible_breakpoint": { + "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", + "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", + "title": "trimethoprim-sulfamethoxazole_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "trimethoprimsulfamethoxazole_intermediate_breakpoint": { + "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", + "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", + "title": "trimethoprim-sulfamethoxazole_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "trimethoprimsulfamethoxazole_resistant_breakpoint": { + "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", + "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", + "title": "trimethoprim-sulfamethoxazole_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, + "authors": { + "name": "authors", + "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", + "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "description": "The DataHarmonizer software and template version provenance.", + "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, GRDI v1.0.0" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "GRDI" + ], + "range": "Provenance" + } + }, + "classes": { + "dh_interface": { + "name": "dh_interface", + "description": "A DataHarmonizer interface", + "from_schema": "https://example.com/GRDI" + }, + "GRDI": { + "name": "GRDI", + "description": "Specification for GRDI virus biosample data gathering", + "from_schema": "https://example.com/GRDI", + "is_a": "dh_interface", + "slot_usage": { + "sample_collector_sample_id": { + "name": "sample_collector_sample_id", + "rank": 1, + "slot_group": "Sample collection and processing" + }, + "alternative_sample_id": { + "name": "alternative_sample_id", + "rank": 2, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 3, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "rank": 4, + "slot_group": "Sample collection and processing" + }, + "sample_collection_project_name": { + "name": "sample_collection_project_name", + "rank": 5, + "slot_group": "Sample collection and processing" + }, + "sample_plan_name": { + "name": "sample_plan_name", + "rank": 6, + "slot_group": "Sample collection and processing" + }, + "sample_plan_id": { + "name": "sample_plan_id", + "rank": 7, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "rank": 8, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 9, + "slot_group": "Sample collection and processing" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "presampling_activity": { + "name": "presampling_activity", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "experimental_protocol_field": { + "name": "experimental_protocol_field", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "specimen_processing": { + "name": "specimen_processing", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "rank": 16, "slot_group": "Sample collection and processing" }, "nucleic_acid_extraction_method": { @@ -25472,3405 +26153,4272 @@ "rank": 110, "slot_group": "Sequence information" }, + "sequencing_date": { + "name": "sequencing_date", + "rank": 111, + "slot_group": "Sequence information" + }, "sequencing_project_name": { "name": "sequencing_project_name", - "rank": 111, + "rank": 112, "slot_group": "Sequence information" }, "sequencing_platform": { "name": "sequencing_platform", - "rank": 112, + "rank": 113, "slot_group": "Sequence information" }, "sequencing_instrument": { "name": "sequencing_instrument", - "rank": 113, + "rank": 114, "slot_group": "Sequence information" }, "sequencing_assay_type": { "name": "sequencing_assay_type", - "rank": 114, + "rank": 115, "slot_group": "Sequence information" }, "library_preparation_kit": { "name": "library_preparation_kit", - "rank": 115, + "rank": 116, "slot_group": "Sequence information" }, "dna_fragment_length": { "name": "dna_fragment_length", - "rank": 116, + "rank": 117, "slot_group": "Sequence information" }, "genomic_target_enrichment_method": { "name": "genomic_target_enrichment_method", - "rank": 117, + "rank": 118, "slot_group": "Sequence information" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", - "rank": 118, + "rank": 119, "slot_group": "Sequence information" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 119, + "rank": 120, "slot_group": "Sequence information" }, "amplicon_size": { "name": "amplicon_size", - "rank": 120, + "rank": 121, "slot_group": "Sequence information" }, "sequencing_flow_cell_version": { "name": "sequencing_flow_cell_version", - "rank": 121, + "rank": 122, "slot_group": "Sequence information" }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 122, + "rank": 123, "slot_group": "Sequence information" }, "r1_fastq_filename": { "name": "r1_fastq_filename", - "rank": 123, + "rank": 124, "slot_group": "Sequence information" }, "r2_fastq_filename": { "name": "r2_fastq_filename", - "rank": 124, + "rank": 125, "slot_group": "Sequence information" }, "fast5_filename": { "name": "fast5_filename", - "rank": 125, + "rank": 126, "slot_group": "Sequence information" }, "genome_sequence_filename": { "name": "genome_sequence_filename", - "rank": 126, + "rank": 127, "slot_group": "Sequence information" }, "quality_control_method_name": { "name": "quality_control_method_name", - 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"rank": 670, + "rank": 699, "slot_group": "Antimicrobial resistance" }, "piperacillintazobactam_resistant_breakpoint": { "name": "piperacillintazobactam_resistant_breakpoint", - "rank": 671, + "rank": 700, "slot_group": "Antimicrobial resistance" }, "polymyxinb_resistance_phenotype": { "name": "polymyxinb_resistance_phenotype", - "rank": 672, + "rank": 701, "slot_group": "Antimicrobial resistance" }, "polymyxinb_measurement": { "name": "polymyxinb_measurement", - "rank": 673, + "rank": 702, "slot_group": "Antimicrobial resistance" }, "polymyxinb_measurement_units": { "name": "polymyxinb_measurement_units", - "rank": 674, + "rank": 703, "slot_group": "Antimicrobial resistance" }, "polymyxinb_measurement_sign": { "name": "polymyxinb_measurement_sign", - "rank": 675, + "rank": 704, "slot_group": "Antimicrobial resistance" }, "polymyxinb_laboratory_typing_method": { "name": "polymyxinb_laboratory_typing_method", - "rank": 676, + "rank": 705, "slot_group": "Antimicrobial resistance" }, "polymyxinb_laboratory_typing_platform": { "name": "polymyxinb_laboratory_typing_platform", - "rank": 677, + "rank": 706, "slot_group": "Antimicrobial resistance" }, "polymyxinb_laboratory_typing_platform_version": { "name": "polymyxinb_laboratory_typing_platform_version", - "rank": 678, + "rank": 707, "slot_group": "Antimicrobial resistance" }, "polymyxinb_vendor_name": { "name": "polymyxinb_vendor_name", - "rank": 679, + "rank": 708, "slot_group": "Antimicrobial resistance" }, "polymyxinb_testing_standard": { "name": "polymyxinb_testing_standard", - "rank": 680, + "rank": 709, "slot_group": "Antimicrobial resistance" }, "polymyxinb_testing_standard_version": { "name": "polymyxinb_testing_standard_version", - "rank": 681, + "rank": 710, "slot_group": "Antimicrobial resistance" }, "polymyxinb_testing_standard_details": { "name": "polymyxinb_testing_standard_details", - "rank": 682, + "rank": 711, "slot_group": "Antimicrobial resistance" }, "polymyxinb_susceptible_breakpoint": { "name": "polymyxinb_susceptible_breakpoint", - "rank": 683, + "rank": 712, "slot_group": "Antimicrobial resistance" }, "polymyxinb_intermediate_breakpoint": { "name": "polymyxinb_intermediate_breakpoint", - "rank": 684, + "rank": 713, "slot_group": "Antimicrobial resistance" }, "polymyxinb_resistant_breakpoint": { "name": "polymyxinb_resistant_breakpoint", - "rank": 685, + "rank": 714, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_resistance_phenotype": { "name": "quinupristindalfopristin_resistance_phenotype", - "rank": 686, + "rank": 715, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_measurement": { "name": "quinupristindalfopristin_measurement", - "rank": 687, + "rank": 716, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_measurement_units": { "name": "quinupristindalfopristin_measurement_units", - "rank": 688, + "rank": 717, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_measurement_sign": { "name": "quinupristindalfopristin_measurement_sign", - "rank": 689, + "rank": 718, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_laboratory_typing_method": { "name": "quinupristindalfopristin_laboratory_typing_method", - "rank": 690, + "rank": 719, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_laboratory_typing_platform": { "name": "quinupristindalfopristin_laboratory_typing_platform", - "rank": 691, + "rank": 720, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_laboratory_typing_platform_version": { "name": "quinupristindalfopristin_laboratory_typing_platform_version", - "rank": 692, + "rank": 721, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_vendor_name": { "name": "quinupristindalfopristin_vendor_name", - "rank": 693, + "rank": 722, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_testing_standard": { "name": "quinupristindalfopristin_testing_standard", - "rank": 694, + "rank": 723, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_testing_standard_version": { "name": "quinupristindalfopristin_testing_standard_version", - "rank": 695, + "rank": 724, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_testing_standard_details": { "name": "quinupristindalfopristin_testing_standard_details", - "rank": 696, + "rank": 725, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_susceptible_breakpoint": { "name": "quinupristindalfopristin_susceptible_breakpoint", - "rank": 697, + "rank": 726, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_intermediate_breakpoint": { "name": "quinupristindalfopristin_intermediate_breakpoint", - "rank": 698, + "rank": 727, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_resistant_breakpoint": { "name": "quinupristindalfopristin_resistant_breakpoint", - "rank": 699, + "rank": 728, "slot_group": "Antimicrobial resistance" }, "streptomycin_resistance_phenotype": { "name": "streptomycin_resistance_phenotype", - "rank": 700, + "rank": 729, "slot_group": "Antimicrobial resistance" }, "streptomycin_measurement": { "name": "streptomycin_measurement", - "rank": 701, + "rank": 730, "slot_group": "Antimicrobial resistance" }, "streptomycin_measurement_units": { "name": "streptomycin_measurement_units", - "rank": 702, + "rank": 731, "slot_group": "Antimicrobial resistance" }, "streptomycin_measurement_sign": { "name": "streptomycin_measurement_sign", - "rank": 703, + "rank": 732, "slot_group": "Antimicrobial resistance" }, "streptomycin_laboratory_typing_method": { "name": "streptomycin_laboratory_typing_method", - "rank": 704, + "rank": 733, "slot_group": "Antimicrobial resistance" }, "streptomycin_laboratory_typing_platform": { "name": "streptomycin_laboratory_typing_platform", - "rank": 705, + "rank": 734, "slot_group": "Antimicrobial resistance" }, "streptomycin_laboratory_typing_platform_version": { "name": "streptomycin_laboratory_typing_platform_version", - "rank": 706, + "rank": 735, "slot_group": "Antimicrobial resistance" }, "streptomycin_vendor_name": { "name": "streptomycin_vendor_name", - "rank": 707, + "rank": 736, "slot_group": "Antimicrobial resistance" }, "streptomycin_testing_standard": { "name": "streptomycin_testing_standard", - "rank": 708, + "rank": 737, "slot_group": "Antimicrobial resistance" }, "streptomycin_testing_standard_version": { "name": "streptomycin_testing_standard_version", - "rank": 709, + "rank": 738, "slot_group": "Antimicrobial resistance" }, "streptomycin_testing_standard_details": { "name": "streptomycin_testing_standard_details", - "rank": 710, + "rank": 739, "slot_group": "Antimicrobial resistance" }, "streptomycin_susceptible_breakpoint": { "name": "streptomycin_susceptible_breakpoint", - "rank": 711, + "rank": 740, "slot_group": "Antimicrobial resistance" }, "streptomycin_intermediate_breakpoint": { "name": "streptomycin_intermediate_breakpoint", - "rank": 712, + "rank": 741, "slot_group": "Antimicrobial resistance" }, "streptomycin_resistant_breakpoint": { "name": "streptomycin_resistant_breakpoint", - "rank": 713, + "rank": 742, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_resistance_phenotype": { "name": "sulfisoxazole_resistance_phenotype", - "rank": 714, + "rank": 743, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_measurement": { "name": "sulfisoxazole_measurement", - "rank": 715, + "rank": 744, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_measurement_units": { "name": "sulfisoxazole_measurement_units", - "rank": 716, + "rank": 745, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_measurement_sign": { "name": "sulfisoxazole_measurement_sign", - "rank": 717, + "rank": 746, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_laboratory_typing_method": { "name": "sulfisoxazole_laboratory_typing_method", - "rank": 718, + "rank": 747, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_laboratory_typing_platform": { "name": "sulfisoxazole_laboratory_typing_platform", - "rank": 719, + "rank": 748, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_laboratory_typing_platform_version": { "name": "sulfisoxazole_laboratory_typing_platform_version", - "rank": 720, + "rank": 749, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_vendor_name": { "name": "sulfisoxazole_vendor_name", - "rank": 721, + "rank": 750, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_testing_standard": { "name": "sulfisoxazole_testing_standard", - "rank": 722, + "rank": 751, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_testing_standard_version": { "name": "sulfisoxazole_testing_standard_version", - "rank": 723, + "rank": 752, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_testing_standard_details": { "name": "sulfisoxazole_testing_standard_details", - "rank": 724, + "rank": 753, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_susceptible_breakpoint": { "name": "sulfisoxazole_susceptible_breakpoint", - "rank": 725, + "rank": 754, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_intermediate_breakpoint": { "name": "sulfisoxazole_intermediate_breakpoint", - "rank": 726, + "rank": 755, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_resistant_breakpoint": { "name": "sulfisoxazole_resistant_breakpoint", - "rank": 727, + "rank": 756, "slot_group": "Antimicrobial resistance" }, "telithromycin_resistance_phenotype": { "name": "telithromycin_resistance_phenotype", - "rank": 728, + "rank": 757, "slot_group": "Antimicrobial resistance" }, "telithromycin_measurement": { "name": "telithromycin_measurement", - "rank": 729, + "rank": 758, "slot_group": "Antimicrobial resistance" }, "telithromycin_measurement_units": { "name": "telithromycin_measurement_units", - "rank": 730, + "rank": 759, "slot_group": "Antimicrobial resistance" }, "telithromycin_measurement_sign": { "name": "telithromycin_measurement_sign", - "rank": 731, + "rank": 760, "slot_group": "Antimicrobial resistance" }, "telithromycin_laboratory_typing_method": { "name": "telithromycin_laboratory_typing_method", - "rank": 732, + "rank": 761, "slot_group": "Antimicrobial resistance" }, "telithromycin_laboratory_typing_platform": { "name": "telithromycin_laboratory_typing_platform", - "rank": 733, + "rank": 762, "slot_group": "Antimicrobial resistance" }, "telithromycin_laboratory_typing_platform_version": { "name": "telithromycin_laboratory_typing_platform_version", - "rank": 734, + "rank": 763, "slot_group": "Antimicrobial resistance" }, "telithromycin_vendor_name": { "name": "telithromycin_vendor_name", - "rank": 735, + "rank": 764, "slot_group": "Antimicrobial resistance" }, "telithromycin_testing_standard": { "name": "telithromycin_testing_standard", - "rank": 736, + "rank": 765, "slot_group": "Antimicrobial resistance" }, "telithromycin_testing_standard_version": { "name": "telithromycin_testing_standard_version", - "rank": 737, + "rank": 766, "slot_group": "Antimicrobial resistance" }, "telithromycin_testing_standard_details": { "name": "telithromycin_testing_standard_details", - "rank": 738, + "rank": 767, "slot_group": "Antimicrobial resistance" }, "telithromycin_susceptible_breakpoint": { "name": "telithromycin_susceptible_breakpoint", - "rank": 739, + "rank": 768, "slot_group": "Antimicrobial resistance" }, "telithromycin_intermediate_breakpoint": { "name": "telithromycin_intermediate_breakpoint", - "rank": 740, + "rank": 769, "slot_group": "Antimicrobial resistance" }, "telithromycin_resistant_breakpoint": { "name": "telithromycin_resistant_breakpoint", - "rank": 741, + "rank": 770, "slot_group": "Antimicrobial resistance" }, "tetracycline_resistance_phenotype": { "name": "tetracycline_resistance_phenotype", - "rank": 742, + "rank": 771, "slot_group": "Antimicrobial resistance" }, "tetracycline_measurement": { "name": "tetracycline_measurement", - "rank": 743, + "rank": 772, "slot_group": "Antimicrobial resistance" }, "tetracycline_measurement_units": { "name": "tetracycline_measurement_units", - "rank": 744, + "rank": 773, "slot_group": "Antimicrobial resistance" }, "tetracycline_measurement_sign": { "name": "tetracycline_measurement_sign", - "rank": 745, + "rank": 774, "slot_group": "Antimicrobial resistance" }, "tetracycline_laboratory_typing_method": { "name": "tetracycline_laboratory_typing_method", - "rank": 746, + "rank": 775, "slot_group": "Antimicrobial resistance" }, "tetracycline_laboratory_typing_platform": { "name": "tetracycline_laboratory_typing_platform", - "rank": 747, + "rank": 776, "slot_group": "Antimicrobial resistance" }, "tetracycline_laboratory_typing_platform_version": { "name": "tetracycline_laboratory_typing_platform_version", - "rank": 748, + "rank": 777, "slot_group": "Antimicrobial resistance" }, "tetracycline_vendor_name": { "name": "tetracycline_vendor_name", - "rank": 749, + "rank": 778, "slot_group": "Antimicrobial resistance" }, "tetracycline_testing_standard": { "name": "tetracycline_testing_standard", - "rank": 750, + "rank": 779, "slot_group": "Antimicrobial resistance" }, "tetracycline_testing_standard_version": { "name": "tetracycline_testing_standard_version", - "rank": 751, + "rank": 780, "slot_group": "Antimicrobial resistance" }, "tetracycline_testing_standard_details": { "name": "tetracycline_testing_standard_details", - "rank": 752, + "rank": 781, "slot_group": "Antimicrobial resistance" }, "tetracycline_susceptible_breakpoint": { "name": "tetracycline_susceptible_breakpoint", - "rank": 753, + "rank": 782, "slot_group": "Antimicrobial resistance" }, "tetracycline_intermediate_breakpoint": { "name": "tetracycline_intermediate_breakpoint", - "rank": 754, + "rank": 783, "slot_group": "Antimicrobial resistance" }, "tetracycline_resistant_breakpoint": { "name": "tetracycline_resistant_breakpoint", - "rank": 755, + "rank": 784, "slot_group": "Antimicrobial resistance" }, "tigecycline_resistance_phenotype": { "name": "tigecycline_resistance_phenotype", - "rank": 756, + "rank": 785, "slot_group": "Antimicrobial resistance" }, "tigecycline_measurement": { "name": "tigecycline_measurement", - "rank": 757, + "rank": 786, "slot_group": "Antimicrobial resistance" }, "tigecycline_measurement_units": { "name": "tigecycline_measurement_units", - "rank": 758, + "rank": 787, "slot_group": "Antimicrobial resistance" }, "tigecycline_measurement_sign": { "name": "tigecycline_measurement_sign", - "rank": 759, + "rank": 788, "slot_group": "Antimicrobial resistance" }, "tigecycline_laboratory_typing_method": { "name": "tigecycline_laboratory_typing_method", - "rank": 760, + "rank": 789, "slot_group": "Antimicrobial resistance" }, "tigecycline_laboratory_typing_platform": { "name": "tigecycline_laboratory_typing_platform", - "rank": 761, + "rank": 790, "slot_group": "Antimicrobial resistance" }, "tigecycline_laboratory_typing_platform_version": { "name": "tigecycline_laboratory_typing_platform_version", - "rank": 762, + "rank": 791, "slot_group": "Antimicrobial resistance" }, "tigecycline_vendor_name": { "name": "tigecycline_vendor_name", - "rank": 763, + "rank": 792, "slot_group": "Antimicrobial resistance" }, "tigecycline_testing_standard": { "name": "tigecycline_testing_standard", - "rank": 764, + "rank": 793, "slot_group": "Antimicrobial resistance" }, "tigecycline_testing_standard_version": { "name": "tigecycline_testing_standard_version", - "rank": 765, + "rank": 794, "slot_group": "Antimicrobial resistance" }, "tigecycline_testing_standard_details": { "name": "tigecycline_testing_standard_details", - "rank": 766, + "rank": 795, "slot_group": "Antimicrobial resistance" }, "tigecycline_susceptible_breakpoint": { "name": "tigecycline_susceptible_breakpoint", - "rank": 767, + "rank": 796, "slot_group": "Antimicrobial resistance" }, "tigecycline_intermediate_breakpoint": { "name": "tigecycline_intermediate_breakpoint", - "rank": 768, + "rank": 797, "slot_group": "Antimicrobial resistance" }, "tigecycline_resistant_breakpoint": { "name": "tigecycline_resistant_breakpoint", - "rank": 769, + "rank": 798, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_resistance_phenotype": { "name": "trimethoprimsulfamethoxazole_resistance_phenotype", - "rank": 770, + "rank": 799, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_measurement": { "name": "trimethoprimsulfamethoxazole_measurement", - "rank": 771, + "rank": 800, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_measurement_units": { "name": "trimethoprimsulfamethoxazole_measurement_units", - "rank": 772, + "rank": 801, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_measurement_sign": { "name": "trimethoprimsulfamethoxazole_measurement_sign", - "rank": 773, + "rank": 802, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_laboratory_typing_method": { "name": "trimethoprimsulfamethoxazole_laboratory_typing_method", - "rank": 774, + "rank": 803, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_laboratory_typing_platform": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", + "rank": 804, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", + "rank": 805, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_vendor_name": { + "name": "trimethoprimsulfamethoxazole_vendor_name", + "rank": 806, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_testing_standard": { + "name": "trimethoprimsulfamethoxazole_testing_standard", + "rank": 807, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_testing_standard_version": { + "name": "trimethoprimsulfamethoxazole_testing_standard_version", + "rank": 808, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_testing_standard_details": { + "name": "trimethoprimsulfamethoxazole_testing_standard_details", + "rank": 809, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_susceptible_breakpoint": { + "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", + "rank": 810, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_intermediate_breakpoint": { + "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", + "rank": 811, + "slot_group": "Antimicrobial resistance" + }, + "trimethoprimsulfamethoxazole_resistant_breakpoint": { + "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", + "rank": 812, "slot_group": "Antimicrobial resistance" }, - "trimethoprimsulfamethoxazole_laboratory_typing_platform": { - "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", - "rank": 775, - "slot_group": "Antimicrobial resistance" + "authors": { + "name": "authors", + "rank": 813, + "slot_group": "Contributor acknowledgement" + }, + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "rank": 814, + "slot_group": "Contributor acknowledgement" + } + }, + "attributes": { + "sample_collector_sample_id": { + "name": "sample_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "sample_collector_sample_ID", + "comments": [ + "The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "ABCD123" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:sample_name", + "NCBI_BIOSAMPLE_Enterics:sample_name", + "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "sample_collector_sample_id", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "alternative_sample_id": { + "name": "alternative_sample_id", + "description": "An alternative sample_ID assigned to the sample by another organization.", + "title": "alternative_sample_ID", + "comments": [ + "\"Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nMultiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.\"" + ], + "examples": [ + { + "value": "ABCD1234[PHAC]" + }, + { + "value": "12345rev[CFIA]" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 2, + "slot_uri": "GENEPIO:0100427", + "alias": "alternative_sample_id", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "required": true + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the agency, organization or institution with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:collected_by", + "NCBI_BIOSAMPLE_Enterics:collected_by" + ], + "rank": 3, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "SampleCollectedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "description": "The specific laboratory affiliation of the sample collector.", + "title": "sample_collected_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 4, + "slot_uri": "GENEPIO:0100428", + "alias": "sample_collected_by_laboratory_name", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_project_name": { + "name": "sample_collection_project_name", + "description": "The name of the project/initiative/program for which the sample was collected.", + "title": "sample_collection_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Watershed Project (HA-120)" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:project_name" + ], + "rank": 5, + "slot_uri": "GENEPIO:0100429", + "alias": "sample_collection_project_name", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_plan_name": { + "name": "sample_plan_name", + "description": "The name of the study design for a surveillance project.", + "title": "sample_plan_name", + "comments": [ + "Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "National Microbiological Baseline Study in Broiler Chicken" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 6, + "slot_uri": "GENEPIO:0100430", + "alias": "sample_plan_name", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sample_plan_id": { + "name": "sample_plan_id", + "description": "The identifier of the study design for a surveillance project.", + "title": "sample_plan_ID", + "comments": [ + "Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2001_M205" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 7, + "slot_uri": "GENEPIO:0100431", + "alias": "sample_plan_id", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "description": "The name or job title of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 8, + "slot_uri": "GENEPIO:0100432", + "alias": "sample_collector_contact_name", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "johnnyblogs@lab.ca" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 9, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Surveillance [GENEPIO:0100004]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:purpose_of_sampling", + "NCBI_BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 10, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The experimental activities or variables that affected the sample collected.", + "title": "presampling_activity", + "comments": [ + "If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Antimicrobial pre-treatment [GENEPIO:0100537]" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 11, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "PresamplingActivityMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the experimental activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the experimental details using free text." + ], + "examples": [ + { + "value": "Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter." + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 12, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol_field": { + "name": "experimental_protocol_field", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol_field", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "examples": [ + { + "value": "OneHealth2024_protocol" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 13, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol_field", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control [GENEPIO:0101018]" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 14, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "ExperimentalSpecimenRoleTypeMenu" + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures.", + "title": "specimen_processing", + "comments": [ + "Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Samples pooled [OBI:0600016]" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 15, + "slot_uri": "GENEPIO:0100435", + "alias": "specimen_processing", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 16, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { - "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", - "rank": 776, - "slot_group": "Antimicrobial resistance" + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic acid extraction method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and Salmonella (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 17, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_vendor_name": { - "name": "trimethoprimsulfamethoxazole_vendor_name", - "rank": 777, - "slot_group": "Antimicrobial resistance" + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic acid extraction kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 18, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_testing_standard": { - "name": "trimethoprimsulfamethoxazole_testing_standard", - "rank": 778, - "slot_group": "Antimicrobial resistance" + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name (country)", + "comments": [ + "Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value." + ], + "examples": [ + { + "value": "Canada [GAZ:00002560]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:geo_loc_name", + "BIOSAMPLE:geo_loc_name%20%28country%29", + "NCBI_BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 19, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "trimethoprimsulfamethoxazole_testing_standard_version": { - "name": "trimethoprimsulfamethoxazole_testing_standard_version", - "rank": 779, - "slot_group": "Antimicrobial resistance" + "geo_loc_name_state_province_region": { + "name": "geo_loc_name_state_province_region", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name (state/province/region)", + "comments": [ + "Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value." + ], + "examples": [ + { + "value": "British Columbia [GAZ:00002562]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:geo_loc_name", + "BIOSAMPLE:geo_loc_name%20%28state/province/region%29", + "NCBI_BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 20, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_region", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "GeoLocNameStateProvinceRegionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "trimethoprimsulfamethoxazole_testing_standard_details": { - "name": "trimethoprimsulfamethoxazole_testing_standard_details", - "rank": 780, - "slot_group": "Antimicrobial resistance" + "geo_loc_name_site": { + "name": "geo_loc_name_site", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name (site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:geo_loc_name", + "BIOSAMPLE:geo_loc_name%20%28site%29" + ], + "rank": 21, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "trimethoprimsulfamethoxazole_susceptible_breakpoint": { - "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", - "rank": 781, - "slot_group": "Antimicrobial resistance" + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", + "description": "The country of origin of a food product.", + "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_origin" + ], + "rank": 22, + "slot_uri": "GENEPIO:0100437", + "alias": "food_product_origin_geo_loc_name_country", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "trimethoprimsulfamethoxazole_intermediate_breakpoint": { - "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", - "rank": 782, - "slot_group": "Antimicrobial resistance" + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", + "description": "The country of origin of the host.", + "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 23, + "slot_uri": "GENEPIO:0100438", + "alias": "host_origin_geo_loc_name_country", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "trimethoprimsulfamethoxazole_resistant_breakpoint": { - "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", - "rank": 783, - "slot_group": "Antimicrobial resistance" + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc latitude", + "comments": [ + "If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 24, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "authors": { - "name": "authors", - "rank": 784, - "slot_group": "Contributor acknowledgement" + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc longitude", + "comments": [ + "If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 25, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "dataharmonizer_provenance": { - "name": "dataharmonizer_provenance", - "rank": 785, - "slot_group": "Contributor acknowledgement" - } - }, - "attributes": { - "sample_collector_sample_id": { - "name": "sample_collector_sample_id", - "description": "The user-defined name for the sample.", - "title": "sample_collector_sample_ID", + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected.", + "title": "sample_collection_date", + "todos": [ + "<={today}" + ], "comments": [ - "The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value." + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], "examples": [ { - "value": "ABCD123" + "value": "2020-10-30" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:sample_name", - "NCBI_BIOSAMPLE_Enterics:sample_name", - "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" + "BIOSAMPLE:sample%20collection%20date", + "NCBI_BIOSAMPLE_Enterics:collection_date" ], - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "sample_collector_sample_id", + "rank": 26, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "date", + "required": true + }, + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", + "description": "The precision to which the \"sample collection date\" was provided.", + "title": "sample_collection_date_precision", + "comments": [ + "Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"." + ], + "examples": [ + { + "value": "day [UO:0000033]" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 27, + "slot_uri": "GENEPIO:0001177", + "alias": "sample_collection_date_precision", "owner": "GRDI", "domain_of": [ "GRDI" @@ -28879,307 +30427,389 @@ "required": true, "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "SampleCollectionDatePrecisionMenu" }, { "range": "NullValueMenu" } ] }, - "alternative_sample_id": { - "name": "alternative_sample_id", - "description": "An alternative sample_ID assigned to the sample by another organization.", - "title": "alternative_sample_ID", + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], "comments": [ - "\"Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nMultiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.\"" + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], "examples": [ { - "value": "ABCD1234[PHAC]" + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" }, { - "value": "12345rev[CFIA]" + "range": "NullValueMenu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample_processing_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" } ], "from_schema": "https://example.com/GRDI", - "rank": 2, - "slot_uri": "GENEPIO:0100427", - "alias": "alternative_sample_id", + "rank": 29, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "required": true + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample_collected_by": { - "name": "sample_collected_by", - "description": "The name of the agency, organization or institution with which the sample collector is affiliated.", - "title": "sample_collected_by", + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", "comments": [ - "Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide this time in ISO 8601 24hr format, in your local time." ], "examples": [ { - "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + "value": "17:15 PST" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:collected_by", - "NCBI_BIOSAMPLE_Enterics:collected_by" - ], - "rank": 3, - "slot_uri": "GENEPIO:0001153", - "alias": "sample_collected_by", + "rank": 30, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, "any_of": [ { - "range": "SampleCollectedByMenu" + "range": "time" }, { "range": "NullValueMenu" } ] }, - "sample_collected_by_laboratory_name": { - "name": "sample_collected_by_laboratory_name", - "description": "The specific laboratory affiliation of the sample collector.", - "title": "sample_collected_by_laboratory_name", + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", "comments": [ - "Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide this time in ISO 8601 24hr format, in your local time." ], "examples": [ { - "value": "Topp Lab" + "value": "19:15 PST" } ], "from_schema": "https://example.com/GRDI", - "rank": 4, - "slot_uri": "GENEPIO:0100428", - "alias": "sample_collected_by_laboratory_name", + "rank": 31, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample_collection_project_name": { - "name": "sample_collection_project_name", - "description": "The name of the project/initiative/program for which the sample was collected.", - "title": "sample_collection_project_name", + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", "comments": [ - "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." ], "examples": [ { - "value": "Watershed Project (HA-120)" + "value": "Morning" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:project_name" - ], - "rank": 5, - "slot_uri": "GENEPIO:0100429", - "alias": "sample_collection_project_name", + "rank": 32, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "SampleCollectionTimeOfDayMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample_plan_name": { - "name": "sample_plan_name", - "description": "The name of the study design for a surveillance project.", - "title": "sample_plan_name", + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", "comments": [ - "Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the numerical value of time." ], "examples": [ { - "value": "National Microbiological Baseline Study in Broiler Chicken" + "value": "1900-01-03" } ], "from_schema": "https://example.com/GRDI", - "rank": 6, - "slot_uri": "GENEPIO:0100430", - "alias": "sample_plan_name", + "rank": 33, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample_plan_id": { - "name": "sample_plan_id", - "description": "The identifier of the study design for a surveillance project.", - "title": "sample_plan_ID", + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", "comments": [ - "Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the units from the pick list." ], "examples": [ { - "value": "2001_M205" + "value": "Hour" } ], "from_schema": "https://example.com/GRDI", - "rank": 7, - "slot_uri": "GENEPIO:0100431", - "alias": "sample_plan_id", + "rank": 34, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "SampleCollectionDurationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample_collector_contact_name": { - "name": "sample_collector_contact_name", - "description": "The name or job title of the contact responsible for follow-up regarding the sample.", - "title": "sample_collector_contact_name", + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample_received_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], "comments": [ - "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], "examples": [ { - "value": "Enterics Lab Manager" + "value": "2020-11-15" } ], "from_schema": "https://example.com/GRDI", - "rank": 8, - "slot_uri": "GENEPIO:0100432", - "alias": "sample_collector_contact_name", + "rank": 35, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "range": "date" }, - "sample_collector_contact_email": { - "name": "sample_collector_contact_email", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "title": "sample_collector_contact_email", + "original_sample_description": { + "name": "original_sample_description", + "description": "The original sample description provided by the sample collector.", + "title": "original_sample_description", "comments": [ - "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications." ], "examples": [ { - "value": "johnnyblogs@lab.ca" + "value": "RTE Prosciutto from deli" } ], "from_schema": "https://example.com/GRDI", - "rank": 9, - "slot_uri": "GENEPIO:0001156", - "alias": "sample_collector_contact_email", + "rank": 36, + "slot_uri": "GENEPIO:0100439", + "alias": "original_sample_description", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "range": "WhitespaceMinimizedString" }, - "purpose_of_sampling": { - "name": "purpose_of_sampling", - "description": "The reason that the sample was collected.", - "title": "purpose_of_sampling", + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", "comments": [ - "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "Surveillance [GENEPIO:0100004]" + "value": "Poultry hatchery [ENVO:01001874]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:purpose_of_sampling", - "NCBI_BIOSAMPLE_Enterics:purpose_of_sampling" + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_site", + "NCBI_BIOSAMPLE_Enterics:isolation_source", + "NCBI_BIOSAMPLE_Enterics:animal_env" ], - "rank": 10, - "slot_uri": "GENEPIO:0001198", - "alias": "purpose_of_sampling", + "rank": 37, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "PurposeOfSamplingMenu" + "range": "EnvironmentalSiteMenu" }, { "range": "NullValueMenu" } ] }, - "presampling_activity": { - "name": "presampling_activity", - "description": "The experimental activities or variables that affected the sample collected.", - "title": "presampling_activity", + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", "comments": [ - "If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "Antimicrobial pre-treatment [GENEPIO:0100537]" + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" } ], "from_schema": "https://example.com/GRDI", - "rank": 11, - "slot_uri": "GENEPIO:0100433", - "alias": "presampling_activity", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_material", + "NCBI_BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "PresamplingActivityMenu" + "range": "EnvironmentalMaterialMenu" }, { "range": "NullValueMenu" } ] }, - "presampling_activity_details": { - "name": "presampling_activity_details", - "description": "The details of the experimental activities or variables that affected the sample collected.", - "title": "presampling_activity_details", + "environmental_material_constituent": { + "name": "environmental_material_constituent", + "description": "The material constituents that comprise an environmental material e.g. lead, plastic, paper.", + "title": "environmental_material_constituent", "comments": [ - "Briefly describe the experimental details using free text." + "If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter." + "value": "lead" + }, + { + "value": "plastic" } ], "from_schema": "https://example.com/GRDI", - "rank": 12, - "slot_uri": "GENEPIO:0100434", - "alias": "presampling_activity_details", + "rank": 39, + "slot_uri": "GENEPIO:0101197", + "alias": "environmental_material_constituent", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29187,299 +30817,361 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "experimental_protocol_field": { - "name": "experimental_protocol_field", - "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", - "title": "experimental_protocol_field", + "animal_or_plant_population": { + "name": "animal_or_plant_population", + "description": "The type of animal or plant population inhabiting an area.", + "title": "animal_or_plant_population", "comments": [ - "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + "This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank." ], "examples": [ { - "value": "OneHealth2024_protocol" + "value": "Turkey [NCBITaxon:9103]" } ], "from_schema": "https://example.com/GRDI", - "rank": 13, - "slot_uri": "GENEPIO:0101029", - "alias": "experimental_protocol_field", + "rank": 40, + "slot_uri": "GENEPIO:0100443", + "alias": "animal_or_plant_population", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "experimental_specimen_role_type": { - "name": "experimental_specimen_role_type", - "description": "The type of role that the sample represents in the experiment.", - "title": "experimental_specimen_role_type", - "comments": [ - "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." - ], - "examples": [ + "recommended": true, + "multivalued": true, + "any_of": [ { - "value": "Positive experimental control [GENEPIO:0101018]" + "range": "AnimalOrPlantPopulationMenu" + }, + { + "range": "NullValueMenu" } - ], - "from_schema": "https://example.com/GRDI", - "rank": 14, - "slot_uri": "GENEPIO:0100921", - "alias": "experimental_specimen_role_type", - "owner": "GRDI", - "domain_of": [ - "GRDI" - ], - "slot_group": "Sample collection and processing", - "range": "ExperimentalSpecimenRoleTypeMenu" + ] }, - "specimen_processing": { - "name": "specimen_processing", - "description": "The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures.", - "title": "specimen_processing", + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical_material", "comments": [ - "Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "Samples pooled [OBI:0600016]" + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" } ], "from_schema": "https://example.com/GRDI", - "rank": 15, - "slot_uri": "GENEPIO:0100435", - "alias": "specimen_processing", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_material", + "NCBI_BIOSAMPLE_Enterics:host_tissue_sampled", + "NCBI_BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 41, + "slot_uri": "GENEPIO:0001211", + "alias": "anatomical_material", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "SpecimenProcessingMenu" + "range": "AnatomicalMaterialMenu" }, { "range": "NullValueMenu" } ] }, - "specimen_processing_details": { - "name": "specimen_processing_details", - "description": "The details of the processing applied to the sample during or after receiving the sample.", - "title": "specimen_processing_details", + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body_product", "comments": [ - "Briefly describe the processes applied to the sample." + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "25 samples were pooled and further prepared as a single sample during library prep." + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" } ], "from_schema": "https://example.com/GRDI", - "rank": 16, - "slot_uri": "GENEPIO:0100311", - "alias": "specimen_processing_details", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:body_product", + "NCBI_BIOSAMPLE_Enterics:host_body_product", + "NCBI_BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 42, + "slot_uri": "GENEPIO:0001216", + "alias": "body_product", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "nucleic_acid_extraction_method": { - "name": "nucleic_acid_extraction_method", - "description": "The process used to extract genomic material from a sample.", - "title": "nucleic acid extraction method", + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical_part", "comments": [ - "Briefly describe the extraction method used." + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and Salmonella (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + "value": "Snout [UBERON:0006333]" } ], "from_schema": "https://example.com/GRDI", - "rank": 17, - "slot_uri": "GENEPIO:0100939", - "alias": "nucleic_acid_extraction_method", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_part", + "NCBI_BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001214", + "alias": "anatomical_part", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "nucleic_acid_extraction_kit": { - "name": "nucleic_acid_extraction_kit", - "description": "The kit used to extract genomic material from a sample", - "title": "nucleic acid extraction kit", + "anatomical_region": { + "name": "anatomical_region", + "description": "A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.", + "title": "anatomical_region", "comments": [ - "Provide the name of the genomic extraction kit used." + "This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist." ], "examples": [ { - "value": "QIAamp PowerFecal Pro DNA Kit" + "value": "Dorso-lateral region [BSPO:0000080]" } ], "from_schema": "https://example.com/GRDI", - "rank": 18, - "slot_uri": "GENEPIO:0100772", - "alias": "nucleic_acid_extraction_kit", + "rank": 44, + "slot_uri": "GENEPIO:0100700", + "alias": "anatomical_region", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalRegionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name_country": { - "name": "geo_loc_name_country", - "description": "The country of origin of the sample.", - "title": "geo_loc_name (country)", + "food_product": { + "name": "food_product", + "description": "A material consumed and digested for nutritional value or enjoyment.", + "title": "food_product", "comments": [ - "Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value." + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "Canada [GAZ:00002560]" + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:geo_loc_name", - "BIOSAMPLE:geo_loc_name%20%28country%29", - "NCBI_BIOSAMPLE_Enterics:geo_loc_name" + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:food_product", + "NCBI_BIOSAMPLE_Enterics:isolation_source", + "NCBI_BIOSAMPLE_Enterics:food_product_type" ], - "rank": 19, - "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_country", + "rank": 45, + "slot_uri": "GENEPIO:0100444", + "alias": "food_product", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "GeoLocNameCountryMenu" + "range": "FoodProductMenu" }, { "range": "NullValueMenu" } ] }, - "geo_loc_name_state_province_region": { - "name": "geo_loc_name_state_province_region", - "description": "The state/province/territory of origin of the sample.", - "title": "geo_loc_name (state/province/region)", + "food_product_properties": { + "name": "food_product_properties", + "description": "Any characteristic of the food product pertaining to its state, processing, or implications for consumers.", + "title": "food_product_properties", "comments": [ - "Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value." + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." ], "examples": [ { - "value": "British Columbia [GAZ:00002562]" + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:geo_loc_name", - "BIOSAMPLE:geo_loc_name%20%28state/province/region%29", - "NCBI_BIOSAMPLE_Enterics:geo_loc_name" + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:food_product_properties", + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], - "rank": 20, - "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_state_province_region", + "rank": 46, + "slot_uri": "GENEPIO:0100445", + "alias": "food_product_properties", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "GeoLocNameStateProvinceRegionMenu" + "range": "FoodProductPropertiesMenu" }, { "range": "NullValueMenu" } ] }, - "geo_loc_name_site": { - "name": "geo_loc_name_site", - "description": "The name of a specific geographical location e.g. Credit River (rather than river).", - "title": "geo_loc_name (site)", + "label_claim": { + "name": "label_claim", + "description": "The claim made by the label that relates to food processing, allergen information etc.", + "title": "label_claim", "comments": [ - "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + "Provide any characteristic of the food product, as described on the label only." ], "examples": [ { - "value": "Credit River" + "value": "Antibiotic free [FOODON:03601063]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:geo_loc_name", - "BIOSAMPLE:geo_loc_name%20%28site%29" + "NCBI_BIOSAMPLE_Enterics:label_claims" ], - "rank": 21, - "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_site", + "rank": 47, + "slot_uri": "FOODON:03602001", + "alias": "label_claim", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "multivalued": true, + "any_of": [ + { + "range": "LabelClaimMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "food_product_origin_geo_loc_name_country": { - "name": "food_product_origin_geo_loc_name_country", - "description": "The country of origin of a food product.", - "title": "food_product_origin_geo_loc_name (country)", + "animal_source_of_food": { + "name": "animal_source_of_food", + "description": "The animal from which the food product was derived.", + "title": "animal_source_of_food", "comments": [ - "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma." ], "examples": [ { - "value": "United States of America [GAZ:00002459]" + "value": "Chicken [NCBITaxon:9031]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:food_origin" + "NCBI_BIOSAMPLE_Enterics:food_source" ], - "rank": 22, - "slot_uri": "GENEPIO:0100437", - "alias": "food_product_origin_geo_loc_name_country", + "rank": 48, + "slot_uri": "GENEPIO:0100446", + "alias": "animal_source_of_food", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "GeoLocNameCountryMenu" + "range": "AnimalSourceOfFoodMenu" }, { "range": "NullValueMenu" } ] }, - "host_origin_geo_loc_name_country": { - "name": "host_origin_geo_loc_name_country", - "description": "The country of origin of the host.", - "title": "host_origin_geo_loc_name (country)", + "food_product_production_stream": { + "name": "food_product_production_stream", + "description": "A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity.", + "title": "food_product_production_stream", "comments": [ - "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the name of the agricultural production stream from the picklist." ], "examples": [ { - "value": "South Africa [GAZ:00001094]" + "value": "Beef cattle production stream [FOODON:03000452]" } ], "from_schema": "https://example.com/GRDI", - "rank": 23, - "slot_uri": "GENEPIO:0100438", - "alias": "host_origin_geo_loc_name_country", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_prod" + ], + "rank": 49, + "slot_uri": "GENEPIO:0100699", + "alias": "food_product_production_stream", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29487,147 +31179,163 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "GeoLocNameCountryMenu" + "range": "FoodProductProductionStreamMenu" }, { "range": "NullValueMenu" } ] }, - "geo_loc_latitude": { - "name": "geo_loc_latitude", - "description": "The latitude coordinates of the geographical location of sample collection.", - "title": "geo_loc latitude", + "food_packaging": { + "name": "food_packaging", + "description": "The type of packaging used to contain a food product.", + "title": "food_packaging", "comments": [ - "If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value." + "If known, provide information regarding how the food product was packaged." ], "examples": [ { - "value": "38.98 N" + "value": "Plastic tray or pan [FOODON:03490126]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:lat_lon" + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:food_packaging", + "NCBI_BIOSAMPLE_Enterics:food_contain_wrap" ], - "rank": 24, - "slot_uri": "GENEPIO:0100309", - "alias": "geo_loc_latitude", + "rank": 50, + "slot_uri": "GENEPIO:0100447", + "alias": "food_packaging", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "FoodPackagingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_longitude": { - "name": "geo_loc_longitude", - "description": "The longitude coordinates of the geographical location of sample collection.", - "title": "geo_loc longitude", + "food_quality_date": { + "name": "food_quality_date", + "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", + "title": "food_quality_date", + "todos": [ + "<={today}" + ], "comments": [ - "If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value." + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." ], "examples": [ { - "value": "77.11 W" + "value": "2020-05-25" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:lat_lon" + "NCBI_BIOSAMPLE_Enterics:food_quality_date" ], - "rank": 25, - "slot_uri": "GENEPIO:0100310", - "alias": "geo_loc_longitude", + "rank": 51, + "slot_uri": "GENEPIO:0100615", + "alias": "food_quality_date", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "range": "date" }, - "sample_collection_date": { - "name": "sample_collection_date", - "description": "The date on which the sample was collected.", - "title": "sample_collection_date", + "food_packaging_date": { + "name": "food_packaging_date", + "description": "A food product's packaging date as marked by a food manufacturer or retailer.", + "title": "food_packaging_date", "todos": [ "<={today}" ], "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." ], "examples": [ { - "value": "2020-10-30" + "value": "2020-05-25" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:sample%20collection%20date", - "NCBI_BIOSAMPLE_Enterics:collection_date" - ], - "rank": 26, - "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", + "rank": 52, + "slot_uri": "GENEPIO:0100616", + "alias": "food_packaging_date", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "date", - "required": true + "range": "date" }, - "sample_collection_date_precision": { - "name": "sample_collection_date_precision", - "description": "The precision to which the \"sample collection date\" was provided.", - "title": "sample_collection_date_precision", + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", "comments": [ - "Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"." + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "day [UO:0000033]" + "value": "Drag swab [OBI:0002822]" } ], "from_schema": "https://example.com/GRDI", - "rank": 27, - "slot_uri": "GENEPIO:0001177", - "alias": "sample_collection_date_precision", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_device", + "NCBI_BIOSAMPLE_Enterics:samp_collect_device", + "NCBI_BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 53, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, "any_of": [ { - "range": "SampleCollectionDatePrecisionMenu" + "range": "CollectionDeviceMenu" }, { "range": "NullValueMenu" } ] }, - "sample_collection_end_date": { - "name": "sample_collection_end_date", - "description": "The date on which sample collection ended for a continuous sample.", - "title": "sample_collection_end_date", - "todos": [ - ">={sample_collection_date}", - "<={today}" - ], + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", "comments": [ - "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." ], "examples": [ { - "value": "2020-03-18" + "value": "Rinsing for specimen collection [GENEPIO_0002116]" } ], "from_schema": "https://example.com/GRDI", - "rank": 28, - "slot_uri": "GENEPIO:0101071", - "alias": "sample_collection_end_date", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_method", + "NCBI_BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 54, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29636,2342 +31344,2166 @@ "recommended": true, "any_of": [ { - "range": "date" + "range": "CollectionMethodMenu" }, { "range": "NullValueMenu" } ] }, - "sample_processing_date": { - "name": "sample_processing_date", - "description": "The date on which the sample was processed.", - "title": "sample_processing_date", - "todos": [ - ">={sample_collection_date}", - "<={today}" - ], + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", "comments": [ - "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + "Provide the numerical value of volume." ], "examples": [ { - "value": "2020-03-16" + "value": "5" } ], "from_schema": "https://example.com/GRDI", - "rank": 29, - "slot_uri": "GENEPIO:0100763", - "alias": "sample_processing_date", + "rank": 55, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "date" - }, - { - "range": "NullValueMenu" - } - ] + "range": "WhitespaceMinimizedString" }, - "sample_collection_start_time": { - "name": "sample_collection_start_time", - "description": "The time at which sample collection began.", - "title": "sample_collection_start_time", + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", "comments": [ - "Provide this time in ISO 8601 24hr format, in your local time." + "Provide the units from the pick list." ], "examples": [ { - "value": "17:15 PST" + "value": "milliliter (mL) [UO:0000098]" } ], "from_schema": "https://example.com/GRDI", - "rank": 30, - "slot_uri": "GENEPIO:0101072", - "alias": "sample_collection_start_time", + "rank": 56, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true, - "any_of": [ - { - "range": "time" - }, - { - "range": "NullValueMenu" - } - ] + "range": "SampleVolumeMeasurementUnitMenu" }, - "sample_collection_end_time": { - "name": "sample_collection_end_time", - "description": "The time at which sample collection ended.", - "title": "sample_collection_end_time", + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", "comments": [ - "Provide this time in ISO 8601 24hr format, in your local time." + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." ], "examples": [ { - "value": "19:15 PST" + "value": "No residual sample (sample all used) [GENEPIO:0101088]" } ], "from_schema": "https://example.com/GRDI", - "rank": 31, - "slot_uri": "GENEPIO:0101073", - "alias": "sample_collection_end_time", + "rank": 57, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true, - "any_of": [ - { - "range": "time" - }, - { - "range": "NullValueMenu" - } - ] + "range": "ResidualSampleStatusMenu" }, - "sample_collection_time_of_day": { - "name": "sample_collection_time_of_day", - "description": "The descriptive time of day during which the sample was collected.", - "title": "sample_collection_time_of_day", + "sample_storage_method": { + "name": "sample_storage_method", + "description": "A specification of the way that a specimen is or was stored.", + "title": "sample_storage_method", "comments": [ - "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + "Provide a description of how the sample was stored." ], "examples": [ { - "value": "Morning" + "value": "packed on ice during transport" } ], "from_schema": "https://example.com/GRDI", - "rank": 32, - "slot_uri": "GENEPIO:0100765", - "alias": "sample_collection_time_of_day", + "rank": 58, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "SampleCollectionTimeOfDayMenu" - }, + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The material or matrix in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide a description of the medium in which the sample was stored." + ], + "examples": [ { - "range": "NullValueMenu" + "value": "PBS + 20% glycerol" } - ] + ], + "from_schema": "https://example.com/GRDI", + "rank": 59, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "sample_collection_time_duration_value": { - "name": "sample_collection_time_duration_value", - "description": "The amount of time over which the sample was collected.", - "title": "sample_collection_time_duration_value", + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", "comments": [ "Provide the numerical value of time." ], "examples": [ { - "value": "1900-01-03" + "value": "5" } ], "from_schema": "https://example.com/GRDI", - "rank": 33, - "slot_uri": "GENEPIO:0100766", - "alias": "sample_collection_time_duration_value", + "rank": 60, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "range": "WhitespaceMinimizedString" }, - "sample_collection_time_duration_unit": { - "name": "sample_collection_time_duration_unit", - "description": "The units of the time duration measurement of sample collection.", - "title": "sample_collection_time_duration_unit", + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", "comments": [ "Provide the units from the pick list." ], "examples": [ { - "value": "Hour" + "value": "Day [UO:0000033]" } ], "from_schema": "https://example.com/GRDI", - "rank": 34, - "slot_uri": "GENEPIO:0100767", - "alias": "sample_collection_time_duration_unit", + "rank": 61, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true, - "any_of": [ - { - "range": "SampleCollectionDurationUnitMenu" - }, - { - "range": "NullValueMenu" - } - ] + "range": "SampleStorageDurationUnitMenu" }, - "sample_received_date": { - "name": "sample_received_date", - "description": "The date on which the sample was received.", - "title": "sample_received_date", - "todos": [ - ">={sample_collection_date}", - "<={today}" - ], + "nucleic_acid_storage_duration_value": { + "name": "nucleic_acid_storage_duration_value", + "description": "The numerical value of the time measurement during which the extracted nucleic acid is in storage.", + "title": "nucleic_acid_storage_duration_value", "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + "Provide the numerical value of time." ], "examples": [ { - "value": "2020-11-15" + "value": "5" } ], "from_schema": "https://example.com/GRDI", - "rank": 35, - "slot_uri": "GENEPIO:0001179", - "alias": "sample_received_date", + "rank": 62, + "slot_uri": "GENEPIO:0101085", + "alias": "nucleic_acid_storage_duration_value", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "date" + "range": "WhitespaceMinimizedString" }, - "original_sample_description": { - "name": "original_sample_description", - "description": "The original sample description provided by the sample collector.", - "title": "original_sample_description", + "nucleic_acid_storage_duration_unit": { + "name": "nucleic_acid_storage_duration_unit", + "description": "The units of a measured extracted nucleic acid storage duration.", + "title": "nucleic_acid_storage_duration_unit", "comments": [ - "Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications." + "Provide the units from the pick list." ], "examples": [ { - "value": "RTE Prosciutto from deli" + "value": "Year [UO:0000036]" } ], "from_schema": "https://example.com/GRDI", - "rank": 36, - "slot_uri": "GENEPIO:0100439", - "alias": "original_sample_description", + "rank": 63, + "slot_uri": "GENEPIO:0101086", + "alias": "nucleic_acid_storage_duration_unit", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "range": "NucleicAcidStorageDurationUnitMenu" }, - "environmental_site": { - "name": "environmental_site", - "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", - "title": "environmental_site", + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", "comments": [ - "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." ], "examples": [ { - "value": "Poultry hatchery [ENVO:01001874]" + "value": "Total coliform count [GENEPIO:0100729]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:environmental_site", - "NCBI_BIOSAMPLE_Enterics:isolation_source", - "NCBI_BIOSAMPLE_Enterics:animal_env" - ], - "rank": 37, - "slot_uri": "GENEPIO:0001232", - "alias": "environmental_site", + "rank": 64, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true, "multivalued": true, "any_of": [ { - "range": "EnvironmentalSiteMenu" + "range": "AvailableDataTypesMenu" }, { "range": "NullValueMenu" } ] }, - "environmental_material": { - "name": "environmental_material", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", - "title": "environmental_material", + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", "comments": [ - "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." ], "examples": [ { - "value": "Soil [ENVO:00001998]" - }, - { - "value": "Water [CHEBI:15377]" - }, - { - "value": "Wastewater [ENVO:00002001]" - }, - { - "value": "Broom [ENVO:03501377]" + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:environmental_material", - "NCBI_BIOSAMPLE_Enterics:isolation_source" - ], - "rank": 38, - "slot_uri": "GENEPIO:0001223", - "alias": "environmental_material", + "rank": 65, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, - "any_of": [ - { - "range": "EnvironmentalMaterialMenu" - }, - { - "range": "NullValueMenu" - } - ] + "range": "WhitespaceMinimizedString" }, - "environmental_material_constituent": { - "name": "environmental_material_constituent", - "description": "The material constituents that comprise an environmental material e.g. lead, plastic, paper.", - "title": "environmental_material_constituent", + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", "comments": [ - "If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon." + "Provide the numerical depth only of water only (without units)." ], "examples": [ { - "value": "lead" - }, - { - "value": "plastic" + "value": "5" } ], "from_schema": "https://example.com/GRDI", - "rank": 39, - "slot_uri": "GENEPIO:0101197", - "alias": "environmental_material_constituent", + "rank": 66, + "slot_uri": "GENEPIO:0100440", + "alias": "water_depth", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "animal_or_plant_population": { - "name": "animal_or_plant_population", - "description": "The type of animal or plant population inhabiting an area.", - "title": "animal_or_plant_population", + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", "comments": [ - "This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank." + "Provide the units of measurement for which the depth was recorded." ], "examples": [ { - "value": "Turkey [NCBITaxon:9103]" + "value": "meter (m) [UO:0000008]" } ], "from_schema": "https://example.com/GRDI", - "rank": 40, - "slot_uri": "GENEPIO:0100443", - "alias": "animal_or_plant_population", + "rank": 67, + "slot_uri": "GENEPIO:0101025", + "alias": "water_depth_units", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, + "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "AnimalOrPlantPopulationMenu" + "range": "WaterDepthUnitsMenu" }, { "range": "NullValueMenu" } ] }, - "anatomical_material": { - "name": "anatomical_material", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "title": "anatomical_material", + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", "comments": [ - "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + "Provide the numerical depth only of the sediment (without units)." ], "examples": [ { - "value": "Tissue [UBERON:0000479]" - }, - { - "value": "Blood [UBERON:0000178]" + "value": "2" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:anatomical_material", - "NCBI_BIOSAMPLE_Enterics:host_tissue_sampled", - "NCBI_BIOSAMPLE_Enterics:isolation_source" - ], - "rank": 41, - "slot_uri": "GENEPIO:0001211", - "alias": "anatomical_material", + "rank": 68, + "slot_uri": "GENEPIO:0100697", + "alias": "sediment_depth", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, - "any_of": [ - { - "range": "AnatomicalMaterialMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "body_product": { - "name": "body_product", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "title": "body_product", + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", "comments": [ - "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + "Provide the units of measurement for which the depth was recorded." ], "examples": [ { - "value": "Feces [UBERON:0001988]" - }, - { - "value": "Urine [UBERON:0001088]" + "value": "meter (m) [UO:0000008]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:body_product", - "NCBI_BIOSAMPLE_Enterics:host_body_product", - "NCBI_BIOSAMPLE_Enterics:isolation_source" - ], - "rank": 42, - "slot_uri": "GENEPIO:0001216", - "alias": "body_product", + "rank": 69, + "slot_uri": "GENEPIO:0101026", + "alias": "sediment_depth_units", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, + "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "BodyProductMenu" + "range": "SedimentDepthUnitsMenu" }, { "range": "NullValueMenu" } ] }, - "anatomical_part": { - "name": "anatomical_part", - "description": "An anatomical part of an organism e.g. oropharynx.", - "title": "anatomical_part", + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", "comments": [ - "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + "Provide the numerical value for the temperature of the air (without units)." ], "examples": [ { - "value": "Snout [UBERON:0006333]" + "value": "25" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:anatomical_part", - "NCBI_BIOSAMPLE_Enterics:isolation_source" - ], - "rank": 43, - "slot_uri": "GENEPIO:0001214", - "alias": "anatomical_part", + "rank": 70, + "slot_uri": "GENEPIO:0100441", + "alias": "air_temperature", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, - "any_of": [ - { - "range": "AnatomicalPartMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "anatomical_region": { - "name": "anatomical_region", - "description": "A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.", - "title": "anatomical_region", + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", "comments": [ - "This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist." + "Provide the units of measurement for which the temperature was recorded." ], "examples": [ { - "value": "Dorso-lateral region [BSPO:0000080]" + "value": "degree Celsius (C) [UO:0000027]" } ], "from_schema": "https://example.com/GRDI", - "rank": 44, - "slot_uri": "GENEPIO:0100700", - "alias": "anatomical_region", + "rank": 71, + "slot_uri": "GENEPIO:0101027", + "alias": "air_temperature_units", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, + "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "AnatomicalRegionMenu" + "range": "AirTemperatureUnitsMenu" }, { "range": "NullValueMenu" } ] }, - "food_product": { - "name": "food_product", - "description": "A material consumed and digested for nutritional value or enjoyment.", - "title": "food_product", + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", "comments": [ - "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + "Provide the numerical value for the temperature of the water (without units)." ], "examples": [ { - "value": "Feather meal [FOODON:00003927]" - }, - { - "value": "Bone meal [ENVO:02000054]" - }, - { - "value": "Chicken breast [FOODON:00002703]" + "value": "4" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_product", - "NCBI_BIOSAMPLE_Enterics:isolation_source", - "NCBI_BIOSAMPLE_Enterics:food_product_type" - ], - "rank": 45, - "slot_uri": "GENEPIO:0100444", - "alias": "food_product", + "rank": 72, + "slot_uri": "GENEPIO:0100698", + "alias": "water_temperature", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, - "any_of": [ - { - "range": "FoodProductMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "food_product_properties": { - "name": "food_product_properties", - "description": "Any characteristic of the food product pertaining to its state, processing, or implications for consumers.", - "title": "food_product_properties", + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", "comments": [ - "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + "Provide the units of measurement for which the temperature was recorded." ], "examples": [ { - "value": "Food (chopped) [FOODON:00002777]" - }, - { - "value": "Ready-to-eat (RTE) [FOODON:03316636]" + "value": "degree Celsius (C) [UO:0000027]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_product_properties", - "NCBI_BIOSAMPLE_Enterics:isolation_source" - ], - "rank": 46, - "slot_uri": "GENEPIO:0100445", - "alias": "food_product_properties", + "rank": 73, + "slot_uri": "GENEPIO:0101028", + "alias": "water_temperature_units", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, + "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "FoodProductPropertiesMenu" + "range": "WaterTemperatureUnitsMenu" }, { "range": "NullValueMenu" } ] }, - "label_claim": { - "name": "label_claim", - "description": "The claim made by the label that relates to food processing, allergen information etc.", - "title": "label_claim", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling_weather_conditions", "comments": [ - "Provide any characteristic of the food product, as described on the label only." + "Provide the weather conditions at the time of sample collection." ], "examples": [ { - "value": "Antibiotic free [FOODON:03601063]" + "value": "Rain [ENVO:01001564]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:label_claims" - ], - "rank": 47, - "slot_uri": "FOODON:03602001", - "alias": "label_claim", + "rank": 74, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Environmental conditions and measurements", "multivalued": true, "any_of": [ { - "range": "LabelClaimMenu" + "range": "SamplingWeatherConditionsMenu" }, { "range": "NullValueMenu" } ] }, - "animal_source_of_food": { - "name": "animal_source_of_food", - "description": "The animal from which the food product was derived.", - "title": "animal_source_of_food", + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling_weather_conditions", "comments": [ - "Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma." + "Provide the weather conditions prior to sample collection." ], "examples": [ { - "value": "Chicken [NCBITaxon:9031]" + "value": "Rain [ENVO:01001564]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:food_source" - ], - "rank": 48, - "slot_uri": "GENEPIO:0100446", - "alias": "animal_source_of_food", + "rank": 75, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, + "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "AnimalSourceOfFoodMenu" + "range": "SamplingWeatherConditionsMenu" }, { "range": "NullValueMenu" } ] }, - "food_product_production_stream": { - "name": "food_product_production_stream", - "description": "A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity.", - "title": "food_product_production_stream", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation_measurement_value", "comments": [ - "Provide the name of the agricultural production stream from the picklist." + "Provide the quantity of precipitation in the area leading up to the time of sample collection." ], "examples": [ { - "value": "Beef cattle production stream [FOODON:03000452]" + "value": "12" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:food_prod" - ], - "rank": 49, - "slot_uri": "GENEPIO:0100699", - "alias": "food_product_production_stream", + "rank": 76, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "FoodProductProductionStreamMenu" + "range": "Whitespaceminimizedstring" }, { "range": "NullValueMenu" } ] }, - "food_packaging": { - "name": "food_packaging", - "description": "The type of packaging used to contain a food product.", - "title": "food_packaging", + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", + "title": "precipitation_measurement_unit", "comments": [ - "If known, provide information regarding how the food product was packaged." + "Provide the units of precipitation by selecting a value from the pick list." ], "examples": [ { - "value": "Plastic tray or pan [FOODON:03490126]" + "value": "inch" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_packaging", - "NCBI_BIOSAMPLE_Enterics:food_contain_wrap" - ], - "rank": 50, - "slot_uri": "GENEPIO:0100447", - "alias": "food_packaging", + "rank": 77, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "multivalued": true, + "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "FoodPackagingMenu" + "range": "PrecipitationMeasurementUnitMenu" }, { "range": "NullValueMenu" } ] }, - "food_quality_date": { - "name": "food_quality_date", - "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", - "title": "food_quality_date", - "todos": [ - "<={today}" - ], + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation_measurement_method", "comments": [ - "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + "Provide the name of the procedure or method used to measure precipitation." ], "examples": [ { - "value": "2020-05-25" + "value": "Rain gauge over a 12 hour period prior to sample collection" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:food_quality_date" - ], - "rank": 51, - "slot_uri": "GENEPIO:0100615", - "alias": "food_quality_date", + "rank": 78, + "slot_uri": "GENEPIO:0100913", + "alias": "precipitation_measurement_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "date" + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "food_packaging_date": { - "name": "food_packaging_date", - "description": "A food product's packaging date as marked by a food manufacturer or retailer.", - "title": "food_packaging_date", - "todos": [ - "<={today}" - ], + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host (common name)", "comments": [ - "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." ], "examples": [ { - "value": "2020-05-25" - } - ], - "from_schema": "https://example.com/GRDI", - "rank": 52, - "slot_uri": "GENEPIO:0100616", - "alias": "food_packaging_date", - "owner": "GRDI", - "domain_of": [ - "GRDI" - ], - "slot_group": "Sample collection and processing", - "range": "date" - }, - "collection_device": { - "name": "collection_device", - "description": "The instrument or container used to collect the sample e.g. swab.", - "title": "collection_device", - "comments": [ - "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." - ], - "examples": [ + "value": "Cow [NCBITaxon:9913]" + }, { - "value": "Drag swab [OBI:0002822]" + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:collection_device", - "NCBI_BIOSAMPLE_Enterics:samp_collect_device", - "NCBI_BIOSAMPLE_Enterics:isolation_source" + "NCBI_BIOSAMPLE_Enterics:host" ], - "rank": 53, - "slot_uri": "GENEPIO:0001234", - "alias": "collection_device", + "rank": 79, + "slot_uri": "GENEPIO:0001386", + "alias": "host_common_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host information", "recommended": true, "any_of": [ { - "range": "CollectionDeviceMenu" + "range": "HostCommonNameMenu" }, { "range": "NullValueMenu" } ] }, - "collection_method": { - "name": "collection_method", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "title": "collection_method", + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host (scientific name)", "comments": [ - "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." ], "examples": [ { - "value": "Rinsing for specimen collection [GENEPIO_0002116]" + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:collection_method", - "NCBI_BIOSAMPLE_Enterics:isolation_source" + "BIOSAMPLE:host", + "NCBI_BIOSAMPLE_Enterics:isolation_source", + "NCBI_BIOSAMPLE_Enterics:host" ], - "rank": 54, - "slot_uri": "GENEPIO:0001241", - "alias": "collection_method", + "rank": 80, + "slot_uri": "GENEPIO:0001387", + "alias": "host_scientific_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host information", "recommended": true, "any_of": [ { - "range": "CollectionMethodMenu" + "range": "HostScientificNameMenu" }, { "range": "NullValueMenu" } ] }, - "sample_volume_measurement_value": { - "name": "sample_volume_measurement_value", - "description": "The numerical value of the volume measurement of the sample collected.", - "title": "sample_volume_measurement_value", + "host_ecotype": { + "name": "host_ecotype", + "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", + "title": "host (ecotype)", "comments": [ - "Provide the numerical value of volume." + "Provide the name of the ecotype of the host organism." ], "examples": [ { - "value": "5" + "value": "Sea ecotype" } ], "from_schema": "https://example.com/GRDI", - "rank": 55, - "slot_uri": "GENEPIO:0100768", - "alias": "sample_volume_measurement_value", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_variety" + ], + "rank": 81, + "slot_uri": "GENEPIO:0100450", + "alias": "host_ecotype", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host information", "range": "WhitespaceMinimizedString" }, - "sample_volume_measurement_unit": { - "name": "sample_volume_measurement_unit", - "description": "The units of the volume measurement of the sample collected.", - "title": "sample_volume_measurement_unit", + "host_breed": { + "name": "host_breed", + "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", + "title": "host (breed)", "comments": [ - "Provide the units from the pick list." + "Provide the name of the breed of the host organism." ], "examples": [ { - "value": "milliliter (mL) [UO:0000098]" + "value": "Holstein" } ], "from_schema": "https://example.com/GRDI", - "rank": 56, - "slot_uri": "GENEPIO:0100769", - "alias": "sample_volume_measurement_unit", + "exact_mappings": [ + "BIOSAMPLE:host_disease", + "NCBI_BIOSAMPLE_Enterics:host_animal_breed" + ], + "rank": 82, + "slot_uri": "GENEPIO:0100451", + "alias": "host_breed", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "SampleVolumeMeasurementUnitMenu" + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" }, - "residual_sample_status": { - "name": "residual_sample_status", - "description": "The status of the residual sample (whether any sample remains after its original use).", - "title": "residual_sample_status", + "host_food_production_name": { + "name": "host_food_production_name", + "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", + "title": "host (food production name)", "comments": [ - "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host" + ], + "rank": 83, + "slot_uri": "GENEPIO:0100452", + "alias": "host_food_production_name", + "owner": "GRDI", + "domain_of": [ + "GRDI" ], - "examples": [ + "slot_group": "Host information", + "any_of": [ { - "value": "No residual sample (sample all used) [GENEPIO:0101088]" + "range": "HostFoodProductionNameMenu" + }, + { + "range": "NullValueMenu" } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "Age of host at the time of sampling, expressed as an age group.", + "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." ], "from_schema": "https://example.com/GRDI", - "rank": 57, - "slot_uri": "GENEPIO:0101090", - "alias": "residual_sample_status", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_age" + ], + "rank": 84, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "ResidualSampleStatusMenu" + "slot_group": "Host information", + "any_of": [ + { + "range": "HostAgeBinMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample_storage_method": { - "name": "sample_storage_method", - "description": "A specification of the way that a specimen is or was stored.", - "title": "sample_storage_method", + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host_disease", "comments": [ - "Provide a description of how the sample was stored." + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." ], "examples": [ { - "value": "packed on ice during transport" + "value": "mastitis, gastroenteritis" } ], "from_schema": "https://example.com/GRDI", - "rank": 58, - "slot_uri": "GENEPIO:0100448", - "alias": "sample_storage_method", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_disease" + ], + "rank": 85, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host information", "range": "WhitespaceMinimizedString" }, - "sample_storage_medium": { - "name": "sample_storage_medium", - "description": "The material or matrix in which a sample is stored.", - "title": "sample_storage_medium", + "microbiological_method": { + "name": "microbiological_method", + "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", + "title": "microbiological_method", "comments": [ - "Provide a description of the medium in which the sample was stored." + "Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure." ], "examples": [ { - "value": "PBS + 20% glycerol" + "value": "MFHPB-30" } ], "from_schema": "https://example.com/GRDI", - "rank": 59, - "slot_uri": "GENEPIO:0100449", - "alias": "sample_storage_medium", + "rank": 86, + "slot_uri": "GENEPIO:0100454", + "alias": "microbiological_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "sample_storage_duration_value": { - "name": "sample_storage_duration_value", - "description": "The numerical value of the time measurement during which a sample is in storage.", - "title": "sample_storage_duration_value", + "strain": { + "name": "strain", + "description": "The strain identifier.", + "title": "strain", "comments": [ - "Provide the numerical value of time." + "If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier." ], "examples": [ { - "value": "5" + "value": "K12" } ], "from_schema": "https://example.com/GRDI", - "rank": 60, - "slot_uri": "GENEPIO:0101014", - "alias": "sample_storage_duration_value", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:strain" + ], + "rank": 87, + "slot_uri": "GENEPIO:0100455", + "alias": "strain", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "sample_storage_duration_unit": { - "name": "sample_storage_duration_unit", - "description": "The units of a measured sample storage duration.", - "title": "sample_storage_duration_unit", + "isolate_id": { + "name": "isolate_id", + "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", + "title": "isolate_ID", "comments": [ - "Provide the units from the pick list." + "Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field." ], "examples": [ { - "value": "Day [UO:0000033]" + "value": "SA20131043" } ], "from_schema": "https://example.com/GRDI", - "rank": 61, - "slot_uri": "GENEPIO:0101015", - "alias": "sample_storage_duration_unit", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:strain", + "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" + ], + "rank": 88, + "slot_uri": "GENEPIO:0100456", + "alias": "isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "SampleStorageDurationUnitMenu" + "slot_group": "Strain and isolation information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "nucleic_acid_storage_duration_value": { - "name": "nucleic_acid_storage_duration_value", - "description": "The numerical value of the time measurement during which the extracted nucleic acid is in storage.", - "title": "nucleic_acid_storage_duration_value", + "alternative_isolate_id": { + "name": "alternative_isolate_id", + "description": "An alternative isolate_ID assigned to the isolate by another organization.", + "title": "alternative_isolate_ID", "comments": [ - "Provide the numerical value of time." + "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nAn example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]\nMultiple alternative isolate IDs can be provided, separated by semi-colons." ], "examples": [ { - "value": "5" + "value": "GHIF3456[PHAC]" + }, + { + "value": "QWICK222[CFIA]" } ], "from_schema": "https://example.com/GRDI", - "rank": 62, - "slot_uri": "GENEPIO:0101085", - "alias": "nucleic_acid_storage_duration_value", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:isolate_name_alias" + ], + "rank": 89, + "slot_uri": "GENEPIO:0100457", + "alias": "alternative_isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "nucleic_acid_storage_duration_unit": { - "name": "nucleic_acid_storage_duration_unit", - "description": "The units of a measured extracted nucleic acid storage duration.", - "title": "nucleic_acid_storage_duration_unit", + "progeny_isolate_id": { + "name": "progeny_isolate_id", + "description": "The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.", + "title": "progeny_isolate_ID", "comments": [ - "Provide the units from the pick list." + "If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID." ], "examples": [ { - "value": "Year [UO:0000036]" + "value": "SUB_ON_1526" } ], "from_schema": "https://example.com/GRDI", - "rank": 63, - "slot_uri": "GENEPIO:0101086", - "alias": "nucleic_acid_storage_duration_unit", + "rank": 90, + "slot_uri": "GENEPIO:0100458", + "alias": "progeny_isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "NucleicAcidStorageDurationUnitMenu" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" }, - "available_data_types": { - "name": "available_data_types", - "description": "The type of data that is available, that may or may not require permission to access.", - "title": "available_data_types", + "irida_isolate_id": { + "name": "irida_isolate_id", + "description": "The identifier of the isolate in the IRIDA platform.", + "title": "IRIDA_isolate_ID", "comments": [ - "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + "Provide the \"sample ID\" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices." ], "examples": [ { - "value": "Total coliform count [GENEPIO:0100729]" + "value": "GRDI_LL_12345" } ], "from_schema": "https://example.com/GRDI", - "rank": 64, - "slot_uri": "GENEPIO:0100690", - "alias": "available_data_types", + "rank": 91, + "slot_uri": "GENEPIO:0100459", + "alias": "irida_isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "multivalued": true, + "slot_group": "Strain and isolation information", + "required": true, "any_of": [ { - "range": "AvailableDataTypesMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" } ] }, - "available_data_type_details": { - "name": "available_data_type_details", - "description": "Detailed information regarding other available data types.", - "title": "available_data_type_details", + "irida_project_id": { + "name": "irida_project_id", + "description": "The identifier of the Project in the iRIDA platform.", + "title": "IRIDA_project_ID", "comments": [ - "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + "Provide the IRIDA \"project ID\"." ], "examples": [ { - "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + "value": "666" } ], "from_schema": "https://example.com/GRDI", - "rank": 65, - "slot_uri": "GENEPIO:0101023", - "alias": "available_data_type_details", + "rank": 92, + "slot_uri": "GENEPIO:0100460", + "alias": "irida_project_id", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "water_depth": { - "name": "water_depth", - "description": "The depth of some water.", - "title": "water_depth", - "comments": [ - "Provide the numerical depth only of water only (without units)." - ], - "examples": [ + "slot_group": "Strain and isolation information", + "required": true, + "any_of": [ { - "value": "5" + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" } - ], - "from_schema": "https://example.com/GRDI", - "rank": 66, - "slot_uri": "GENEPIO:0100440", - "alias": "water_depth", - "owner": "GRDI", - "domain_of": [ - "GRDI" - ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + ] }, - "water_depth_units": { - "name": "water_depth_units", - "description": "The units of measurement for water depth.", - "title": "water_depth_units", + "isolated_by": { + "name": "isolated_by", + "description": "The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated.", + "title": "isolated_by", "comments": [ - "Provide the units of measurement for which the depth was recorded." + "Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "meter (m) [UO:0000008]" + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" } ], "from_schema": "https://example.com/GRDI", - "rank": 67, - "slot_uri": "GENEPIO:0101025", - "alias": "water_depth_units", + "rank": 93, + "slot_uri": "GENEPIO:0100461", + "alias": "isolated_by", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", - "any_of": [ - { - "range": "WaterDepthUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Strain and isolation information", + "range": "IsolatedByMenu" }, - "sediment_depth": { - "name": "sediment_depth", - "description": "The depth of some sediment.", - "title": "sediment_depth", + "isolated_by_laboratory_name": { + "name": "isolated_by_laboratory_name", + "description": "The specific laboratory affiliation of the individual who performed the isolation procedure.", + "title": "isolated_by_laboratory_name", "comments": [ - "Provide the numerical depth only of the sediment (without units)." + "Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "2" + "value": "Topp Lab" } ], "from_schema": "https://example.com/GRDI", - "rank": 68, - "slot_uri": "GENEPIO:0100697", - "alias": "sediment_depth", + "rank": 94, + "slot_uri": "GENEPIO:0100462", + "alias": "isolated_by_laboratory_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "sediment_depth_units": { - "name": "sediment_depth_units", - "description": "The units of measurement for sediment depth.", - "title": "sediment_depth_units", + "isolated_by_contact_name": { + "name": "isolated_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the isolate.", + "title": "isolated_by_contact_name", "comments": [ - "Provide the units of measurement for which the depth was recorded." + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "meter (m) [UO:0000008]" + "value": "Enterics Lab Manager" } ], "from_schema": "https://example.com/GRDI", - "rank": 69, - "slot_uri": "GENEPIO:0101026", - "alias": "sediment_depth_units", + "rank": 95, + "slot_uri": "GENEPIO:0100463", + "alias": "isolated_by_contact_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", - "any_of": [ - { - "range": "SedimentDepthUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" }, - "air_temperature": { - "name": "air_temperature", - "description": "The temperature of some air.", - "title": "air_temperature", + "isolated_by_contact_email": { + "name": "isolated_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the isolate.", + "title": "isolated_by_contact_email", "comments": [ - "Provide the numerical value for the temperature of the air (without units)." + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "25" + "value": "enterics@lab.ca" } ], "from_schema": "https://example.com/GRDI", - "rank": 70, - "slot_uri": "GENEPIO:0100441", - "alias": "air_temperature", + "rank": 96, + "slot_uri": "GENEPIO:0100464", + "alias": "isolated_by_contact_email", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "air_temperature_units": { - "name": "air_temperature_units", - "description": "The units of measurement for air temperature.", - "title": "air_temperature_units", + "isolation_date": { + "name": "isolation_date", + "description": "The date on which the isolate was isolated from a sample.", + "title": "isolation_date", + "todos": [ + "<={today}" + ], "comments": [ - "Provide the units of measurement for which the temperature was recorded." + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], "examples": [ { - "value": "degree Celsius (C) [UO:0000027]" + "value": "2020-10-30" } ], "from_schema": "https://example.com/GRDI", - "rank": 71, - "slot_uri": "GENEPIO:0101027", - "alias": "air_temperature_units", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:cult_isol_date" + ], + "rank": 97, + "slot_uri": "GENEPIO:0100465", + "alias": "isolation_date", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", - "any_of": [ - { - "range": "AirTemperatureUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Strain and isolation information", + "range": "date" }, - "water_temperature": { - "name": "water_temperature", - "description": "The temperature of some water.", - "title": "water_temperature", + "isolate_received_date": { + "name": "isolate_received_date", + "description": "The date on which the isolate was received by the laboratory.", + "title": "isolate_received_date", + "todos": [ + "<={today}" + ], "comments": [ - "Provide the numerical value for the temperature of the water (without units)." + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], "examples": [ { - "value": "4" + "value": "2020-11-15" } ], "from_schema": "https://example.com/GRDI", - "rank": 72, - "slot_uri": "GENEPIO:0100698", - "alias": "water_temperature", + "rank": 98, + "slot_uri": "GENEPIO:0100466", + "alias": "isolate_received_date", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "water_temperature_units": { - "name": "water_temperature_units", - "description": "The units of measurement for water temperature.", - "title": "water_temperature_units", + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", "comments": [ - "Provide the units of measurement for which the temperature was recorded." + "Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used." ], "examples": [ { - "value": "degree Celsius (C) [UO:0000027]" + "value": "Salmonella enterica subsp. enterica [NCBITaxon:59201]" } ], "from_schema": "https://example.com/GRDI", - "rank": 73, - "slot_uri": "GENEPIO:0101028", - "alias": "water_temperature_units", + "exact_mappings": [ + "BIOSAMPLE:organism", + "NCBI_BIOSAMPLE_Enterics:organism" + ], + "rank": 99, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Strain and isolation information", + "required": true, + "multivalued": true, "any_of": [ { - "range": "WaterTemperatureUnitsMenu" + "range": "OrganismMenu" }, { "range": "NullValueMenu" } ] }, - "sampling_weather_conditions": { - "name": "sampling_weather_conditions", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "sampling_weather_conditions", + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "description": "The type of planned process by which an organismal entity is associated with a taxon or taxa.", + "title": "taxonomic_identification_process", "comments": [ - "Provide the weather conditions at the time of sample collection." + "Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "PCR assay [OBI:0002740]" } ], "from_schema": "https://example.com/GRDI", - "rank": 74, - "slot_uri": "GENEPIO:0100779", - "alias": "sampling_weather_conditions", + "rank": 100, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", - "multivalued": true, + "slot_group": "Strain and isolation information", + "recommended": true, "any_of": [ { - "range": "SamplingWeatherConditionsMenu" + "range": "TaxonomicIdentificationProcessMenu" }, { "range": "NullValueMenu" } ] }, - "presampling_weather_conditions": { - "name": "presampling_weather_conditions", - "description": "Weather conditions prior to collection that may affect the sample.", - "title": "presampling_weather_conditions", + "taxonomic_identification_process_details": { + "name": "taxonomic_identification_process_details", + "description": "The details of the process used to determine the taxonomic identification of an organism.", + "title": "taxonomic_identification_process_details", "comments": [ - "Provide the weather conditions prior to sample collection." + "Briefly describe the taxonomic identififcation method details using free text." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "Biolog instrument" } ], "from_schema": "https://example.com/GRDI", - "rank": 75, - "slot_uri": "GENEPIO:0100780", - "alias": "presampling_weather_conditions", + "rank": 101, + "slot_uri": "GENEPIO:0100584", + "alias": "taxonomic_identification_process_details", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", - "any_of": [ - { - "range": "SamplingWeatherConditionsMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation_measurement_value", + "serovar": { + "name": "serovar", + "description": "The serovar of the organism.", + "title": "serovar", "comments": [ - "Provide the quantity of precipitation in the area leading up to the time of sample collection." + "Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR." ], "examples": [ { - "value": "12" + "value": "Heidelberg" } ], "from_schema": "https://example.com/GRDI", - "rank": 76, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:serovar" + ], + "rank": 102, + "slot_uri": "GENEPIO:0100467", + "alias": "serovar", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", - "any_of": [ - { - "range": "Whitespaceminimizedstring" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "precipitation_measurement_unit": { - "name": "precipitation_measurement_unit", - "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", - "title": "precipitation_measurement_unit", + "serotyping_method": { + "name": "serotyping_method", + "description": "The method used to determine the serovar.", + "title": "serotyping_method", "comments": [ - "Provide the units of precipitation by selecting a value from the pick list." + "If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software." ], "examples": [ { - "value": "inch" + "value": "SISTR 1.0.1" } ], "from_schema": "https://example.com/GRDI", - "rank": 77, - "slot_uri": "GENEPIO:0100912", - "alias": "precipitation_measurement_unit", + "rank": 103, + "slot_uri": "GENEPIO:0100468", + "alias": "serotyping_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", - "any_of": [ - { - "range": "PrecipitationMeasurementUnitMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "precipitation_measurement_method": { - "name": "precipitation_measurement_method", - "description": "The process used to measure the amount of water which has fallen during a precipitation process.", - "title": "precipitation_measurement_method", + "phagetype": { + "name": "phagetype", + "description": "The phagetype of the organism.", + "title": "phagetype", "comments": [ - "Provide the name of the procedure or method used to measure precipitation." + "Provide if known. If unknown, put “missing”." ], "examples": [ { - "value": "Rain gauge over a 12 hour period prior to sample collection" + "value": "47" } ], "from_schema": "https://example.com/GRDI", - "rank": 78, - "slot_uri": "GENEPIO:0100913", - "alias": "precipitation_measurement_method", + "rank": 104, + "slot_uri": "GENEPIO:0100469", + "alias": "phagetype", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "host_common_name": { - "name": "host_common_name", - "description": "The commonly used name of the host.", - "title": "host (common name)", + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", "comments": [ - "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." ], "examples": [ { - "value": "Cow [NCBITaxon:9913]" - }, - { - "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + "value": "LS_2010_NP_123446" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:host" - ], - "rank": 79, - "slot_uri": "GENEPIO:0001386", - "alias": "host_common_name", + "rank": 105, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information", - "recommended": true, - "any_of": [ - { - "range": "HostCommonNameMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "host_scientific_name": { - "name": "host_scientific_name", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", "comments": [ - "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "Bos taurus [NCBITaxon:9913]" - }, - { - "value": "Homo sapiens [NCBITaxon:9103]" + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:host", - "NCBI_BIOSAMPLE_Enterics:isolation_source", - "NCBI_BIOSAMPLE_Enterics:host" + "BIOSAMPLE:sequenced_by", + "NCBI_BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 80, - "slot_uri": "GENEPIO:0001387", - "alias": "host_scientific_name", + "rank": 106, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information", - "recommended": true, + "slot_group": "Sequence information", + "required": true, "any_of": [ { - "range": "HostScientificNameMenu" + "range": "SequencedByMenu" }, { "range": "NullValueMenu" } ] }, - "host_ecotype": { - "name": "host_ecotype", - "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", - "title": "host (ecotype)", + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", "comments": [ - "Provide the name of the ecotype of the host organism." + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "Sea ecotype" + "value": "Topp Lab" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:host_variety" - ], - "rank": 81, - "slot_uri": "GENEPIO:0100450", - "alias": "host_ecotype", + "rank": 107, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "host_breed": { - "name": "host_breed", - "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", - "title": "host (breed)", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", "comments": [ - "Provide the name of the breed of the host organism." + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "Holstein" + "value": "Enterics Lab Manager" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:host_disease", - "NCBI_BIOSAMPLE_Enterics:host_animal_breed" - ], - "rank": 82, - "slot_uri": "GENEPIO:0100451", - "alias": "host_breed", + "rank": 108, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "host_food_production_name": { - "name": "host_food_production_name", - "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", - "title": "host (food production name)", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", "comments": [ - "Select the host's food production name from the pick list." + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "Calf [FOODON:03411349]" + "value": "enterics@lab.ca" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:host" - ], - "rank": 83, - "slot_uri": "GENEPIO:0100452", - "alias": "host_food_production_name", + "rank": 109, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information", + "slot_group": "Sequence information", + "required": true, "any_of": [ { - "range": "HostFoodProductionNameMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" } ] }, - "host_age_bin": { - "name": "host_age_bin", - "description": "Age of host at the time of sampling, expressed as an age group.", - "title": "host_age_bin", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", "comments": [ - "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + "Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Research [GENEPIO:0100003]" + } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:host_age" + "BIOSAMPLE:purpose_of_sequencing" ], - "rank": 84, - "slot_uri": "GENEPIO:0001394", - "alias": "host_age_bin", + "rank": 110, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information", + "slot_group": "Sequence information", + "required": true, + "multivalued": true, "any_of": [ { - "range": "HostAgeBinMenu" + "range": "PurposeOfSequencingMenu" }, { "range": "NullValueMenu" } ] }, - "host_disease": { - "name": "host_disease", - "description": "The name of the disease experienced by the host.", - "title": "host_disease", + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], "comments": [ - "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + "ISO 8601 standard \"YYYY-MM-DD\"." ], "examples": [ { - "value": "mastitis, gastroenteritis" + "value": "2020-06-22" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:host_disease" - ], - "rank": 85, - "slot_uri": "GENEPIO:0001391", - "alias": "host_disease", + "rank": 111, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "microbiological_method": { - "name": "microbiological_method", - "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", - "title": "microbiological_method", + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", "comments": [ - "Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure." + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "MFHPB-30" + "value": "AMR-GRDI (PA-1356)" } ], "from_schema": "https://example.com/GRDI", - "rank": 86, - "slot_uri": "GENEPIO:0100454", - "alias": "microbiological_method", + "rank": 112, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "strain": { - "name": "strain", - "description": "The strain identifier.", - "title": "strain", + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", "comments": [ - "If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier." + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "K12" + "value": "Illumina [GENEPIO:0001923]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain" - ], - "rank": 87, - "slot_uri": "GENEPIO:0100455", - "alias": "strain", + "rank": 113, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "any_of": [ + { + "range": "SequencingPlatformMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "isolate_id": { - "name": "isolate_id", - "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", - "title": "isolate_ID", + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", "comments": [ - "Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field." + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "SA20131043" + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain", - "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" - ], - "rank": 88, - "slot_uri": "GENEPIO:0100456", - "alias": "isolate_id", + "rank": 114, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "required": true, + "slot_group": "Sequence information", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "SequencingInstrumentMenu" }, { "range": "NullValueMenu" } ] }, - "alternative_isolate_id": { - "name": "alternative_isolate_id", - "description": "An alternative isolate_ID assigned to the isolate by another organization.", - "title": "alternative_isolate_ID", + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", "comments": [ - "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nAn example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]\nMultiple alternative isolate IDs can be provided, separated by semi-colons." + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." ], "examples": [ { - "value": "GHIF3456[PHAC]" - }, - { - "value": "QWICK222[CFIA]" + "value": "whole genome sequencing assay [OBI:0002117]" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:isolate_name_alias" - ], - "rank": 89, - "slot_uri": "GENEPIO:0100457", - "alias": "alternative_isolate_id", + "rank": 115, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Sequence information", + "range": "SequencingAssayTypeMenu" }, - "progeny_isolate_id": { - "name": "progeny_isolate_id", - "description": "The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.", - "title": "progeny_isolate_ID", + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", "comments": [ - "If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID." + "Provide the name of the library preparation kit used." ], "examples": [ { - "value": "SUB_ON_1526" + "value": "Nextera XT" } ], "from_schema": "https://example.com/GRDI", - "rank": 90, - "slot_uri": "GENEPIO:0100458", - "alias": "progeny_isolate_id", + "rank": 116, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "irida_isolate_id": { - "name": "irida_isolate_id", - "description": "The identifier of the isolate in the IRIDA platform.", - "title": "IRIDA_isolate_ID", + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", "comments": [ - "Provide the \"sample ID\" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices." + "Provide the fragment length in base pairs (do not include the units)." ], "examples": [ { - "value": "GRDI_LL_12345" + "value": "400" } ], "from_schema": "https://example.com/GRDI", - "rank": 91, - "slot_uri": "GENEPIO:0100459", - "alias": "irida_isolate_id", + "rank": 117, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Sequence information", + "range": "integer" }, - "irida_project_id": { - "name": "irida_project_id", - "description": "The identifier of the Project in the iRIDA platform.", - "title": "IRIDA_project_ID", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", "comments": [ - "Provide the IRIDA \"project ID\"." + "Provide the name of the enrichment method" ], "examples": [ { - "value": "666" + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" } ], "from_schema": "https://example.com/GRDI", - "rank": 92, - "slot_uri": "GENEPIO:0100460", - "alias": "irida_project_id", + "rank": 118, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, + "slot_group": "Sequence information", + "range": "GenomicTargetEnrichmentMethodMenu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ { - "range": "NullValueMenu" + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" } - ] + ], + "from_schema": "https://example.com/GRDI", + "rank": 119, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "isolated_by": { - "name": "isolated_by", - "description": "The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated.", - "title": "isolated_by", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", "comments": [ - "Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." ], "examples": [ { - "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + "value": "artic v3" } ], "from_schema": "https://example.com/GRDI", - "rank": 93, - "slot_uri": "GENEPIO:0100461", - "alias": "isolated_by", + "rank": 120, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "IsolatedByMenu" + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "isolated_by_laboratory_name": { - "name": "isolated_by_laboratory_name", - "description": "The specific laboratory affiliation of the individual who performed the isolation procedure.", - "title": "isolated_by_laboratory_name", + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", "comments": [ - "Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the amplicon size expressed in base pairs." ], "examples": [ { - "value": "Topp Lab" + "value": "300" } ], "from_schema": "https://example.com/GRDI", - "rank": 94, - "slot_uri": "GENEPIO:0100462", - "alias": "isolated_by_laboratory_name", + "rank": 121, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "range": "integer" }, - "isolated_by_contact_name": { - "name": "isolated_by_contact_name", - "description": "The name or title of the contact responsible for follow-up regarding the isolate.", - "title": "isolated_by_contact_name", + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", "comments": [ - "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." ], "examples": [ { - "value": "Enterics Lab Manager" + "value": "R.9.4.1" } ], "from_schema": "https://example.com/GRDI", - "rank": 95, - "slot_uri": "GENEPIO:0100463", - "alias": "isolated_by_contact_name", + "rank": 122, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "isolated_by_contact_email": { - "name": "isolated_by_contact_email", - "description": "The email address of the contact responsible for follow-up regarding the isolate.", - "title": "isolated_by_contact_email", + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", "comments": [ - "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." ], "examples": [ { - "value": "enterics@lab.ca" + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" } ], "from_schema": "https://example.com/GRDI", - "rank": 96, - "slot_uri": "GENEPIO:0100464", - "alias": "isolated_by_contact_email", + "rank": 123, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "isolation_date": { - "name": "isolation_date", - "description": "The date on which the isolate was isolated from a sample.", - "title": "isolation_date", - "todos": [ - "<={today}" - ], + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + "Provide the r1 FASTQ filename." ], "examples": [ { - "value": "2020-10-30" + "value": "ABC123_S1_L001_R1_001.fastq.gz" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:cult_isol_date" - ], - "rank": 97, - "slot_uri": "GENEPIO:0100465", - "alias": "isolation_date", + "rank": 124, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "date" + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "isolate_received_date": { - "name": "isolate_received_date", - "description": "The date on which the isolate was received by the laboratory.", - "title": "isolate_received_date", - "todos": [ - "<={today}" - ], + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + "Provide the r2 FASTQ filename." ], "examples": [ { - "value": "2020-11-15" + "value": "ABC123_S1_L001_R2_001.fastq.gz" } ], "from_schema": "https://example.com/GRDI", - "rank": 98, - "slot_uri": "GENEPIO:0100466", - "alias": "isolate_received_date", + "rank": 125, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "organism": { - "name": "organism", - "description": "Taxonomic name of the organism.", - "title": "organism", + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", "comments": [ - "Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used." + "Provide the FAST5 filename." ], "examples": [ { - "value": "Salmonella enterica subsp. enterica [NCBITaxon:59201]" + "value": "batch1a_sequences.fast5" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:organism", - "NCBI_BIOSAMPLE_Enterics:organism" - ], - "rank": 99, - "slot_uri": "GENEPIO:0001191", - "alias": "organism", + "rank": 126, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "required": true, - "multivalued": true, - "any_of": [ - { - "range": "OrganismMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "taxonomic_identification_process": { - "name": "taxonomic_identification_process", - "description": "The type of planned process by which an organismal entity is associated with a taxon or taxa.", - "title": "taxonomic_identification_process", + "genome_sequence_filename": { + "name": "genome_sequence_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "genome_sequence_filename", "comments": [ - "Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the FASTA filename." ], "examples": [ { - "value": "PCR assay [OBI:0002740]" + "value": "pathogenassembly123.fasta" } ], "from_schema": "https://example.com/GRDI", - "rank": 100, - "slot_uri": "GENEPIO:0100583", - "alias": "taxonomic_identification_process", + "rank": 127, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_filename", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "recommended": true, - "any_of": [ - { - "range": "TaxonomicIdentificationProcessMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "taxonomic_identification_process_details": { - "name": "taxonomic_identification_process_details", - "description": "The details of the process used to determine the taxonomic identification of an organism.", - "title": "taxonomic_identification_process_details", + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality_control_method_name", "comments": [ - "Briefly describe the taxonomic identififcation method details using free text." + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." ], "examples": [ { - "value": "Biolog instrument" + "value": "ncov-tools" } ], "from_schema": "https://example.com/GRDI", - "rank": 101, - "slot_uri": "GENEPIO:0100584", - "alias": "taxonomic_identification_process_details", + "rank": 128, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "serovar": { - "name": "serovar", - "description": "The serovar of the organism.", - "title": "serovar", + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality_control_method_version", "comments": [ - "Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR." + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." ], "examples": [ { - "value": "Heidelberg" + "value": "1.2.3" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:serovar" - ], - "rank": 102, - "slot_uri": "GENEPIO:0100467", - "alias": "serovar", + "rank": 129, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "serotyping_method": { - "name": "serotyping_method", - "description": "The method used to determine the serovar.", - "title": "serotyping_method", + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality_control_determination", "comments": [ - "If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software." + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." ], "examples": [ { - "value": "SISTR 1.0.1" + "value": "sequence failed quality control" } ], "from_schema": "https://example.com/GRDI", - "rank": 103, - "slot_uri": "GENEPIO:0100468", - "alias": "serotyping_method", + "rank": 130, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlDeterminationMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "phagetype": { - "name": "phagetype", - "description": "The phagetype of the organism.", - "title": "phagetype", + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality_control_issues", "comments": [ - "Provide if known. If unknown, put “missing”." + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." ], "examples": [ { - "value": "47" + "value": "low average genome coverage" } ], "from_schema": "https://example.com/GRDI", - "rank": 104, - "slot_uri": "GENEPIO:0100469", - "alias": "phagetype", + "rank": 131, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlIssuesMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "library_id": { - "name": "library_id", - "description": "The user-specified identifier for the library prepared for sequencing.", - "title": "library_ID", + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality_control_details", "comments": [ - "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + "Provide notes or details regarding QC results using free text." ], "examples": [ { - "value": "LS_2010_NP_123446" + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." } ], "from_schema": "https://example.com/GRDI", - "rank": 105, - "slot_uri": "GENEPIO:0001448", - "alias": "library_id", + "rank": 132, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "sequenced_by": { - "name": "sequenced_by", - "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", - "title": "sequenced_by", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw_sequence_data_processing_method", "comments": [ - "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." ], "examples": [ { - "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + "value": "Porechop 0.2.3" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:sequenced_by", - "NCBI_BIOSAMPLE_Enterics:sequenced_by" - ], - "rank": 106, - "slot_uri": "GENEPIO:0100416", - "alias": "sequenced_by", + "rank": 133, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "required": true, + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, "any_of": [ { - "range": "SequencedByMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" } ] }, - "sequenced_by_laboratory_name": { - "name": "sequenced_by_laboratory_name", - "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", - "title": "sequenced_by_laboratory_name", + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting_method", "comments": [ - "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the name and version number of the software used to remove host reads." ], "examples": [ { - "value": "Topp Lab" + "value": "Nanostripper" } ], "from_schema": "https://example.com/GRDI", - "rank": 107, - "slot_uri": "GENEPIO:0100470", - "alias": "sequenced_by_laboratory_name", + "rank": 134, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequenced_by_contact_name": { - "name": "sequenced_by_contact_name", - "description": "The name or title of the contact responsible for follow-up regarding the sequence.", - "title": "sequenced_by_contact_name", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence_assembly_software_name", "comments": [ - "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the name of the software used to assemble the sequence." ], "examples": [ { - "value": "Enterics Lab Manager" + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" } ], "from_schema": "https://example.com/GRDI", - "rank": 108, - "slot_uri": "GENEPIO:0100471", - "alias": "sequenced_by_contact_name", + "rank": 135, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "required": true, + "slot_group": "Bioinformatics and QC metrics", "any_of": [ { "range": "WhitespaceMinimizedString" @@ -31981,28 +33513,27 @@ } ] }, - "sequenced_by_contact_email": { - "name": "sequenced_by_contact_email", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "title": "sequenced_by_contact_email", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence_assembly_software_version", "comments": [ - "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the version of the software used to assemble the sequence." ], "examples": [ { - "value": "enterics@lab.ca" + "value": "3.15.5" } ], "from_schema": "https://example.com/GRDI", - "rank": 109, - "slot_uri": "GENEPIO:0100422", - "alias": "sequenced_by_contact_email", + "rank": 136, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "required": true, + "slot_group": "Bioinformatics and QC metrics", "any_of": [ { "range": "WhitespaceMinimizedString" @@ -32012,439 +33543,427 @@ } ] }, - "purpose_of_sequencing": { - "name": "purpose_of_sequencing", - "description": "The reason that the sample was sequenced.", - "title": "purpose_of_sequencing", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus_sequence_software_name", "comments": [ - "Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the name of the software used to generate the consensus sequence." ], "examples": [ { - "value": "Research [GENEPIO:0100003]" + "value": "iVar" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:purpose_of_sequencing" - ], - "rank": 110, - "slot_uri": "GENEPIO:0001445", - "alias": "purpose_of_sequencing", + "rank": 137, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "required": true, - "multivalued": true, + "slot_group": "Bioinformatics and QC metrics", "any_of": [ { - "range": "PurposeOfSequencingMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" } ] }, - "sequencing_project_name": { - "name": "sequencing_project_name", - "description": "The name of the project/initiative/program for which sequencing was performed.", - "title": "sequencing_project_name", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus_sequence_software_version", "comments": [ - "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the version of the software used to generate the consensus sequence." ], "examples": [ { - "value": "AMR-GRDI (PA-1356)" + "value": "1.3" } ], "from_schema": "https://example.com/GRDI", - "rank": 111, - "slot_uri": "GENEPIO:0100472", - "alias": "sequencing_project_name", + "rank": 138, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing_platform": { - "name": "sequencing_platform", - "description": "The platform technology used to perform the sequencing.", - "title": "sequencing_platform", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth_of_coverage_value", "comments": [ - "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide value as a percent." ], "examples": [ { - "value": "Illumina [GENEPIO:0001923]" + "value": "95" } ], "from_schema": "https://example.com/GRDI", - "rank": 112, - "slot_uri": "GENEPIO:0100473", - "alias": "sequencing_platform", + "rank": 139, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "any_of": [ - { - "range": "SequencingPlatformMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "sequencing_instrument": { - "name": "sequencing_instrument", - "description": "The model of the sequencing instrument used.", - "title": "sequencing_instrument", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth_of_coverage_value", "comments": [ - "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide value as a fold of coverage." ], "examples": [ { - "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + "value": "400" } ], "from_schema": "https://example.com/GRDI", - "rank": 113, - "slot_uri": "GENEPIO:0001452", - "alias": "sequencing_instrument", + "rank": 140, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "any_of": [ - { - "range": "SequencingInstrumentMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "sequencing_assay_type": { - "name": "sequencing_assay_type", - "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", - "title": "sequencing_assay_type", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth_of_coverage_threshold", "comments": [ - "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + "Provide the threshold fold coverage." ], "examples": [ { - "value": "whole genome sequencing assay [OBI:0002117]" + "value": "100" } ], "from_schema": "https://example.com/GRDI", - "rank": 114, - "slot_uri": "GENEPIO:0100997", - "alias": "sequencing_assay_type", + "rank": 141, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "SequencingAssayTypeMenu" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "library_preparation_kit": { - "name": "library_preparation_kit", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "title": "library_preparation_kit", + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome_completeness", "comments": [ - "Provide the name of the library preparation kit used." + "Provide the genome completeness as a percent (no need to include units)." ], "examples": [ { - "value": "Nextera XT" + "value": "85" } ], "from_schema": "https://example.com/GRDI", - "rank": 115, - "slot_uri": "GENEPIO:0001450", - "alias": "library_preparation_kit", + "rank": 142, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "dna_fragment_length": { - "name": "dna_fragment_length", - "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", - "title": "DNA_fragment_length", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number_of_base_pairs_sequenced", "comments": [ - "Provide the fragment length in base pairs (do not include the units)." + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "400" + "value": "387566" } ], "from_schema": "https://example.com/GRDI", - "rank": 116, - "slot_uri": "GENEPIO:0100843", - "alias": "dna_fragment_length", + "rank": 143, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "genomic_target_enrichment_method": { - "name": "genomic_target_enrichment_method", - "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", - "title": "genomic_target_enrichment_method", + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number_of_total_reads", "comments": [ - "Provide the name of the enrichment method" + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + "value": "423867" } ], "from_schema": "https://example.com/GRDI", - "rank": 117, - "slot_uri": "GENEPIO:0100966", - "alias": "genomic_target_enrichment_method", + "rank": 144, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "GenomicTargetEnrichmentMethodMenu" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "genomic_target_enrichment_method_details": { - "name": "genomic_target_enrichment_method_details", - "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", - "title": "genomic_target_enrichment_method_details", + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number_of_unique_reads", "comments": [ - "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + "value": "248236" } ], "from_schema": "https://example.com/GRDI", - "rank": 118, - "slot_uri": "GENEPIO:0100967", - "alias": "genomic_target_enrichment_method_details", + "rank": 145, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "amplicon_pcr_primer_scheme": { - "name": "amplicon_pcr_primer_scheme", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "title": "amplicon_pcr_primer_scheme", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum_post-trimming_read_length", "comments": [ - "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "artic v3" + "value": "150" } ], "from_schema": "https://example.com/GRDI", - "rank": 119, - "slot_uri": "GENEPIO:0001456", - "alias": "amplicon_pcr_primer_scheme", + "rank": 146, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "amplicon_size": { - "name": "amplicon_size", - "description": "The length of the amplicon generated by PCR amplification.", - "title": "amplicon_size", + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number_of_contigs", "comments": [ - "Provide the amplicon size expressed in base pairs." + "Provide a numerical value." ], "examples": [ { - "value": "300" + "value": "10" } ], "from_schema": "https://example.com/GRDI", - "rank": 120, - "slot_uri": "GENEPIO:0001449", - "alias": "amplicon_size", + "rank": 147, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "sequencing_flow_cell_version": { - "name": "sequencing_flow_cell_version", - "description": "The version number of the flow cell used for generating sequence data.", - "title": "sequencing_flow_cell_version", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent_Ns_across_total_genome_length", "comments": [ - "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "R.9.4.1" + "value": "2" } ], "from_schema": "https://example.com/GRDI", - "rank": 121, - "slot_uri": "GENEPIO:0101102", - "alias": "sequencing_flow_cell_version", + "rank": 148, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "sequencing_protocol": { - "name": "sequencing_protocol", - "description": "The protocol or method used for sequencing.", - "title": "sequencing_protocol", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns_per_100_kbp", "comments": [ - "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + "value": "342" } ], "from_schema": "https://example.com/GRDI", - "rank": 122, - "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol", + "rank": 149, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "r1_fastq_filename": { - "name": "r1_fastq_filename", - "description": "The user-specified filename of the r1 FASTQ file.", - "title": "r1_fastq_filename", + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", "comments": [ - "Provide the r1 FASTQ filename." + "Provide the N50 value in Mb." ], "examples": [ { - "value": "ABC123_S1_L001_R1_001.fastq.gz" + "value": "150" } ], "from_schema": "https://example.com/GRDI", - "rank": 123, - "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename", + "rank": 150, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "r2_fastq_filename": { - "name": "r2_fastq_filename", - "description": "The user-specified filename of the r2 FASTQ file.", - "title": "r2_fastq_filename", + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent_read_contamination_", "comments": [ - "Provide the r2 FASTQ filename." + "Provide the percent contamination value (no need to include units)." ], "examples": [ { - "value": "ABC123_S1_L001_R2_001.fastq.gz" + "value": "2" } ], "from_schema": "https://example.com/GRDI", - "rank": 124, - "slot_uri": "GENEPIO:0001477", - "alias": "r2_fastq_filename", + "rank": 151, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "fast5_filename": { - "name": "fast5_filename", - "description": "The user-specified filename of the FAST5 file.", - "title": "fast5_filename", + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence_assembly_length", "comments": [ - "Provide the FAST5 filename." + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "batch1a_sequences.fast5" + "value": "34272" } ], "from_schema": "https://example.com/GRDI", - "rank": 125, - "slot_uri": "GENEPIO:0001480", - "alias": "fast5_filename", + "rank": 152, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "genome_sequence_filename": { - "name": "genome_sequence_filename", - "description": "The user-defined filename of the FASTA file.", - "title": "genome_sequence_filename", + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus_genome_length", "comments": [ - "Provide the FASTA filename." + "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "pathogenassembly123.fasta" + "value": "38677" } ], "from_schema": "https://example.com/GRDI", - "rank": 126, - "slot_uri": "GENEPIO:0101715", - "alias": "genome_sequence_filename", + "rank": 153, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "quality_control_method_name": { - "name": "quality_control_method_name", - "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", - "title": "quality_control_method_name", + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference_genome_accession", "comments": [ - "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + "Provide the accession number of the reference genome." ], "examples": [ { - "value": "ncov-tools" + "value": "NC_045512.2" } ], "from_schema": "https://example.com/GRDI", - "rank": 127, - "slot_uri": "GENEPIO:0100557", - "alias": "quality_control_method_name", + "rank": 154, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", "owner": "GRDI", "domain_of": [ "GRDI" @@ -32452,22 +33971,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality_control_method_version": { - "name": "quality_control_method_version", - "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", - "title": "quality_control_method_version", + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication_method", "comments": [ - "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + "Provide the deduplication software name followed by the version, or a link to a tool or method." ], "examples": [ { - "value": "1.2.3" + "value": "DeDup 0.12.8" } ], "from_schema": "https://example.com/GRDI", - "rank": 128, - "slot_uri": "GENEPIO:0100558", - "alias": "quality_control_method_version", + "rank": 155, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -32475,1363 +33994,1491 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality_control_determination": { - "name": "quality_control_determination", - "description": "The determination of a quality control assessment.", - "title": "quality_control_determination", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics_protocol", "comments": [ - "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." ], "examples": [ { - "value": "sequence failed quality control" + "value": "https://github.com/phac-nml/ncov2019-artic-nf" } ], "from_schema": "https://example.com/GRDI", - "rank": 129, - "slot_uri": "GENEPIO:0100559", - "alias": "quality_control_determination", + "rank": 156, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "multivalued": true, - "any_of": [ - { - "range": "QualityControlDeterminationMenu" - }, - { - "range": "NullValueMenu" - } - ] + "range": "WhitespaceMinimizedString" }, - "quality_control_issues": { - "name": "quality_control_issues", - "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", - "title": "quality_control_issues", + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read_mapping_software_name", "comments": [ - "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + "Provide the name of the read mapping software." ], "examples": [ { - "value": "low average genome coverage" + "value": "Bowtie2, BWA-MEM, TopHat" } ], "from_schema": "https://example.com/GRDI", - "rank": 130, - "slot_uri": "GENEPIO:0100560", - "alias": "quality_control_issues", + "rank": 157, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "multivalued": true, - "any_of": [ - { - "range": "QualityControlIssuesMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" }, - "quality_control_details": { - "name": "quality_control_details", - "description": "The details surrounding a low quality determination in a quality control assessment.", - "title": "quality_control_details", + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read_mapping_software_version", "comments": [ - "Provide notes or details regarding QC results using free text." + "Provide the version number of the read mapping software." ], "examples": [ { - "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + "value": "2.5.1" } ], "from_schema": "https://example.com/GRDI", - "rank": 131, - "slot_uri": "GENEPIO:0100561", - "alias": "quality_control_details", + "rank": 158, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "raw_sequence_data_processing_method": { - "name": "raw_sequence_data_processing_method", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "title": "raw_sequence_data_processing_method", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic_reference_database_name", "comments": [ - "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + "Provide the name of the taxonomic reference database." ], "examples": [ { - "value": "Porechop 0.2.3" + "value": "NCBITaxon" } ], "from_schema": "https://example.com/GRDI", - "rank": 132, - "slot_uri": "GENEPIO:0001458", - "alias": "raw_sequence_data_processing_method", + "rank": 159, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" }, - "dehosting_method": { - "name": "dehosting_method", - "description": "The method used to remove host reads from the pathogen sequence.", - "title": "dehosting_method", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic_reference_database_version", "comments": [ - "Provide the name and version number of the software used to remove host reads." + "Provide the version number of the taxonomic reference database." ], "examples": [ { - "value": "Nanostripper" + "value": "1.3" } ], "from_schema": "https://example.com/GRDI", - "rank": 133, - "slot_uri": "GENEPIO:0001459", - "alias": "dehosting_method", + "rank": 160, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" }, - "sequence_assembly_software_name": { - "name": "sequence_assembly_software_name", - "description": "The name of the software used to assemble a sequence.", - "title": "sequence_assembly_software_name", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic_analysis_report_filename", "comments": [ - "Provide the name of the software used to assemble the sequence." + "Provide the filename of the report containing the results of the taxonomic analysis." ], "examples": [ { - "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + "value": "WWtax_report_Feb1_2024.doc" } ], "from_schema": "https://example.com/GRDI", - "rank": 134, - "slot_uri": "GENEPIO:0100825", - "alias": "sequence_assembly_software_name", + "rank": 161, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" }, - "sequence_assembly_software_version": { - "name": "sequence_assembly_software_version", - "description": "The version of the software used to assemble a sequence.", - "title": "sequence_assembly_software_version", + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic_analysis_date", + "todos": [ + "<={today}" + ], "comments": [ - "Provide the version of the software used to assemble the sequence." + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], "examples": [ { - "value": "3.15.5" + "value": "2024-02-01" } ], "from_schema": "https://example.com/GRDI", - "rank": 135, - "slot_uri": "GENEPIO:0100826", - "alias": "sequence_assembly_software_version", + "rank": 162, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Taxonomic identification information", + "range": "date" }, - "consensus_sequence_software_name": { - "name": "consensus_sequence_software_name", - "description": "The name of the software used to generate the consensus sequence.", - "title": "consensus_sequence_software_name", + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read_mapping_criteria", "comments": [ - "Provide the name of the software used to generate the consensus sequence." + "Provide a description of the read mapping criteria." ], "examples": [ { - "value": "iVar" + "value": "Phred score >20" } ], "from_schema": "https://example.com/GRDI", - "rank": 136, - "slot_uri": "GENEPIO:0001463", - "alias": "consensus_sequence_software_name", + "rank": 163, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" }, - "consensus_sequence_software_version": { - "name": "consensus_sequence_software_version", - "description": "The version of the software used to generate the consensus sequence.", - "title": "consensus_sequence_software_version", + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", "comments": [ - "Provide the version of the software used to generate the consensus sequence." + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." ], "examples": [ { - "value": "1.3" + "value": "Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]" } ], "from_schema": "https://example.com/GRDI", - "rank": 137, - "slot_uri": "GENEPIO:0001469", - "alias": "consensus_sequence_software_version", + "rank": 164, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Public repository information", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "SequenceSubmittedByMenu" }, { "range": "NullValueMenu" } ] }, - "breadth_of_coverage_value": { - "name": "breadth_of_coverage_value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "title": "breadth_of_coverage_value", + "sequence_submitted_by_contact_name": { + "name": "sequence_submitted_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database.", + "title": "sequence_submitted_by_contact_name", "comments": [ - "Provide value as a percent." + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "95" + "value": "Enterics Lab Manager" } ], "from_schema": "https://example.com/GRDI", - "rank": 138, - "slot_uri": "GENEPIO:0001472", - "alias": "breadth_of_coverage_value", + "rank": 165, + "slot_uri": "GENEPIO:0100474", + "alias": "sequence_submitted_by_contact_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Public repository information", "range": "WhitespaceMinimizedString" }, - "depth_of_coverage_value": { - "name": "depth_of_coverage_value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth_of_coverage_value", + "sequence_submitted_by_contact_email": { + "name": "sequence_submitted_by_contact_email", + "description": "The email address of the agency responsible for submission of the sequence.", + "title": "sequence_submitted_by_contact_email", "comments": [ - "Provide value as a fold of coverage." + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" ], "examples": [ { - "value": "400" + "value": "RespLab@lab.ca" } ], "from_schema": "https://example.com/GRDI", - "rank": 139, - "slot_uri": "GENEPIO:0001474", - "alias": "depth_of_coverage_value", + "rank": 166, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitted_by_contact_email", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Public repository information", "range": "WhitespaceMinimizedString" }, - "depth_of_coverage_threshold": { - "name": "depth_of_coverage_threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", - "title": "depth_of_coverage_threshold", + "publication_id": { + "name": "publication_id", + "description": "The identifier for a publication.", + "title": "publication_ID", "comments": [ - "Provide the threshold fold coverage." + "If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable." ], "examples": [ { - "value": "100" + "value": "PMID: 33205991" } ], "from_schema": "https://example.com/GRDI", - "rank": 140, - "slot_uri": "GENEPIO:0001475", - "alias": "depth_of_coverage_threshold", + "rank": 167, + "slot_uri": "GENEPIO:0100475", + "alias": "publication_id", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Public repository information", "range": "WhitespaceMinimizedString" }, - "genome_completeness": { - "name": "genome_completeness", - "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", - "title": "genome_completeness", + "attribute_package": { + "name": "attribute_package", + "description": "The attribute package used to structure metadata in an INSDC BioSample.", + "title": "attribute_package", "comments": [ - "Provide the genome completeness as a percent (no need to include units)." + "If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”." ], "examples": [ { - "value": "85" + "value": "Pathogen.env [GENEPIO:0100581]" } ], "from_schema": "https://example.com/GRDI", - "rank": 141, - "slot_uri": "GENEPIO:0100844", - "alias": "genome_completeness", + "rank": 168, + "slot_uri": "GENEPIO:0100476", + "alias": "attribute_package", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Public repository information", + "any_of": [ + { + "range": "AttributePackageMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "number_of_base_pairs_sequenced": { - "name": "number_of_base_pairs_sequenced", - "description": "The number of total base pairs generated by the sequencing process.", - "title": "number_of_base_pairs_sequenced", + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "title": "bioproject_accession", "comments": [ - "Provide a numerical value (no need to include units)." + "Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects." ], "examples": [ { - "value": "387566" + "value": "PRJNA12345" } ], "from_schema": "https://example.com/GRDI", - "rank": 142, - "slot_uri": "GENEPIO:0001482", - "alias": "number_of_base_pairs_sequenced", + "exact_mappings": [ + "BIOSAMPLE:bioproject_accession", + "NCBI_BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 169, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Public repository information", + "range": "WhitespaceMinimizedString" }, - "number_of_total_reads": { - "name": "number_of_total_reads", - "description": "The total number of non-unique reads generated by the sequencing process.", - "title": "number_of_total_reads", + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "title": "biosample_accession", "comments": [ - "Provide a numerical value (no need to include units)." + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA." ], "examples": [ { - "value": "423867" + "value": "SAMN14180202" } ], "from_schema": "https://example.com/GRDI", - "rank": 143, - "slot_uri": "GENEPIO:0100827", - "alias": "number_of_total_reads", + "exact_mappings": [ + "ENA_ANTIBIOGRAM:bioSample_ID" + ], + "rank": 170, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Public repository information", + "range": "WhitespaceMinimizedString" }, - "number_of_unique_reads": { - "name": "number_of_unique_reads", - "description": "The number of unique reads generated by the sequencing process.", - "title": "number_of_unique_reads", + "sra_accession": { + "name": "sra_accession", + "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", + "title": "SRA_accession", "comments": [ - "Provide a numerical value (no need to include units)." + "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR." ], "examples": [ { - "value": "248236" + "value": "SRR11177792" } ], "from_schema": "https://example.com/GRDI", - "rank": 144, - "slot_uri": "GENEPIO:0100828", - "alias": "number_of_unique_reads", + "rank": 171, + "slot_uri": "GENEPIO:0001142", + "alias": "sra_accession", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Public repository information", + "range": "WhitespaceMinimizedString" }, - "minimum_posttrimming_read_length": { - "name": "minimum_posttrimming_read_length", - "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", - "title": "minimum_post-trimming_read_length", + "genbank_accession": { + "name": "genbank_accession", + "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", + "title": "GenBank_accession", "comments": [ - "Provide a numerical value (no need to include units)." + "Store the accession returned from a GenBank/ENA/DDBJ submission." ], "examples": [ { - "value": "150" + "value": "MN908947.3" } ], "from_schema": "https://example.com/GRDI", - "rank": 145, - "slot_uri": "GENEPIO:0100829", - "alias": "minimum_posttrimming_read_length", + "rank": 172, + "slot_uri": "GENEPIO:0001145", + "alias": "genbank_accession", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Public repository information", + "range": "WhitespaceMinimizedString" }, - "number_of_contigs": { - "name": "number_of_contigs", - "description": "The number of contigs (contiguous sequences) in a sequence assembly.", - "title": "number_of_contigs", + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", "comments": [ - "Provide a numerical value." + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." ], "examples": [ { - "value": "10" + "value": "Number of total samples collected, Number of positive samples" } ], "from_schema": "https://example.com/GRDI", - "rank": 146, - "slot_uri": "GENEPIO:0100937", - "alias": "number_of_contigs", + "rank": 173, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "percent_ns_across_total_genome_length": { - "name": "percent_ns_across_total_genome_length", - "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", - "title": "percent_Ns_across_total_genome_length", + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", "comments": [ - "Provide a numerical value (no need to include units)." + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." ], "examples": [ { - "value": "2" + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." } ], "from_schema": "https://example.com/GRDI", - "rank": 147, - "slot_uri": "GENEPIO:0100830", - "alias": "percent_ns_across_total_genome_length", + "rank": 174, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "ns_per_100_kbp": { - "name": "ns_per_100_kbp", - "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", - "title": "Ns_per_100_kbp", + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the stage of food production as free text." ], "examples": [ { - "value": "342" + "value": "Abattoir [ENVO:01000925]" } ], "from_schema": "https://example.com/GRDI", - "rank": 148, - "slot_uri": "GENEPIO:0001484", - "alias": "ns_per_100_kbp", + "rank": 175, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "n50": { - "name": "n50", - "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", - "title": "N50", + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", "comments": [ - "Provide the N50 value in Mb." + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." ], "examples": [ { - "value": "150" + "value": "Vaccination [NCIT:C15346]" } ], "from_schema": "https://example.com/GRDI", - "rank": 149, - "slot_uri": "GENEPIO:0100938", - "alias": "n50", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:upstream_intervention" + ], + "rank": 176, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "ExperimentalInterventionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "percent_read_contamination_": { - "name": "percent_read_contamination_", - "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", - "title": "percent_read_contamination_", + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", "comments": [ - "Provide the percent contamination value (no need to include units)." + "If an experimental intervention was applied in the survey, provide details in this field as free text." ], "examples": [ { - "value": "2" + "value": "2% cranberry solution mixed in feed" } ], "from_schema": "https://example.com/GRDI", - "rank": 150, - "slot_uri": "GENEPIO:0100845", - "alias": "percent_read_contamination_", + "rank": 177, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "sequence_assembly_length": { - "name": "sequence_assembly_length", - "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", - "title": "sequence_assembly_length", + "amr_testing_by": { + "name": "amr_testing_by", + "description": "The name of the organization that performed the antimicrobial resistance testing.", + "title": "AMR_testing_by", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "34272" + "value": "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]" } ], "from_schema": "https://example.com/GRDI", - "rank": 151, - "slot_uri": "GENEPIO:0100846", - "alias": "sequence_assembly_length", + "rank": 178, + "slot_uri": "GENEPIO:0100511", + "alias": "amr_testing_by", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "AmrTestingByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "consensus_genome_length": { - "name": "consensus_genome_length", - "description": "The length of the genome defined by the most common nucleotides at each position.", - "title": "consensus_genome_length", + "amr_testing_by_laboratory_name": { + "name": "amr_testing_by_laboratory_name", + "description": "The name of the lab within the organization that performed the antimicrobial resistance testing.", + "title": "AMR_testing_by_laboratory_name", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "38677" + "value": "Topp Lab" } ], "from_schema": "https://example.com/GRDI", - "rank": 152, - "slot_uri": "GENEPIO:0001483", - "alias": "consensus_genome_length", + "rank": 179, + "slot_uri": "GENEPIO:0100512", + "alias": "amr_testing_by_laboratory_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Antimicrobial resistance", + "range": "WhitespaceMinimizedString" }, - "reference_genome_accession": { - "name": "reference_genome_accession", - "description": "A persistent, unique identifier of a genome database entry.", - "title": "reference_genome_accession", + "amr_testing_by_contact_name": { + "name": "amr_testing_by_contact_name", + "description": "The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", + "title": "AMR_testing_by_contact_name", "comments": [ - "Provide the accession number of the reference genome." + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "NC_045512.2" + "value": "Enterics Lab Manager" } ], "from_schema": "https://example.com/GRDI", - "rank": 153, - "slot_uri": "GENEPIO:0001485", - "alias": "reference_genome_accession", + "rank": 180, + "slot_uri": "GENEPIO:0100513", + "alias": "amr_testing_by_contact_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "deduplication_method": { - "name": "deduplication_method", - "description": "The method used to remove duplicated reads in a sequence read dataset.", - "title": "deduplication_method", + "amr_testing_by_contact_email": { + "name": "amr_testing_by_contact_email", + "description": "The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", + "title": "AMR_testing_by_contact_email", "comments": [ - "Provide the deduplication software name followed by the version, or a link to a tool or method." + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "DeDup 0.12.8" + "value": "johnnyblogs@lab.ca" } ], "from_schema": "https://example.com/GRDI", - "rank": 154, - "slot_uri": "GENEPIO:0100831", - "alias": "deduplication_method", + "rank": 181, + "slot_uri": "GENEPIO:0100514", + "alias": "amr_testing_by_contact_email", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "bioinformatics_protocol": { - "name": "bioinformatics_protocol", - "description": "A description of the overall bioinformatics strategy used.", - "title": "bioinformatics_protocol", + "amr_testing_date": { + "name": "amr_testing_date", + "description": "The date the antimicrobial resistance testing was performed.", + "title": "AMR_testing_date", + "todos": [ + "<={today}" + ], "comments": [ - "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], "examples": [ { - "value": "https://github.com/phac-nml/ncov2019-artic-nf" + "value": "2022-04-03" } ], "from_schema": "https://example.com/GRDI", - "rank": 155, - "slot_uri": "GENEPIO:0001489", - "alias": "bioinformatics_protocol", + "rank": 182, + "slot_uri": "GENEPIO:0100515", + "alias": "amr_testing_date", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "range": "date" }, - "read_mapping_software_name": { - "name": "read_mapping_software_name", - "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", - "title": "read_mapping_software_name", + "amikacin_resistance_phenotype": { + "name": "amikacin_resistance_phenotype", + "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", + "title": "amikacin_resistance_phenotype", "comments": [ - "Provide the name of the read mapping software." + "Select a phenotype from the pick list provided." ], "examples": [ { - "value": "Bowtie2, BWA-MEM, TopHat" + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" } ], "from_schema": "https://example.com/GRDI", - "rank": 156, - "slot_uri": "GENEPIO:0100832", - "alias": "read_mapping_software_name", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:resistance_phenotype" + ], + "rank": 183, + "alias": "amikacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialPhenotypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "read_mapping_software_version": { - "name": "read_mapping_software_version", - "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", - "title": "read_mapping_software_version", + "amikacin_measurement": { + "name": "amikacin_measurement", + "description": "The measured value of amikacin resistance.", + "title": "amikacin_measurement", "comments": [ - "Provide the version number of the read mapping software." + "This field should only contain a number (either an integer or a number with decimals)." ], "examples": [ { - "value": "2.5.1" + "value": "4" } ], "from_schema": "https://example.com/GRDI", - "rank": 157, - "slot_uri": "GENEPIO:0100833", - "alias": "read_mapping_software_version", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement" + ], + "rank": 184, + "alias": "amikacin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic_reference_database_name": { - "name": "taxonomic_reference_database_name", - "description": "The name of the taxonomic reference database used to identify the organism.", - "title": "taxonomic_reference_database_name", + "amikacin_measurement_units": { + "name": "amikacin_measurement_units", + "description": "The units of the antimicrobial resistance measurement.", + "title": "amikacin_measurement_units", "comments": [ - "Provide the name of the taxonomic reference database." + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], "examples": [ { - "value": "NCBITaxon" + "value": "ug/mL [UO:0000274]" } ], "from_schema": "https://example.com/GRDI", - "rank": 158, - "slot_uri": "GENEPIO:0100834", - "alias": "taxonomic_reference_database_name", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_units" + ], + "rank": 185, + "alias": "amikacin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic_reference_database_version": { - "name": "taxonomic_reference_database_version", - "description": "The version of the taxonomic reference database used to identify the organism.", - "title": "taxonomic_reference_database_version", + "amikacin_measurement_sign": { + "name": "amikacin_measurement_sign", + "description": "The qualifier associated with the antimicrobial resistance measurement", + "title": "amikacin_measurement_sign", "comments": [ - "Provide the version number of the taxonomic reference database." + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], "examples": [ { - "value": "1.3" + "value": "greater than (>) [GENEPIO:0001006]" } ], "from_schema": "https://example.com/GRDI", - "rank": 159, - "slot_uri": "GENEPIO:0100835", - "alias": "taxonomic_reference_database_version", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_sign" + ], + "rank": 186, + "alias": "amikacin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementSignMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic_analysis_report_filename": { - "name": "taxonomic_analysis_report_filename", - "description": "The filename of the report containing the results of a taxonomic analysis.", - "title": "taxonomic_analysis_report_filename", + "amikacin_laboratory_typing_method": { + "name": "amikacin_laboratory_typing_method", + "description": "The general method used for antimicrobial susceptibility testing.", + "title": "amikacin_laboratory_typing_method", "comments": [ - "Provide the filename of the report containing the results of the taxonomic analysis." + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], "examples": [ { - "value": "WWtax_report_Feb1_2024.doc" + "value": "Broth dilution [ARO:3004397]" } ], "from_schema": "https://example.com/GRDI", - "rank": 160, - "slot_uri": "GENEPIO:0101074", - "alias": "taxonomic_analysis_report_filename", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_method" + ], + "rank": 187, + "alias": "amikacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "AntimicrobialLaboratoryTypingMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic_analysis_date": { - "name": "taxonomic_analysis_date", - "description": "The date a taxonomic analysis was performed.", - "title": "taxonomic_analysis_date", - "todos": [ - "<={today}" - ], + "amikacin_laboratory_typing_platform": { + "name": "amikacin_laboratory_typing_platform", + "description": "The brand/platform used for antimicrobial susceptibility testing.", + "title": "amikacin_laboratory_typing_platform", "comments": [ - "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], "examples": [ { - "value": "2024-02-01" + "value": "Sensitire [ARO:3004402]" } ], "from_schema": "https://example.com/GRDI", - "rank": 161, - "slot_uri": "GENEPIO:0101075", - "alias": "taxonomic_analysis_date", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "rank": 188, + "alias": "amikacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Taxonomic identification information", - "range": "date" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "AntimicrobialLaboratoryTypingPlatformMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "read_mapping_criteria": { - "name": "read_mapping_criteria", - "description": "A description of the criteria used to map reads to a reference sequence.", - "title": "read_mapping_criteria", + "amikacin_laboratory_typing_platform_version": { + "name": "amikacin_laboratory_typing_platform_version", + "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", + "title": "amikacin_laboratory_typing_platform_version", "comments": [ - "Provide a description of the read mapping criteria." + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], "examples": [ { - "value": "Phred score >20" + "value": "CMV3AGNF" } ], "from_schema": "https://example.com/GRDI", - "rank": 162, - "slot_uri": "GENEPIO:0100836", - "alias": "read_mapping_criteria", + "rank": 189, + "alias": "amikacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Taxonomic identification information", + "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "sequence_submitted_by": { - "name": "sequence_submitted_by", - "description": "The name of the agency that submitted the sequence to a database.", - "title": "sequence_submitted_by", + "amikacin_vendor_name": { + "name": "amikacin_vendor_name", + "description": "The name of the vendor of the testing platform used.", + "title": "amikacin_vendor_name", "comments": [ - "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + "Provide the full name of the company (avoid abbreviations)." ], "examples": [ { - "value": "Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]" + "value": "Sensititre" } ], "from_schema": "https://example.com/GRDI", - "rank": 163, - "slot_uri": "GENEPIO:0001159", - "alias": "sequence_submitted_by", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "rank": 190, + "alias": "amikacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", + "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "SequenceSubmittedByMenu" + "range": "AntimicrobialVendorName" }, { "range": "NullValueMenu" } ] }, - "sequence_submitted_by_contact_name": { - "name": "sequence_submitted_by_contact_name", - "description": "The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database.", - "title": "sequence_submitted_by_contact_name", + "amikacin_testing_standard": { + "name": "amikacin_testing_standard", + "description": "The testing standard used for determination of resistance phenotype", + "title": "amikacin_testing_standard", "comments": [ - "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "Select a testing standard from the pick list provided." ], "examples": [ { - "value": "Enterics Lab Manager" + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" } ], "from_schema": "https://example.com/GRDI", - "rank": 164, - "slot_uri": "GENEPIO:0100474", - "alias": "sequence_submitted_by_contact_name", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:testing_standard" + ], + "rank": 191, + "alias": "amikacin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialTestingStandardMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence_submitted_by_contact_email": { - "name": "sequence_submitted_by_contact_email", - "description": "The email address of the agency responsible for submission of the sequence.", - "title": "sequence_submitted_by_contact_email", + "amikacin_testing_standard_version": { + "name": "amikacin_testing_standard_version", + "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", + "title": "amikacin_testing_standard_version", "comments": [ - "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + "If applicable, include a version number for the testing standard used." ], "examples": [ { - "value": "RespLab@lab.ca" + "value": "M100" } ], "from_schema": "https://example.com/GRDI", - "rank": 165, - "slot_uri": "GENEPIO:0001165", - "alias": "sequence_submitted_by_contact_email", + "rank": 192, + "alias": "amikacin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", + "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "publication_id": { - "name": "publication_id", - "description": "The identifier for a publication.", - "title": "publication_ID", + "amikacin_testing_standard_details": { + "name": "amikacin_testing_standard_details", + "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", + "title": "amikacin_testing_standard_details", "comments": [ - "If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable." + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], "examples": [ { - "value": "PMID: 33205991" + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." } ], "from_schema": "https://example.com/GRDI", - "rank": 166, - "slot_uri": "GENEPIO:0100475", - "alias": "publication_id", + "rank": 193, + "alias": "amikacin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", + "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "attribute_package": { - "name": "attribute_package", - "description": "The attribute package used to structure metadata in an INSDC BioSample.", - "title": "attribute_package", + "amikacin_susceptible_breakpoint": { + "name": "amikacin_susceptible_breakpoint", + "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", + "title": "amikacin_susceptible_breakpoint", "comments": [ - "If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”." + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], "examples": [ { - "value": "Pathogen.env [GENEPIO:0100581]" + "value": "8" } ], "from_schema": "https://example.com/GRDI", - "rank": 167, - "slot_uri": "GENEPIO:0100476", - "alias": "attribute_package", + "rank": 194, + "alias": "amikacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", - "any_of": [ - { - "range": "AttributePackageMenu" - }, - { - "range": "NullValueMenu" - } - ] + "slot_group": "Antimicrobial resistance", + "range": "WhitespaceMinimizedString" }, - "bioproject_accession": { - "name": "bioproject_accession", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "title": "bioproject_accession", - "comments": [ - "Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects." - ], + "amikacin_intermediate_breakpoint": { + "name": "amikacin_intermediate_breakpoint", + "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", + "title": "amikacin_intermediate_breakpoint", "examples": [ { - "value": "PRJNA12345" + "value": "16" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:bioproject_accession", - "NCBI_BIOSAMPLE_Enterics:bioproject_accession" - ], - "rank": 168, - "slot_uri": "GENEPIO:0001136", - "alias": "bioproject_accession", + "rank": 195, + "alias": "amikacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", + "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "biosample_accession": { - "name": "biosample_accession", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "title": "biosample_accession", + "amikacin_resistant_breakpoint": { + "name": "amikacin_resistant_breakpoint", + "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", + "title": "amikacin_resistant_breakpoint", "comments": [ - "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA." + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], "examples": [ { - "value": "SAMN14180202" + "value": "32" } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "ENA_ANTIBIOGRAM:bioSample_ID" - ], - "rank": 169, - "slot_uri": "GENEPIO:0001139", - "alias": "biosample_accession", + "rank": 196, + "alias": "amikacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", + "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "sra_accession": { - "name": "sra_accession", - "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA_accession", + "amoxicillinclavulanic_acid_resistance_phenotype": { + "name": "amoxicillinclavulanic_acid_resistance_phenotype", + "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", + "title": "amoxicillin-clavulanic_acid_resistance_phenotype", "comments": [ - "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR." + "Select a phenotype from the pick list provided." ], "examples": [ { - "value": "SRR11177792" + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" } ], "from_schema": "https://example.com/GRDI", - "rank": 170, - "slot_uri": "GENEPIO:0001142", - "alias": "sra_accession", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:resistance_phenotype" + ], + "rank": 197, + "alias": "amoxicillinclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialPhenotypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "genbank_accession": { - "name": "genbank_accession", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "title": "GenBank_accession", + "amoxicillinclavulanic_acid_measurement": { + "name": "amoxicillinclavulanic_acid_measurement", + "description": "The measured value of amoxicillin-clavulanic acid resistance.", + "title": "amoxicillin-clavulanic_acid_measurement", "comments": [ - "Store the accession returned from a GenBank/ENA/DDBJ submission." + "This field should only contain a number (either an integer or a number with decimals)." ], "examples": [ { - "value": "MN908947.3" + "value": "4" } ], "from_schema": "https://example.com/GRDI", - "rank": 171, - "slot_uri": "GENEPIO:0001145", - "alias": "genbank_accession", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement" + ], + "rank": 198, + "alias": "amoxicillinclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "prevalence_metrics": { - "name": "prevalence_metrics", - "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", - "title": "prevalence_metrics", + "amoxicillinclavulanic_acid_measurement_units": { + "name": "amoxicillinclavulanic_acid_measurement_units", + "description": "The units of the antimicrobial resistance measurement.", + "title": "amoxicillin-clavulanic_acid_measurement_units", "comments": [ - "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], "examples": [ { - "value": "Number of total samples collected, Number of positive samples" + "value": "ug/mL [UO:0000274]" } ], "from_schema": "https://example.com/GRDI", - "rank": 172, - "slot_uri": "GENEPIO:0100480", - "alias": "prevalence_metrics", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_units" + ], + "rank": 199, + "alias": "amoxicillinclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Risk assessment information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "prevalence_metrics_details": { - "name": "prevalence_metrics_details", - "description": "The details pertaining to the prevalence metrics from a surveillance project.", - "title": "prevalence_metrics_details", + "amoxicillinclavulanic_acid_measurement_sign": { + "name": "amoxicillinclavulanic_acid_measurement_sign", + "description": "The qualifier associated with the antimicrobial resistance measurement", + "title": "amoxicillin-clavulanic_acid_measurement_sign", "comments": [ - "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], "examples": [ { - "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + "value": "greater than (>) [GENEPIO:0001006]" } ], "from_schema": "https://example.com/GRDI", - "rank": 173, - "slot_uri": "GENEPIO:0100481", - "alias": "prevalence_metrics_details", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:measurement_sign" + ], + "rank": 200, + "alias": "amoxicillinclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Risk assessment information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Antimicrobial resistance", + "required": true, + "any_of": [ + { + "range": "AntimicrobialMeasurementSignMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "stage_of_production": { - "name": "stage_of_production", - "description": "The stage of food production.", - "title": "stage_of_production", + "amoxicillinclavulanic_acid_laboratory_typing_method": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_method", + "description": "The general method used for antimicrobial susceptibility testing.", + "title": "amoxicillin-clavulanic_acid_laboratory_typing_method", "comments": [ - "Provide the stage of food production as free text." + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], "examples": [ { - "value": "Abattoir [ENVO:01000925]" + "value": "Broth dilution [ARO:3004397]" } ], "from_schema": "https://example.com/GRDI", - "rank": 174, - "slot_uri": "GENEPIO:0100482", - "alias": "stage_of_production", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_method" + ], + "rank": 201, + "alias": "amoxicillinclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Risk assessment information", - "recommended": true, + "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { "range": "NullValueMenu" } ] }, - "experimental_intervention": { - "name": "experimental_intervention", - "description": "The category of the experimental intervention applied in the food production system.", - "title": "experimental_intervention", + "amoxicillinclavulanic_acid_laboratory_typing_platform": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform", + "description": "The brand/platform used for antimicrobial susceptibility testing.", + "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform", "comments": [ - "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], "examples": [ { - "value": "Vaccination [NCIT:C15346]" + "value": "Sensitire [ARO:3004402]" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:upstream_intervention" + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 175, - "slot_uri": "GENEPIO:0100483", - "alias": "experimental_intervention", + "rank": 202, + "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Risk assessment information", - "recommended": true, - "multivalued": true, + "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "ExperimentalInterventionMenu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { "range": "NullValueMenu" } ] }, - "experiment_intervention_details": { - "name": "experiment_intervention_details", - "description": "The details of the experimental intervention applied in the food production system.", - "title": "experiment_intervention_details", + "amoxicillinclavulanic_acid_laboratory_typing_platform_version": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", + "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", + "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform_version", "comments": [ - "If an experimental intervention was applied in the survey, provide details in this field as free text." + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], "examples": [ { - "value": "2% cranberry solution mixed in feed" + "value": "CMV3AGNF" } ], "from_schema": "https://example.com/GRDI", - "rank": 176, - "slot_uri": "GENEPIO:0100484", - "alias": "experiment_intervention_details", + "rank": 203, + "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Risk assessment information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Antimicrobial resistance", + "range": "WhitespaceMinimizedString" }, - "amr_testing_by": { - "name": "amr_testing_by", - "description": "The name of the organization that performed the antimicrobial resistance testing.", - "title": "AMR_testing_by", + "amoxicillinclavulanic_acid_vendor_name": { + "name": "amoxicillinclavulanic_acid_vendor_name", + "description": "The name of the vendor of the testing platform used.", + "title": "amoxicillin-clavulanic_acid_vendor_name", "comments": [ - "Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Provide the full name of the company (avoid abbreviations)." ], "examples": [ { - "value": "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]" + "value": "Sensititre" } ], "from_schema": "https://example.com/GRDI", - "rank": 177, - "slot_uri": "GENEPIO:0100511", - "alias": "amr_testing_by", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "rank": 204, + "alias": "amoxicillinclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true, "any_of": [ { - "range": "AmrTestingByMenu" + "range": "AntimicrobialVendorNameMenu" }, { "range": "NullValueMenu" } ] }, - "amr_testing_by_laboratory_name": { - "name": "amr_testing_by_laboratory_name", - "description": "The name of the lab within the organization that performed the antimicrobial resistance testing.", - "title": "AMR_testing_by_laboratory_name", + "amoxicillinclavulanic_acid_testing_standard": { + "name": "amoxicillinclavulanic_acid_testing_standard", + "description": "The testing standard used for determination of resistance phenotype", + "title": "amoxicillin-clavulanic_acid_testing_standard", "comments": [ - "Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + "Select a testing standard from the pick list provided." ], "examples": [ { - "value": "Topp Lab" + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" } ], "from_schema": "https://example.com/GRDI", - "rank": 178, - "slot_uri": "GENEPIO:0100512", - "alias": "amr_testing_by_laboratory_name", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:testing_standard" + ], + "rank": 205, + "alias": "amoxicillinclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "range": "WhitespaceMinimizedString" + "recommended": true, + "any_of": [ + { + "range": "AntimicrobialTestingStandardMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "amr_testing_by_contact_name": { - "name": "amr_testing_by_contact_name", - "description": "The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", - "title": "AMR_testing_by_contact_name", + "amoxicillinclavulanic_acid_testing_standard_version": { + "name": "amoxicillinclavulanic_acid_testing_standard_version", + "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", + "title": "amoxicillin-clavulanic_acid_testing_standard_version", "comments": [ - "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "If applicable, include a version number for the testing standard used." ], "examples": [ { - "value": "Enterics Lab Manager" + "value": "M100" } ], "from_schema": "https://example.com/GRDI", - "rank": 179, - "slot_uri": "GENEPIO:0100513", - "alias": "amr_testing_by_contact_name", + "rank": 206, + "alias": "amoxicillinclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true, - "any_of": [ + "range": "WhitespaceMinimizedString" + }, + "amoxicillinclavulanic_acid_testing_standard_details": { + "name": "amoxicillinclavulanic_acid_testing_standard_details", + "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", + "title": "amoxicillin-clavulanic_acid_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ { - "range": "WhitespaceMinimizedString" + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" }, { - "range": "NullValueMenu" + "value": "2017." } - ] + ], + "from_schema": "https://example.com/GRDI", + "rank": 207, + "alias": "amoxicillinclavulanic_acid_testing_standard_details", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Antimicrobial resistance", + "range": "WhitespaceMinimizedString" }, - "amr_testing_by_contact_email": { - "name": "amr_testing_by_contact_email", - "description": "The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", - "title": "AMR_testing_by_contact_email", + "amoxicillinclavulanic_acid_susceptible_breakpoint": { + "name": "amoxicillinclavulanic_acid_susceptible_breakpoint", + "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", + "title": "amoxicillin-clavulanic_acid_susceptible_breakpoint", "comments": [ - "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], "examples": [ { - "value": "johnnyblogs@lab.ca" + "value": "8" } ], "from_schema": "https://example.com/GRDI", - "rank": 180, - "slot_uri": "GENEPIO:0100514", - "alias": "amr_testing_by_contact_email", + "rank": 208, + "alias": "amoxicillinclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, + "range": "WhitespaceMinimizedString" + }, + "amoxicillinclavulanic_acid_intermediate_breakpoint": { + "name": "amoxicillinclavulanic_acid_intermediate_breakpoint", + "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", + "title": "amoxicillin-clavulanic_acid_intermediate_breakpoint", + "examples": [ { - "range": "NullValueMenu" + "value": "16" } - ] - }, - "amr_testing_date": { - "name": "amr_testing_date", - "description": "The date the antimicrobial resistance testing was performed.", - "title": "AMR_testing_date", - "todos": [ - "<={today}" ], + "from_schema": "https://example.com/GRDI", + "rank": 209, + "alias": "amoxicillinclavulanic_acid_intermediate_breakpoint", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Antimicrobial resistance", + "range": "WhitespaceMinimizedString" + }, + "amoxicillinclavulanic_acid_resistant_breakpoint": { + "name": "amoxicillinclavulanic_acid_resistant_breakpoint", + "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", + "title": "amoxicillin-clavulanic_acid_resistant_breakpoint", "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], "examples": [ { - "value": "2022-04-03" + "value": "32" } ], "from_schema": "https://example.com/GRDI", - "rank": 181, - "slot_uri": "GENEPIO:0100515", - "alias": "amr_testing_date", + "rank": 210, + "alias": "amoxicillinclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "range": "date" + "range": "WhitespaceMinimizedString" }, - "amikacin_resistance_phenotype": { - "name": "amikacin_resistance_phenotype", + "ampicillin_resistance_phenotype": { + "name": "ampicillin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "amikacin_resistance_phenotype", + "title": "ampicillin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -33844,8 +35491,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 182, - "alias": "amikacin_resistance_phenotype", + "rank": 211, + "alias": "ampicillin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33861,10 +35508,10 @@ } ] }, - "amikacin_measurement": { - "name": "amikacin_measurement", - "description": "The measured value of amikacin resistance.", - "title": "amikacin_measurement", + "ampicillin_measurement": { + "name": "ampicillin_measurement", + "description": "The measured value of ampicillin resistance.", + "title": "ampicillin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -33877,8 +35524,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 183, - "alias": "amikacin_measurement", + "rank": 212, + "alias": "ampicillin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33894,10 +35541,10 @@ } ] }, - "amikacin_measurement_units": { - "name": "amikacin_measurement_units", + "ampicillin_measurement_units": { + "name": "ampicillin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "amikacin_measurement_units", + "title": "ampicillin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -33910,8 +35557,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 184, - "alias": "amikacin_measurement_units", + "rank": 213, + "alias": "ampicillin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33927,10 +35574,10 @@ } ] }, - "amikacin_measurement_sign": { - "name": "amikacin_measurement_sign", + "ampicillin_measurement_sign": { + "name": "ampicillin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "amikacin_measurement_sign", + "title": "ampicillin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -33943,8 +35590,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 185, - "alias": "amikacin_measurement_sign", + "rank": 214, + "alias": "ampicillin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33960,10 +35607,10 @@ } ] }, - "amikacin_laboratory_typing_method": { - "name": "amikacin_laboratory_typing_method", + "ampicillin_laboratory_typing_method": { + "name": "ampicillin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "amikacin_laboratory_typing_method", + "title": "ampicillin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -33976,8 +35623,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 186, - "alias": "amikacin_laboratory_typing_method", + "rank": 215, + "alias": "ampicillin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33992,10 +35639,10 @@ } ] }, - "amikacin_laboratory_typing_platform": { - "name": "amikacin_laboratory_typing_platform", + "ampicillin_laboratory_typing_platform": { + "name": "ampicillin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "amikacin_laboratory_typing_platform", + "title": "ampicillin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -34008,8 +35655,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 187, - "alias": "amikacin_laboratory_typing_platform", + "rank": 216, + "alias": "ampicillin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34024,10 +35671,10 @@ } ] }, - "amikacin_laboratory_typing_platform_version": { - "name": "amikacin_laboratory_typing_platform_version", + "ampicillin_laboratory_typing_platform_version": { + "name": "ampicillin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "amikacin_laboratory_typing_platform_version", + "title": "ampicillin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -34037,8 +35684,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 188, - "alias": "amikacin_laboratory_typing_platform_version", + "rank": 217, + "alias": "ampicillin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34046,10 +35693,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amikacin_vendor_name": { - "name": "amikacin_vendor_name", + "ampicillin_vendor_name": { + "name": "ampicillin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "amikacin_vendor_name", + "title": "ampicillin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -34062,8 +35709,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 189, - "alias": "amikacin_vendor_name", + "rank": 218, + "alias": "ampicillin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34071,17 +35718,17 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "AntimicrobialVendorName" + "range": "AntimicrobialVendorNameMenu" }, { "range": "NullValueMenu" } ] }, - "amikacin_testing_standard": { - "name": "amikacin_testing_standard", + "ampicillin_testing_standard": { + "name": "ampicillin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "amikacin_testing_standard", + "title": "ampicillin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -34094,8 +35741,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 190, - "alias": "amikacin_testing_standard", + "rank": 219, + "alias": "ampicillin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34111,10 +35758,10 @@ } ] }, - "amikacin_testing_standard_version": { - "name": "amikacin_testing_standard_version", + "ampicillin_testing_standard_version": { + "name": "ampicillin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "amikacin_testing_standard_version", + "title": "ampicillin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -34124,8 +35771,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 191, - "alias": "amikacin_testing_standard_version", + "rank": 220, + "alias": "ampicillin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34133,10 +35780,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amikacin_testing_standard_details": { - "name": "amikacin_testing_standard_details", + "ampicillin_testing_standard_details": { + "name": "ampicillin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "amikacin_testing_standard_details", + "title": "ampicillin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -34149,8 +35796,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 192, - "alias": "amikacin_testing_standard_details", + "rank": 221, + "alias": "ampicillin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34158,10 +35805,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amikacin_susceptible_breakpoint": { - "name": "amikacin_susceptible_breakpoint", + "ampicillin_susceptible_breakpoint": { + "name": "ampicillin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "amikacin_susceptible_breakpoint", + "title": "ampicillin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -34171,8 +35818,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 193, - "alias": "amikacin_susceptible_breakpoint", + "rank": 222, + "alias": "ampicillin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34180,18 +35827,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amikacin_intermediate_breakpoint": { - "name": "amikacin_intermediate_breakpoint", + "ampicillin_intermediate_breakpoint": { + "name": "ampicillin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "amikacin_intermediate_breakpoint", + "title": "ampicillin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 194, - "alias": "amikacin_intermediate_breakpoint", + "rank": 223, + "alias": "ampicillin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34199,10 +35846,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amikacin_resistant_breakpoint": { - "name": "amikacin_resistant_breakpoint", + "ampicillin_resistant_breakpoint": { + "name": "ampicillin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "amikacin_resistant_breakpoint", + "title": "ampicillin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -34212,8 +35859,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 195, - "alias": "amikacin_resistant_breakpoint", + "rank": 224, + "alias": "ampicillin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34221,10 +35868,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillinclavulanic_acid_resistance_phenotype": { - "name": "amoxicillinclavulanic_acid_resistance_phenotype", + "azithromycin_resistance_phenotype": { + "name": "azithromycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "amoxicillin-clavulanic_acid_resistance_phenotype", + "title": "azithromycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -34237,8 +35884,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 196, - "alias": "amoxicillinclavulanic_acid_resistance_phenotype", + "rank": 225, + "alias": "azithromycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34254,10 +35901,10 @@ } ] }, - "amoxicillinclavulanic_acid_measurement": { - "name": "amoxicillinclavulanic_acid_measurement", - "description": "The measured value of amoxicillin-clavulanic acid resistance.", - "title": "amoxicillin-clavulanic_acid_measurement", + "azithromycin_measurement": { + "name": "azithromycin_measurement", + "description": "The measured value of azithromycin resistance.", + "title": "azithromycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -34270,8 +35917,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 197, - "alias": "amoxicillinclavulanic_acid_measurement", + "rank": 226, + "alias": "azithromycin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34287,10 +35934,10 @@ } ] }, - "amoxicillinclavulanic_acid_measurement_units": { - "name": "amoxicillinclavulanic_acid_measurement_units", + "azithromycin_measurement_units": { + "name": "azithromycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "amoxicillin-clavulanic_acid_measurement_units", + "title": "azithromycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -34303,8 +35950,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 198, - "alias": "amoxicillinclavulanic_acid_measurement_units", + "rank": 227, + "alias": "azithromycin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34320,10 +35967,10 @@ } ] }, - "amoxicillinclavulanic_acid_measurement_sign": { - "name": "amoxicillinclavulanic_acid_measurement_sign", + "azithromycin_measurement_sign": { + "name": "azithromycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "amoxicillin-clavulanic_acid_measurement_sign", + "title": "azithromycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -34336,8 +35983,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 199, - "alias": "amoxicillinclavulanic_acid_measurement_sign", + "rank": 228, + "alias": "azithromycin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34353,10 +36000,10 @@ } ] }, - "amoxicillinclavulanic_acid_laboratory_typing_method": { - "name": "amoxicillinclavulanic_acid_laboratory_typing_method", + "azithromycin_laboratory_typing_method": { + "name": "azithromycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "amoxicillin-clavulanic_acid_laboratory_typing_method", + "title": "azithromycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -34369,8 +36016,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 200, - "alias": "amoxicillinclavulanic_acid_laboratory_typing_method", + "rank": 229, + "alias": "azithromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34385,10 +36032,10 @@ } ] }, - "amoxicillinclavulanic_acid_laboratory_typing_platform": { - "name": "amoxicillinclavulanic_acid_laboratory_typing_platform", + "azithromycin_laboratory_typing_platform": { + "name": "azithromycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform", + "title": "azithromycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -34401,8 +36048,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 201, - "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform", + "rank": 230, + "alias": "azithromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34417,10 +36064,10 @@ } ] }, - "amoxicillinclavulanic_acid_laboratory_typing_platform_version": { - "name": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", + "azithromycin_laboratory_typing_platform_version": { + "name": "azithromycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform_version", + "title": "azithromycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -34430,8 +36077,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 202, - "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", + "rank": 231, + "alias": "azithromycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34439,10 +36086,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillinclavulanic_acid_vendor_name": { - "name": "amoxicillinclavulanic_acid_vendor_name", + "azithromycin_vendor_name": { + "name": "azithromycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "amoxicillin-clavulanic_acid_vendor_name", + "title": "azithromycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -34455,8 +36102,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 203, - "alias": "amoxicillinclavulanic_acid_vendor_name", + "rank": 232, + "alias": "azithromycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34471,10 +36118,10 @@ } ] }, - "amoxicillinclavulanic_acid_testing_standard": { - "name": "amoxicillinclavulanic_acid_testing_standard", + "azithromycin_testing_standard": { + "name": "azithromycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "amoxicillin-clavulanic_acid_testing_standard", + "title": "azithromycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -34487,8 +36134,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 204, - "alias": "amoxicillinclavulanic_acid_testing_standard", + "rank": 233, + "alias": "azithromycin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34504,10 +36151,10 @@ } ] }, - "amoxicillinclavulanic_acid_testing_standard_version": { - "name": "amoxicillinclavulanic_acid_testing_standard_version", + "azithromycin_testing_standard_version": { + "name": "azithromycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "amoxicillin-clavulanic_acid_testing_standard_version", + "title": "azithromycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -34517,8 +36164,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 205, - "alias": "amoxicillinclavulanic_acid_testing_standard_version", + "rank": 234, + "alias": "azithromycin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34526,10 +36173,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillinclavulanic_acid_testing_standard_details": { - "name": "amoxicillinclavulanic_acid_testing_standard_details", + "azithromycin_testing_standard_details": { + "name": "azithromycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "amoxicillin-clavulanic_acid_testing_standard_details", + "title": "azithromycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -34542,8 +36189,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 206, - "alias": "amoxicillinclavulanic_acid_testing_standard_details", + "rank": 235, + "alias": "azithromycin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34551,10 +36198,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillinclavulanic_acid_susceptible_breakpoint": { - "name": "amoxicillinclavulanic_acid_susceptible_breakpoint", + "azithromycin_susceptible_breakpoint": { + "name": "azithromycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "amoxicillin-clavulanic_acid_susceptible_breakpoint", + "title": "azithromycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -34564,8 +36211,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 207, - "alias": "amoxicillinclavulanic_acid_susceptible_breakpoint", + "rank": 236, + "alias": "azithromycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34573,18 +36220,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillinclavulanic_acid_intermediate_breakpoint": { - "name": "amoxicillinclavulanic_acid_intermediate_breakpoint", + "azithromycin_intermediate_breakpoint": { + "name": "azithromycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "amoxicillin-clavulanic_acid_intermediate_breakpoint", + "title": "azithromycin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 208, - "alias": "amoxicillinclavulanic_acid_intermediate_breakpoint", + "rank": 237, + "alias": "azithromycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34592,10 +36239,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillinclavulanic_acid_resistant_breakpoint": { - "name": "amoxicillinclavulanic_acid_resistant_breakpoint", + "azithromycin_resistant_breakpoint": { + "name": "azithromycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "amoxicillin-clavulanic_acid_resistant_breakpoint", + "title": "azithromycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -34605,8 +36252,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 209, - "alias": "amoxicillinclavulanic_acid_resistant_breakpoint", + "rank": 238, + "alias": "azithromycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34614,10 +36261,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ampicillin_resistance_phenotype": { - "name": "ampicillin_resistance_phenotype", + "cefazolin_resistance_phenotype": { + "name": "cefazolin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "ampicillin_resistance_phenotype", + "title": "cefazolin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -34630,8 +36277,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 210, - "alias": "ampicillin_resistance_phenotype", + "rank": 239, + "alias": "cefazolin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34647,10 +36294,10 @@ } ] }, - "ampicillin_measurement": { - "name": "ampicillin_measurement", - "description": "The measured value of ampicillin resistance.", - "title": "ampicillin_measurement", + "cefazolin_measurement": { + "name": "cefazolin_measurement", + "description": "The measured value of cefazolin resistance.", + "title": "cefazolin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -34663,8 +36310,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 211, - "alias": "ampicillin_measurement", + "rank": 240, + "alias": "cefazolin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34680,10 +36327,10 @@ } ] }, - "ampicillin_measurement_units": { - "name": "ampicillin_measurement_units", + "cefazolin_measurement_units": { + "name": "cefazolin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "ampicillin_measurement_units", + "title": "cefazolin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -34696,8 +36343,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 212, - "alias": "ampicillin_measurement_units", + "rank": 241, + "alias": "cefazolin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34713,10 +36360,10 @@ } ] }, - "ampicillin_measurement_sign": { - "name": "ampicillin_measurement_sign", + "cefazolin_measurement_sign": { + "name": "cefazolin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "ampicillin_measurement_sign", + "title": "cefazolin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -34729,8 +36376,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 213, - "alias": "ampicillin_measurement_sign", + "rank": 242, + "alias": "cefazolin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34746,10 +36393,10 @@ } ] }, - "ampicillin_laboratory_typing_method": { - "name": "ampicillin_laboratory_typing_method", + "cefazolin_laboratory_typing_method": { + "name": "cefazolin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "ampicillin_laboratory_typing_method", + "title": "cefazolin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -34762,8 +36409,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 214, - "alias": "ampicillin_laboratory_typing_method", + "rank": 243, + "alias": "cefazolin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34778,10 +36425,10 @@ } ] }, - "ampicillin_laboratory_typing_platform": { - "name": "ampicillin_laboratory_typing_platform", + "cefazolin_laboratory_typing_platform": { + "name": "cefazolin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "ampicillin_laboratory_typing_platform", + "title": "cefazolin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -34794,8 +36441,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 215, - "alias": "ampicillin_laboratory_typing_platform", + "rank": 244, + "alias": "cefazolin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34810,10 +36457,10 @@ } ] }, - "ampicillin_laboratory_typing_platform_version": { - "name": "ampicillin_laboratory_typing_platform_version", + "cefazolin_laboratory_typing_platform_version": { + "name": "cefazolin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "ampicillin_laboratory_typing_platform_version", + "title": "cefazolin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -34823,8 +36470,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 216, - "alias": "ampicillin_laboratory_typing_platform_version", + "rank": 245, + "alias": "cefazolin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34832,10 +36479,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ampicillin_vendor_name": { - "name": "ampicillin_vendor_name", + "cefazolin_vendor_name": { + "name": "cefazolin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "ampicillin_vendor_name", + "title": "cefazolin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -34848,8 +36495,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 217, - "alias": "ampicillin_vendor_name", + "rank": 246, + "alias": "cefazolin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34864,10 +36511,10 @@ } ] }, - "ampicillin_testing_standard": { - "name": "ampicillin_testing_standard", + "cefazolin_testing_standard": { + "name": "cefazolin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "ampicillin_testing_standard", + "title": "cefazolin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -34880,8 +36527,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 218, - "alias": "ampicillin_testing_standard", + "rank": 247, + "alias": "cefazolin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34897,10 +36544,10 @@ } ] }, - "ampicillin_testing_standard_version": { - "name": "ampicillin_testing_standard_version", + "cefazolin_testing_standard_version": { + "name": "cefazolin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "ampicillin_testing_standard_version", + "title": "cefazolin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -34910,8 +36557,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 219, - "alias": "ampicillin_testing_standard_version", + "rank": 248, + "alias": "cefazolin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34919,10 +36566,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ampicillin_testing_standard_details": { - "name": "ampicillin_testing_standard_details", + "cefazolin_testing_standard_details": { + "name": "cefazolin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "ampicillin_testing_standard_details", + "title": "cefazolin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -34935,8 +36582,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 220, - "alias": "ampicillin_testing_standard_details", + "rank": 249, + "alias": "cefazolin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34944,10 +36591,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ampicillin_susceptible_breakpoint": { - "name": "ampicillin_susceptible_breakpoint", + "cefazolin_susceptible_breakpoint": { + "name": "cefazolin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "ampicillin_susceptible_breakpoint", + "title": "cefazolin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -34957,8 +36604,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 221, - "alias": "ampicillin_susceptible_breakpoint", + "rank": 250, + "alias": "cefazolin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34966,18 +36613,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ampicillin_intermediate_breakpoint": { - "name": "ampicillin_intermediate_breakpoint", + "cefazolin_intermediate_breakpoint": { + "name": "cefazolin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "ampicillin_intermediate_breakpoint", + "title": "cefazolin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 222, - "alias": "ampicillin_intermediate_breakpoint", + "rank": 251, + "alias": "cefazolin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34985,10 +36632,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ampicillin_resistant_breakpoint": { - "name": "ampicillin_resistant_breakpoint", + "cefazolin_resistant_breakpoint": { + "name": "cefazolin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "ampicillin_resistant_breakpoint", + "title": "cefazolin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -34998,8 +36645,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 223, - "alias": "ampicillin_resistant_breakpoint", + "rank": 252, + "alias": "cefazolin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35007,10 +36654,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "azithromycin_resistance_phenotype": { - "name": "azithromycin_resistance_phenotype", + "cefepime_resistance_phenotype": { + "name": "cefepime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "azithromycin_resistance_phenotype", + "title": "cefepime_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -35023,8 +36670,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 224, - "alias": "azithromycin_resistance_phenotype", + "rank": 253, + "alias": "cefepime_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35040,10 +36687,10 @@ } ] }, - "azithromycin_measurement": { - "name": "azithromycin_measurement", - "description": "The measured value of azithromycin resistance.", - "title": "azithromycin_measurement", + "cefepime_measurement": { + "name": "cefepime_measurement", + "description": "The measured value of cefepime resistance.", + "title": "cefepime_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -35056,8 +36703,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 225, - "alias": "azithromycin_measurement", + "rank": 254, + "alias": "cefepime_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35073,10 +36720,10 @@ } ] }, - "azithromycin_measurement_units": { - "name": "azithromycin_measurement_units", + "cefepime_measurement_units": { + "name": "cefepime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "azithromycin_measurement_units", + "title": "cefepime_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -35089,8 +36736,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 226, - "alias": "azithromycin_measurement_units", + "rank": 255, + "alias": "cefepime_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35106,10 +36753,10 @@ } ] }, - "azithromycin_measurement_sign": { - "name": "azithromycin_measurement_sign", + "cefepime_measurement_sign": { + "name": "cefepime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "azithromycin_measurement_sign", + "title": "cefepime_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -35122,8 +36769,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 227, - "alias": "azithromycin_measurement_sign", + "rank": 256, + "alias": "cefepime_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35139,10 +36786,10 @@ } ] }, - "azithromycin_laboratory_typing_method": { - "name": "azithromycin_laboratory_typing_method", + "cefepime_laboratory_typing_method": { + "name": "cefepime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "azithromycin_laboratory_typing_method", + "title": "cefepime_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -35155,8 +36802,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 228, - "alias": "azithromycin_laboratory_typing_method", + "rank": 257, + "alias": "cefepime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35171,10 +36818,10 @@ } ] }, - "azithromycin_laboratory_typing_platform": { - "name": "azithromycin_laboratory_typing_platform", + "cefepime_laboratory_typing_platform": { + "name": "cefepime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "azithromycin_laboratory_typing_platform", + "title": "cefepime_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -35187,8 +36834,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 229, - "alias": "azithromycin_laboratory_typing_platform", + "rank": 258, + "alias": "cefepime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35203,10 +36850,10 @@ } ] }, - "azithromycin_laboratory_typing_platform_version": { - "name": "azithromycin_laboratory_typing_platform_version", + "cefepime_laboratory_typing_platform_version": { + "name": "cefepime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "azithromycin_laboratory_typing_platform_version", + "title": "cefepime_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -35216,8 +36863,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 230, - "alias": "azithromycin_laboratory_typing_platform_version", + "rank": 259, + "alias": "cefepime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35225,10 +36872,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "azithromycin_vendor_name": { - "name": "azithromycin_vendor_name", + "cefepime_vendor_name": { + "name": "cefepime_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "azithromycin_vendor_name", + "title": "cefepime_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -35241,8 +36888,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 231, - "alias": "azithromycin_vendor_name", + "rank": 260, + "alias": "cefepime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35257,10 +36904,10 @@ } ] }, - "azithromycin_testing_standard": { - "name": "azithromycin_testing_standard", + "cefepime_testing_standard": { + "name": "cefepime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "azithromycin_testing_standard", + "title": "cefepime_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -35273,8 +36920,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 232, - "alias": "azithromycin_testing_standard", + "rank": 261, + "alias": "cefepime_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35290,10 +36937,10 @@ } ] }, - "azithromycin_testing_standard_version": { - "name": "azithromycin_testing_standard_version", + "cefepime_testing_standard_version": { + "name": "cefepime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "azithromycin_testing_standard_version", + "title": "cefepime_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -35303,8 +36950,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 233, - "alias": "azithromycin_testing_standard_version", + "rank": 262, + "alias": "cefepime_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35312,10 +36959,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "azithromycin_testing_standard_details": { - "name": "azithromycin_testing_standard_details", + "cefepime_testing_standard_details": { + "name": "cefepime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "azithromycin_testing_standard_details", + "title": "cefepime_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -35328,8 +36975,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 234, - "alias": "azithromycin_testing_standard_details", + "rank": 263, + "alias": "cefepime_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35337,10 +36984,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "azithromycin_susceptible_breakpoint": { - "name": "azithromycin_susceptible_breakpoint", + "cefepime_susceptible_breakpoint": { + "name": "cefepime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "azithromycin_susceptible_breakpoint", + "title": "cefepime_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -35350,8 +36997,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 235, - "alias": "azithromycin_susceptible_breakpoint", + "rank": 264, + "alias": "cefepime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35359,18 +37006,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "azithromycin_intermediate_breakpoint": { - "name": "azithromycin_intermediate_breakpoint", + "cefepime_intermediate_breakpoint": { + "name": "cefepime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "azithromycin_intermediate_breakpoint", + "title": "cefepime_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 236, - "alias": "azithromycin_intermediate_breakpoint", + "rank": 265, + "alias": "cefepime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35378,10 +37025,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "azithromycin_resistant_breakpoint": { - "name": "azithromycin_resistant_breakpoint", + "cefepime_resistant_breakpoint": { + "name": "cefepime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "azithromycin_resistant_breakpoint", + "title": "cefepime_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -35391,8 +37038,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 237, - "alias": "azithromycin_resistant_breakpoint", + "rank": 266, + "alias": "cefepime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35400,10 +37047,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefazolin_resistance_phenotype": { - "name": "cefazolin_resistance_phenotype", + "cefotaxime_resistance_phenotype": { + "name": "cefotaxime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "cefazolin_resistance_phenotype", + "title": "cefotaxime_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -35416,8 +37063,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 238, - "alias": "cefazolin_resistance_phenotype", + "rank": 267, + "alias": "cefotaxime_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35433,10 +37080,10 @@ } ] }, - "cefazolin_measurement": { - "name": "cefazolin_measurement", - "description": "The measured value of cefazolin resistance.", - "title": "cefazolin_measurement", + "cefotaxime_measurement": { + "name": "cefotaxime_measurement", + "description": "The measured value of cefotaxime resistance.", + "title": "cefotaxime_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -35449,8 +37096,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 239, - "alias": "cefazolin_measurement", + "rank": 268, + "alias": "cefotaxime_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35466,10 +37113,10 @@ } ] }, - "cefazolin_measurement_units": { - "name": "cefazolin_measurement_units", + "cefotaxime_measurement_units": { + "name": "cefotaxime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "cefazolin_measurement_units", + "title": "cefotaxime_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -35482,8 +37129,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 240, - "alias": "cefazolin_measurement_units", + "rank": 269, + "alias": "cefotaxime_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35499,10 +37146,10 @@ } ] }, - "cefazolin_measurement_sign": { - "name": "cefazolin_measurement_sign", + "cefotaxime_measurement_sign": { + "name": "cefotaxime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "cefazolin_measurement_sign", + "title": "cefotaxime_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -35515,8 +37162,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 241, - "alias": "cefazolin_measurement_sign", + "rank": 270, + "alias": "cefotaxime_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35532,10 +37179,10 @@ } ] }, - "cefazolin_laboratory_typing_method": { - "name": "cefazolin_laboratory_typing_method", + "cefotaxime_laboratory_typing_method": { + "name": "cefotaxime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "cefazolin_laboratory_typing_method", + "title": "cefotaxime_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -35548,8 +37195,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 242, - "alias": "cefazolin_laboratory_typing_method", + "rank": 271, + "alias": "cefotaxime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35564,10 +37211,10 @@ } ] }, - "cefazolin_laboratory_typing_platform": { - "name": "cefazolin_laboratory_typing_platform", + "cefotaxime_laboratory_typing_platform": { + "name": "cefotaxime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "cefazolin_laboratory_typing_platform", + "title": "cefotaxime_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -35580,8 +37227,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 243, - "alias": "cefazolin_laboratory_typing_platform", + "rank": 272, + "alias": "cefotaxime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35596,10 +37243,10 @@ } ] }, - "cefazolin_laboratory_typing_platform_version": { - "name": "cefazolin_laboratory_typing_platform_version", + "cefotaxime_laboratory_typing_platform_version": { + "name": "cefotaxime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "cefazolin_laboratory_typing_platform_version", + "title": "cefotaxime_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -35609,8 +37256,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 244, - "alias": "cefazolin_laboratory_typing_platform_version", + "rank": 273, + "alias": "cefotaxime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35618,10 +37265,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefazolin_vendor_name": { - "name": "cefazolin_vendor_name", + "cefotaxime_vendor_name": { + "name": "cefotaxime_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "cefazolin_vendor_name", + "title": "cefotaxime_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -35634,8 +37281,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 245, - "alias": "cefazolin_vendor_name", + "rank": 274, + "alias": "cefotaxime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35650,10 +37297,10 @@ } ] }, - "cefazolin_testing_standard": { - "name": "cefazolin_testing_standard", + "cefotaxime_testing_standard": { + "name": "cefotaxime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "cefazolin_testing_standard", + "title": "cefotaxime_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -35666,8 +37313,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 246, - "alias": "cefazolin_testing_standard", + "rank": 275, + "alias": "cefotaxime_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35683,10 +37330,10 @@ } ] }, - "cefazolin_testing_standard_version": { - "name": "cefazolin_testing_standard_version", + "cefotaxime_testing_standard_version": { + "name": "cefotaxime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "cefazolin_testing_standard_version", + "title": "cefotaxime_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -35696,8 +37343,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 247, - "alias": "cefazolin_testing_standard_version", + "rank": 276, + "alias": "cefotaxime_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35705,10 +37352,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefazolin_testing_standard_details": { - "name": "cefazolin_testing_standard_details", + "cefotaxime_testing_standard_details": { + "name": "cefotaxime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "cefazolin_testing_standard_details", + "title": "cefotaxime_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -35721,8 +37368,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 248, - "alias": "cefazolin_testing_standard_details", + "rank": 277, + "alias": "cefotaxime_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35730,10 +37377,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefazolin_susceptible_breakpoint": { - "name": "cefazolin_susceptible_breakpoint", + "cefotaxime_susceptible_breakpoint": { + "name": "cefotaxime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "cefazolin_susceptible_breakpoint", + "title": "cefotaxime_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -35743,8 +37390,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 249, - "alias": "cefazolin_susceptible_breakpoint", + "rank": 278, + "alias": "cefotaxime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35752,18 +37399,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefazolin_intermediate_breakpoint": { - "name": "cefazolin_intermediate_breakpoint", + "cefotaxime_intermediate_breakpoint": { + "name": "cefotaxime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "cefazolin_intermediate_breakpoint", + "title": "cefotaxime_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 250, - "alias": "cefazolin_intermediate_breakpoint", + "rank": 279, + "alias": "cefotaxime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35771,10 +37418,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefazolin_resistant_breakpoint": { - "name": "cefazolin_resistant_breakpoint", + "cefotaxime_resistant_breakpoint": { + "name": "cefotaxime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "cefazolin_resistant_breakpoint", + "title": "cefotaxime_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -35784,8 +37431,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 251, - "alias": "cefazolin_resistant_breakpoint", + "rank": 280, + "alias": "cefotaxime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35793,10 +37440,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefepime_resistance_phenotype": { - "name": "cefepime_resistance_phenotype", + "cefotaximeclavulanic_acid_resistance_phenotype": { + "name": "cefotaximeclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "cefepime_resistance_phenotype", + "title": "cefotaxime-clavulanic_acid_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -35809,8 +37456,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 252, - "alias": "cefepime_resistance_phenotype", + "rank": 281, + "alias": "cefotaximeclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35826,10 +37473,10 @@ } ] }, - "cefepime_measurement": { - "name": "cefepime_measurement", - "description": "The measured value of cefepime resistance.", - "title": "cefepime_measurement", + "cefotaximeclavulanic_acid_measurement": { + "name": "cefotaximeclavulanic_acid_measurement", + "description": "The measured value of cefotaxime-clavulanic acid resistance.", + "title": "cefotaxime-clavulanic_acid_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -35842,8 +37489,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 253, - "alias": "cefepime_measurement", + "rank": 282, + "alias": "cefotaximeclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35859,10 +37506,10 @@ } ] }, - "cefepime_measurement_units": { - "name": "cefepime_measurement_units", + "cefotaximeclavulanic_acid_measurement_units": { + "name": "cefotaximeclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "cefepime_measurement_units", + "title": "cefotaxime-clavulanic_acid_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -35875,8 +37522,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 254, - "alias": "cefepime_measurement_units", + "rank": 283, + "alias": "cefotaximeclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35892,10 +37539,10 @@ } ] }, - "cefepime_measurement_sign": { - "name": "cefepime_measurement_sign", + "cefotaximeclavulanic_acid_measurement_sign": { + "name": "cefotaximeclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "cefepime_measurement_sign", + "title": "cefotaxime-clavulanic_acid_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -35908,8 +37555,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 255, - "alias": "cefepime_measurement_sign", + "rank": 284, + "alias": "cefotaximeclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35925,10 +37572,10 @@ } ] }, - "cefepime_laboratory_typing_method": { - "name": "cefepime_laboratory_typing_method", + "cefotaximeclavulanic_acid_laboratory_typing_method": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "cefepime_laboratory_typing_method", + "title": "cefotaxime-clavulanic_acid_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -35941,8 +37588,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 256, - "alias": "cefepime_laboratory_typing_method", + "rank": 285, + "alias": "cefotaximeclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35957,10 +37604,10 @@ } ] }, - "cefepime_laboratory_typing_platform": { - "name": "cefepime_laboratory_typing_platform", + "cefotaximeclavulanic_acid_laboratory_typing_platform": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "cefepime_laboratory_typing_platform", + "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -35973,8 +37620,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 257, - "alias": "cefepime_laboratory_typing_platform", + "rank": 286, + "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35989,10 +37636,10 @@ } ] }, - "cefepime_laboratory_typing_platform_version": { - "name": "cefepime_laboratory_typing_platform_version", + "cefotaximeclavulanic_acid_laboratory_typing_platform_version": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "cefepime_laboratory_typing_platform_version", + "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -36002,8 +37649,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 258, - "alias": "cefepime_laboratory_typing_platform_version", + "rank": 287, + "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36011,10 +37658,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefepime_vendor_name": { - "name": "cefepime_vendor_name", + "cefotaximeclavulanic_acid_vendor_name": { + "name": "cefotaximeclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "cefepime_vendor_name", + "title": "cefotaxime-clavulanic_acid_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -36027,8 +37674,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 259, - "alias": "cefepime_vendor_name", + "rank": 288, + "alias": "cefotaximeclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36043,10 +37690,10 @@ } ] }, - "cefepime_testing_standard": { - "name": "cefepime_testing_standard", + "cefotaximeclavulanic_acid_testing_standard": { + "name": "cefotaximeclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "cefepime_testing_standard", + "title": "cefotaxime-clavulanic_acid_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -36059,8 +37706,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 260, - "alias": "cefepime_testing_standard", + "rank": 289, + "alias": "cefotaximeclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36076,10 +37723,10 @@ } ] }, - "cefepime_testing_standard_version": { - "name": "cefepime_testing_standard_version", + "cefotaximeclavulanic_acid_testing_standard_version": { + "name": "cefotaximeclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "cefepime_testing_standard_version", + "title": "cefotaxime-clavulanic_acid_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -36089,8 +37736,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 261, - "alias": "cefepime_testing_standard_version", + "rank": 290, + "alias": "cefotaximeclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36098,10 +37745,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefepime_testing_standard_details": { - "name": "cefepime_testing_standard_details", + "cefotaximeclavulanic_acid_testing_standard_details": { + "name": "cefotaximeclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "cefepime_testing_standard_details", + "title": "cefotaxime-clavulanic_acid_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -36114,8 +37761,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 262, - "alias": "cefepime_testing_standard_details", + "rank": 291, + "alias": "cefotaximeclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36123,10 +37770,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefepime_susceptible_breakpoint": { - "name": "cefepime_susceptible_breakpoint", + "cefotaximeclavulanic_acid_susceptible_breakpoint": { + "name": "cefotaximeclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "cefepime_susceptible_breakpoint", + "title": "cefotaxime-clavulanic_acid_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -36136,8 +37783,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 263, - "alias": "cefepime_susceptible_breakpoint", + "rank": 292, + "alias": "cefotaximeclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36145,18 +37792,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefepime_intermediate_breakpoint": { - "name": "cefepime_intermediate_breakpoint", + "cefotaximeclavulanic_acid_intermediate_breakpoint": { + "name": "cefotaximeclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "cefepime_intermediate_breakpoint", + "title": "cefotaxime-clavulanic_acid_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 264, - "alias": "cefepime_intermediate_breakpoint", + "rank": 293, + "alias": "cefotaximeclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36164,10 +37811,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefepime_resistant_breakpoint": { - "name": "cefepime_resistant_breakpoint", + "cefotaximeclavulanic_acid_resistant_breakpoint": { + "name": "cefotaximeclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "cefepime_resistant_breakpoint", + "title": "cefotaxime-clavulanic_acid_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -36177,8 +37824,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 265, - "alias": "cefepime_resistant_breakpoint", + "rank": 294, + "alias": "cefotaximeclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36186,10 +37833,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime_resistance_phenotype": { - "name": "cefotaxime_resistance_phenotype", + "cefoxitin_resistance_phenotype": { + "name": "cefoxitin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "cefotaxime_resistance_phenotype", + "title": "cefoxitin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -36202,8 +37849,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 266, - "alias": "cefotaxime_resistance_phenotype", + "rank": 295, + "alias": "cefoxitin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36219,10 +37866,10 @@ } ] }, - "cefotaxime_measurement": { - "name": "cefotaxime_measurement", - "description": "The measured value of cefotaxime resistance.", - "title": "cefotaxime_measurement", + "cefoxitin_measurement": { + "name": "cefoxitin_measurement", + "description": "The measured value of cefoxitin resistance.", + "title": "cefoxitin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -36235,8 +37882,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 267, - "alias": "cefotaxime_measurement", + "rank": 296, + "alias": "cefoxitin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36252,10 +37899,10 @@ } ] }, - "cefotaxime_measurement_units": { - "name": "cefotaxime_measurement_units", + "cefoxitin_measurement_units": { + "name": "cefoxitin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "cefotaxime_measurement_units", + "title": "cefoxitin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -36268,8 +37915,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 268, - "alias": "cefotaxime_measurement_units", + "rank": 297, + "alias": "cefoxitin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36285,10 +37932,10 @@ } ] }, - "cefotaxime_measurement_sign": { - "name": "cefotaxime_measurement_sign", + "cefoxitin_measurement_sign": { + "name": "cefoxitin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "cefotaxime_measurement_sign", + "title": "cefoxitin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -36301,8 +37948,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 269, - "alias": "cefotaxime_measurement_sign", + "rank": 298, + "alias": "cefoxitin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36318,10 +37965,10 @@ } ] }, - "cefotaxime_laboratory_typing_method": { - "name": "cefotaxime_laboratory_typing_method", + "cefoxitin_laboratory_typing_method": { + "name": "cefoxitin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "cefotaxime_laboratory_typing_method", + "title": "cefoxitin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -36334,8 +37981,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 270, - "alias": "cefotaxime_laboratory_typing_method", + "rank": 299, + "alias": "cefoxitin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36350,10 +37997,10 @@ } ] }, - "cefotaxime_laboratory_typing_platform": { - "name": "cefotaxime_laboratory_typing_platform", + "cefoxitin_laboratory_typing_platform": { + "name": "cefoxitin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "cefotaxime_laboratory_typing_platform", + "title": "cefoxitin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -36366,8 +38013,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 271, - "alias": "cefotaxime_laboratory_typing_platform", + "rank": 300, + "alias": "cefoxitin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36382,10 +38029,10 @@ } ] }, - "cefotaxime_laboratory_typing_platform_version": { - "name": "cefotaxime_laboratory_typing_platform_version", + "cefoxitin_laboratory_typing_platform_version": { + "name": "cefoxitin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "cefotaxime_laboratory_typing_platform_version", + "title": "cefoxitin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -36395,8 +38042,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 272, - "alias": "cefotaxime_laboratory_typing_platform_version", + "rank": 301, + "alias": "cefoxitin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36404,10 +38051,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime_vendor_name": { - "name": "cefotaxime_vendor_name", + "cefoxitin_vendor_name": { + "name": "cefoxitin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "cefotaxime_vendor_name", + "title": "cefoxitin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -36420,8 +38067,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 273, - "alias": "cefotaxime_vendor_name", + "rank": 302, + "alias": "cefoxitin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36436,10 +38083,10 @@ } ] }, - "cefotaxime_testing_standard": { - "name": "cefotaxime_testing_standard", + "cefoxitin_testing_standard": { + "name": "cefoxitin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "cefotaxime_testing_standard", + "title": "cefoxitin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -36452,8 +38099,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 274, - "alias": "cefotaxime_testing_standard", + "rank": 303, + "alias": "cefoxitin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36469,10 +38116,10 @@ } ] }, - "cefotaxime_testing_standard_version": { - "name": "cefotaxime_testing_standard_version", + "cefoxitin_testing_standard_version": { + "name": "cefoxitin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "cefotaxime_testing_standard_version", + "title": "cefoxitin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -36482,8 +38129,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 275, - "alias": "cefotaxime_testing_standard_version", + "rank": 304, + "alias": "cefoxitin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36491,10 +38138,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime_testing_standard_details": { - "name": "cefotaxime_testing_standard_details", + "cefoxitin_testing_standard_details": { + "name": "cefoxitin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "cefotaxime_testing_standard_details", + "title": "cefoxitin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -36507,8 +38154,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 276, - "alias": "cefotaxime_testing_standard_details", + "rank": 305, + "alias": "cefoxitin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36516,10 +38163,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime_susceptible_breakpoint": { - "name": "cefotaxime_susceptible_breakpoint", + "cefoxitin_susceptible_breakpoint": { + "name": "cefoxitin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "cefotaxime_susceptible_breakpoint", + "title": "cefoxitin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -36529,8 +38176,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 277, - "alias": "cefotaxime_susceptible_breakpoint", + "rank": 306, + "alias": "cefoxitin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36538,18 +38185,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime_intermediate_breakpoint": { - "name": "cefotaxime_intermediate_breakpoint", + "cefoxitin_intermediate_breakpoint": { + "name": "cefoxitin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "cefotaxime_intermediate_breakpoint", + "title": "cefoxitin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 278, - "alias": "cefotaxime_intermediate_breakpoint", + "rank": 307, + "alias": "cefoxitin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36557,10 +38204,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime_resistant_breakpoint": { - "name": "cefotaxime_resistant_breakpoint", + "cefoxitin_resistant_breakpoint": { + "name": "cefoxitin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "cefotaxime_resistant_breakpoint", + "title": "cefoxitin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -36570,8 +38217,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 279, - "alias": "cefotaxime_resistant_breakpoint", + "rank": 308, + "alias": "cefoxitin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36579,10 +38226,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaximeclavulanic_acid_resistance_phenotype": { - "name": "cefotaximeclavulanic_acid_resistance_phenotype", + "cefpodoxime_resistance_phenotype": { + "name": "cefpodoxime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "cefotaxime-clavulanic_acid_resistance_phenotype", + "title": "cefpodoxime_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -36595,8 +38242,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 280, - "alias": "cefotaximeclavulanic_acid_resistance_phenotype", + "rank": 309, + "alias": "cefpodoxime_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36612,10 +38259,10 @@ } ] }, - "cefotaximeclavulanic_acid_measurement": { - "name": "cefotaximeclavulanic_acid_measurement", - "description": "The measured value of cefotaxime-clavulanic acid resistance.", - "title": "cefotaxime-clavulanic_acid_measurement", + "cefpodoxime_measurement": { + "name": "cefpodoxime_measurement", + "description": "The measured value of cefpodoxime resistance.", + "title": "cefpodoxime_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -36628,8 +38275,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 281, - "alias": "cefotaximeclavulanic_acid_measurement", + "rank": 310, + "alias": "cefpodoxime_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36645,10 +38292,10 @@ } ] }, - "cefotaximeclavulanic_acid_measurement_units": { - "name": "cefotaximeclavulanic_acid_measurement_units", + "cefpodoxime_measurement_units": { + "name": "cefpodoxime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "cefotaxime-clavulanic_acid_measurement_units", + "title": "cefpodoxime_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -36661,8 +38308,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 282, - "alias": "cefotaximeclavulanic_acid_measurement_units", + "rank": 311, + "alias": "cefpodoxime_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36678,10 +38325,10 @@ } ] }, - "cefotaximeclavulanic_acid_measurement_sign": { - "name": "cefotaximeclavulanic_acid_measurement_sign", + "cefpodoxime_measurement_sign": { + "name": "cefpodoxime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "cefotaxime-clavulanic_acid_measurement_sign", + "title": "cefpodoxime_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -36694,8 +38341,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 283, - "alias": "cefotaximeclavulanic_acid_measurement_sign", + "rank": 312, + "alias": "cefpodoxime_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36711,10 +38358,10 @@ } ] }, - "cefotaximeclavulanic_acid_laboratory_typing_method": { - "name": "cefotaximeclavulanic_acid_laboratory_typing_method", + "cefpodoxime_laboratory_typing_method": { + "name": "cefpodoxime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "cefotaxime-clavulanic_acid_laboratory_typing_method", + "title": "cefpodoxime_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -36727,8 +38374,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 284, - "alias": "cefotaximeclavulanic_acid_laboratory_typing_method", + "rank": 313, + "alias": "cefpodoxime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36743,10 +38390,10 @@ } ] }, - "cefotaximeclavulanic_acid_laboratory_typing_platform": { - "name": "cefotaximeclavulanic_acid_laboratory_typing_platform", + "cefpodoxime_laboratory_typing_platform": { + "name": "cefpodoxime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform", + "title": "cefpodoxime_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -36759,8 +38406,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 285, - "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform", + "rank": 314, + "alias": "cefpodoxime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36775,10 +38422,10 @@ } ] }, - "cefotaximeclavulanic_acid_laboratory_typing_platform_version": { - "name": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", + "cefpodoxime_laboratory_typing_platform_version": { + "name": "cefpodoxime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform_version", + "title": "cefpodoxime_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -36788,8 +38435,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 286, - "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", + "rank": 315, + "alias": "cefpodoxime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36797,10 +38444,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaximeclavulanic_acid_vendor_name": { - "name": "cefotaximeclavulanic_acid_vendor_name", + "cefpodoxime_vendor_name": { + "name": "cefpodoxime_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "cefotaxime-clavulanic_acid_vendor_name", + "title": "cefpodoxime_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -36813,8 +38460,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 287, - "alias": "cefotaximeclavulanic_acid_vendor_name", + "rank": 316, + "alias": "cefpodoxime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36829,10 +38476,10 @@ } ] }, - "cefotaximeclavulanic_acid_testing_standard": { - "name": "cefotaximeclavulanic_acid_testing_standard", + "cefpodoxime_testing_standard": { + "name": "cefpodoxime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "cefotaxime-clavulanic_acid_testing_standard", + "title": "cefpodoxime_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -36845,8 +38492,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 288, - "alias": "cefotaximeclavulanic_acid_testing_standard", + "rank": 317, + "alias": "cefpodoxime_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36862,10 +38509,10 @@ } ] }, - "cefotaximeclavulanic_acid_testing_standard_version": { - "name": "cefotaximeclavulanic_acid_testing_standard_version", + "cefpodoxime_testing_standard_version": { + "name": "cefpodoxime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "cefotaxime-clavulanic_acid_testing_standard_version", + "title": "cefpodoxime_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -36875,8 +38522,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 289, - "alias": "cefotaximeclavulanic_acid_testing_standard_version", + "rank": 318, + "alias": "cefpodoxime_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36884,10 +38531,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaximeclavulanic_acid_testing_standard_details": { - "name": "cefotaximeclavulanic_acid_testing_standard_details", + "cefpodoxime_testing_standard_details": { + "name": "cefpodoxime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "cefotaxime-clavulanic_acid_testing_standard_details", + "title": "cefpodoxime_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -36900,8 +38547,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 290, - "alias": "cefotaximeclavulanic_acid_testing_standard_details", + "rank": 319, + "alias": "cefpodoxime_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36909,10 +38556,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaximeclavulanic_acid_susceptible_breakpoint": { - "name": "cefotaximeclavulanic_acid_susceptible_breakpoint", + "cefpodoxime_susceptible_breakpoint": { + "name": "cefpodoxime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "cefotaxime-clavulanic_acid_susceptible_breakpoint", + "title": "cefpodoxime_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -36922,8 +38569,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 291, - "alias": "cefotaximeclavulanic_acid_susceptible_breakpoint", + "rank": 320, + "alias": "cefpodoxime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36931,18 +38578,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaximeclavulanic_acid_intermediate_breakpoint": { - "name": "cefotaximeclavulanic_acid_intermediate_breakpoint", + "cefpodoxime_intermediate_breakpoint": { + "name": "cefpodoxime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "cefotaxime-clavulanic_acid_intermediate_breakpoint", + "title": "cefpodoxime_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 292, - "alias": "cefotaximeclavulanic_acid_intermediate_breakpoint", + "rank": 321, + "alias": "cefpodoxime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36950,10 +38597,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaximeclavulanic_acid_resistant_breakpoint": { - "name": "cefotaximeclavulanic_acid_resistant_breakpoint", + "cefpodoxime_resistant_breakpoint": { + "name": "cefpodoxime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "cefotaxime-clavulanic_acid_resistant_breakpoint", + "title": "cefpodoxime_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -36963,8 +38610,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 293, - "alias": "cefotaximeclavulanic_acid_resistant_breakpoint", + "rank": 322, + "alias": "cefpodoxime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -36972,10 +38619,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefoxitin_resistance_phenotype": { - "name": "cefoxitin_resistance_phenotype", + "ceftazidime_resistance_phenotype": { + "name": "ceftazidime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "cefoxitin_resistance_phenotype", + "title": "ceftazidime_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -36988,8 +38635,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 294, - "alias": "cefoxitin_resistance_phenotype", + "rank": 323, + "alias": "ceftazidime_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37005,10 +38652,10 @@ } ] }, - "cefoxitin_measurement": { - "name": "cefoxitin_measurement", - "description": "The measured value of cefoxitin resistance.", - "title": "cefoxitin_measurement", + "ceftazidime_measurement": { + "name": "ceftazidime_measurement", + "description": "The measured value of ceftazidime resistance.", + "title": "ceftazidime_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -37021,8 +38668,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 295, - "alias": "cefoxitin_measurement", + "rank": 324, + "alias": "ceftazidime_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37038,10 +38685,10 @@ } ] }, - "cefoxitin_measurement_units": { - "name": "cefoxitin_measurement_units", + "ceftazidime_measurement_units": { + "name": "ceftazidime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "cefoxitin_measurement_units", + "title": "ceftazidime_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -37054,8 +38701,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 296, - "alias": "cefoxitin_measurement_units", + "rank": 325, + "alias": "ceftazidime_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37071,10 +38718,10 @@ } ] }, - "cefoxitin_measurement_sign": { - "name": "cefoxitin_measurement_sign", + "ceftazidime_measurement_sign": { + "name": "ceftazidime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "cefoxitin_measurement_sign", + "title": "ceftazidime_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -37087,8 +38734,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 297, - "alias": "cefoxitin_measurement_sign", + "rank": 326, + "alias": "ceftazidime_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37104,10 +38751,10 @@ } ] }, - "cefoxitin_laboratory_typing_method": { - "name": "cefoxitin_laboratory_typing_method", + "ceftazidime_laboratory_typing_method": { + "name": "ceftazidime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "cefoxitin_laboratory_typing_method", + "title": "ceftazidime_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -37120,8 +38767,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 298, - "alias": "cefoxitin_laboratory_typing_method", + "rank": 327, + "alias": "ceftazidime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37136,10 +38783,10 @@ } ] }, - "cefoxitin_laboratory_typing_platform": { - "name": "cefoxitin_laboratory_typing_platform", + "ceftazidime_laboratory_typing_platform": { + "name": "ceftazidime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "cefoxitin_laboratory_typing_platform", + "title": "ceftazidime_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -37152,8 +38799,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 299, - "alias": "cefoxitin_laboratory_typing_platform", + "rank": 328, + "alias": "ceftazidime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37168,10 +38815,10 @@ } ] }, - "cefoxitin_laboratory_typing_platform_version": { - "name": "cefoxitin_laboratory_typing_platform_version", + "ceftazidime_laboratory_typing_platform_version": { + "name": "ceftazidime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "cefoxitin_laboratory_typing_platform_version", + "title": "ceftazidime_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -37181,8 +38828,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 300, - "alias": "cefoxitin_laboratory_typing_platform_version", + "rank": 329, + "alias": "ceftazidime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37190,10 +38837,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefoxitin_vendor_name": { - "name": "cefoxitin_vendor_name", + "ceftazidime_vendor_name": { + "name": "ceftazidime_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "cefoxitin_vendor_name", + "title": "ceftazidime_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -37206,8 +38853,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 301, - "alias": "cefoxitin_vendor_name", + "rank": 330, + "alias": "ceftazidime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37222,10 +38869,10 @@ } ] }, - "cefoxitin_testing_standard": { - "name": "cefoxitin_testing_standard", + "ceftazidime_testing_standard": { + "name": "ceftazidime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "cefoxitin_testing_standard", + "title": "ceftazidime_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -37238,8 +38885,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 302, - "alias": "cefoxitin_testing_standard", + "rank": 331, + "alias": "ceftazidime_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37255,10 +38902,10 @@ } ] }, - "cefoxitin_testing_standard_version": { - "name": "cefoxitin_testing_standard_version", + "ceftazidime_testing_standard_version": { + "name": "ceftazidime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "cefoxitin_testing_standard_version", + "title": "ceftazidime_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -37268,8 +38915,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 303, - "alias": "cefoxitin_testing_standard_version", + "rank": 332, + "alias": "ceftazidime_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37277,10 +38924,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefoxitin_testing_standard_details": { - "name": "cefoxitin_testing_standard_details", + "ceftazidime_testing_standard_details": { + "name": "ceftazidime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "cefoxitin_testing_standard_details", + "title": "ceftazidime_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -37293,8 +38940,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 304, - "alias": "cefoxitin_testing_standard_details", + "rank": 333, + "alias": "ceftazidime_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37302,10 +38949,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefoxitin_susceptible_breakpoint": { - "name": "cefoxitin_susceptible_breakpoint", + "ceftazidime_susceptible_breakpoint": { + "name": "ceftazidime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "cefoxitin_susceptible_breakpoint", + "title": "ceftazidime_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -37315,8 +38962,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 305, - "alias": "cefoxitin_susceptible_breakpoint", + "rank": 334, + "alias": "ceftazidime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37324,18 +38971,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefoxitin_intermediate_breakpoint": { - "name": "cefoxitin_intermediate_breakpoint", + "ceftazidime_intermediate_breakpoint": { + "name": "ceftazidime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "cefoxitin_intermediate_breakpoint", + "title": "ceftazidime_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 306, - "alias": "cefoxitin_intermediate_breakpoint", + "rank": 335, + "alias": "ceftazidime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37343,10 +38990,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefoxitin_resistant_breakpoint": { - "name": "cefoxitin_resistant_breakpoint", + "ceftazidime_resistant_breakpoint": { + "name": "ceftazidime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "cefoxitin_resistant_breakpoint", + "title": "ceftazidime_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -37356,8 +39003,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 307, - "alias": "cefoxitin_resistant_breakpoint", + "rank": 336, + "alias": "ceftazidime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37365,10 +39012,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefpodoxime_resistance_phenotype": { - "name": "cefpodoxime_resistance_phenotype", + "ceftazidimeclavulanic_acid_resistance_phenotype": { + "name": "ceftazidimeclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "cefpodoxime_resistance_phenotype", + "title": "ceftazidime-clavulanic_acid_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -37381,8 +39028,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 308, - "alias": "cefpodoxime_resistance_phenotype", + "rank": 337, + "alias": "ceftazidimeclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37398,10 +39045,10 @@ } ] }, - "cefpodoxime_measurement": { - "name": "cefpodoxime_measurement", - "description": "The measured value of cefpodoxime resistance.", - "title": "cefpodoxime_measurement", + "ceftazidimeclavulanic_acid_measurement": { + "name": "ceftazidimeclavulanic_acid_measurement", + "description": "The measured value of ceftazidime-clavulanic acid resistance.", + "title": "ceftazidime-clavulanic_acid_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -37414,8 +39061,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 309, - "alias": "cefpodoxime_measurement", + "rank": 338, + "alias": "ceftazidimeclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37431,10 +39078,10 @@ } ] }, - "cefpodoxime_measurement_units": { - "name": "cefpodoxime_measurement_units", + "ceftazidimeclavulanic_acid_measurement_units": { + "name": "ceftazidimeclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "cefpodoxime_measurement_units", + "title": "ceftazidime-clavulanic_acid_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -37447,8 +39094,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 310, - "alias": "cefpodoxime_measurement_units", + "rank": 339, + "alias": "ceftazidimeclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37464,10 +39111,10 @@ } ] }, - "cefpodoxime_measurement_sign": { - "name": "cefpodoxime_measurement_sign", + "ceftazidimeclavulanic_acid_measurement_sign": { + "name": "ceftazidimeclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "cefpodoxime_measurement_sign", + "title": "ceftazidime-clavulanic_acid_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -37480,8 +39127,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 311, - "alias": "cefpodoxime_measurement_sign", + "rank": 340, + "alias": "ceftazidimeclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37497,10 +39144,10 @@ } ] }, - "cefpodoxime_laboratory_typing_method": { - "name": "cefpodoxime_laboratory_typing_method", + "ceftazidimeclavulanic_acid_laboratory_typing_method": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "cefpodoxime_laboratory_typing_method", + "title": "ceftazidime-clavulanic_acid_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -37513,8 +39160,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 312, - "alias": "cefpodoxime_laboratory_typing_method", + "rank": 341, + "alias": "ceftazidimeclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37529,10 +39176,10 @@ } ] }, - "cefpodoxime_laboratory_typing_platform": { - "name": "cefpodoxime_laboratory_typing_platform", + "ceftazidimeclavulanic_acid_laboratory_typing_platform": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "cefpodoxime_laboratory_typing_platform", + "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -37545,8 +39192,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 313, - "alias": "cefpodoxime_laboratory_typing_platform", + "rank": 342, + "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37561,10 +39208,10 @@ } ] }, - "cefpodoxime_laboratory_typing_platform_version": { - "name": "cefpodoxime_laboratory_typing_platform_version", + "ceftazidimeclavulanic_acid_laboratory_typing_platform_version": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "cefpodoxime_laboratory_typing_platform_version", + "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -37574,8 +39221,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 314, - "alias": "cefpodoxime_laboratory_typing_platform_version", + "rank": 343, + "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37583,10 +39230,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefpodoxime_vendor_name": { - "name": "cefpodoxime_vendor_name", + "ceftazidimeclavulanic_acid_vendor_name": { + "name": "ceftazidimeclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "cefpodoxime_vendor_name", + "title": "ceftazidime-clavulanic_acid_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -37599,8 +39246,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 315, - "alias": "cefpodoxime_vendor_name", + "rank": 344, + "alias": "ceftazidimeclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37615,10 +39262,10 @@ } ] }, - "cefpodoxime_testing_standard": { - "name": "cefpodoxime_testing_standard", + "ceftazidimeclavulanic_acid_testing_standard": { + "name": "ceftazidimeclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "cefpodoxime_testing_standard", + "title": "ceftazidime-clavulanic_acid_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -37631,8 +39278,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 316, - "alias": "cefpodoxime_testing_standard", + "rank": 345, + "alias": "ceftazidimeclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37648,10 +39295,10 @@ } ] }, - "cefpodoxime_testing_standard_version": { - "name": "cefpodoxime_testing_standard_version", + "ceftazidimeclavulanic_acid_testing_standard_version": { + "name": "ceftazidimeclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "cefpodoxime_testing_standard_version", + "title": "ceftazidime-clavulanic_acid_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -37661,8 +39308,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 317, - "alias": "cefpodoxime_testing_standard_version", + "rank": 346, + "alias": "ceftazidimeclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37670,10 +39317,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefpodoxime_testing_standard_details": { - "name": "cefpodoxime_testing_standard_details", + "ceftazidimeclavulanic_acid_testing_standard_details": { + "name": "ceftazidimeclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "cefpodoxime_testing_standard_details", + "title": "ceftazidime-clavulanic_acid_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -37686,8 +39333,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 318, - "alias": "cefpodoxime_testing_standard_details", + "rank": 347, + "alias": "ceftazidimeclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37695,10 +39342,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefpodoxime_susceptible_breakpoint": { - "name": "cefpodoxime_susceptible_breakpoint", + "ceftazidimeclavulanic_acid_susceptible_breakpoint": { + "name": "ceftazidimeclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "cefpodoxime_susceptible_breakpoint", + "title": "ceftazidime-clavulanic_acid_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -37708,8 +39355,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 319, - "alias": "cefpodoxime_susceptible_breakpoint", + "rank": 348, + "alias": "ceftazidimeclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37717,18 +39364,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefpodoxime_intermediate_breakpoint": { - "name": "cefpodoxime_intermediate_breakpoint", + "ceftazidimeclavulanic_acid_intermediate_breakpoint": { + "name": "ceftazidimeclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "cefpodoxime_intermediate_breakpoint", + "title": "ceftazidime-clavulanic_acid_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 320, - "alias": "cefpodoxime_intermediate_breakpoint", + "rank": 349, + "alias": "ceftazidimeclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37736,10 +39383,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefpodoxime_resistant_breakpoint": { - "name": "cefpodoxime_resistant_breakpoint", + "ceftazidimeclavulanic_acid_resistant_breakpoint": { + "name": "ceftazidimeclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "cefpodoxime_resistant_breakpoint", + "title": "ceftazidime-clavulanic_acid_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -37749,8 +39396,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 321, - "alias": "cefpodoxime_resistant_breakpoint", + "rank": 350, + "alias": "ceftazidimeclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37758,10 +39405,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime_resistance_phenotype": { - "name": "ceftazidime_resistance_phenotype", + "ceftiofur_resistance_phenotype": { + "name": "ceftiofur_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "ceftazidime_resistance_phenotype", + "title": "ceftiofur_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -37774,8 +39421,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 322, - "alias": "ceftazidime_resistance_phenotype", + "rank": 351, + "alias": "ceftiofur_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37791,10 +39438,10 @@ } ] }, - "ceftazidime_measurement": { - "name": "ceftazidime_measurement", - "description": "The measured value of ceftazidime resistance.", - "title": "ceftazidime_measurement", + "ceftiofur_measurement": { + "name": "ceftiofur_measurement", + "description": "The measured value of ceftiofur resistance.", + "title": "ceftiofur_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -37807,8 +39454,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 323, - "alias": "ceftazidime_measurement", + "rank": 352, + "alias": "ceftiofur_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37824,10 +39471,10 @@ } ] }, - "ceftazidime_measurement_units": { - "name": "ceftazidime_measurement_units", + "ceftiofur_measurement_units": { + "name": "ceftiofur_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "ceftazidime_measurement_units", + "title": "ceftiofur_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -37840,8 +39487,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 324, - "alias": "ceftazidime_measurement_units", + "rank": 353, + "alias": "ceftiofur_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37857,10 +39504,10 @@ } ] }, - "ceftazidime_measurement_sign": { - "name": "ceftazidime_measurement_sign", + "ceftiofur_measurement_sign": { + "name": "ceftiofur_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "ceftazidime_measurement_sign", + "title": "ceftiofur_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -37873,8 +39520,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 325, - "alias": "ceftazidime_measurement_sign", + "rank": 354, + "alias": "ceftiofur_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37890,10 +39537,10 @@ } ] }, - "ceftazidime_laboratory_typing_method": { - "name": "ceftazidime_laboratory_typing_method", + "ceftiofur_laboratory_typing_method": { + "name": "ceftiofur_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "ceftazidime_laboratory_typing_method", + "title": "ceftiofur_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -37906,8 +39553,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 326, - "alias": "ceftazidime_laboratory_typing_method", + "rank": 355, + "alias": "ceftiofur_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37922,10 +39569,10 @@ } ] }, - "ceftazidime_laboratory_typing_platform": { - "name": "ceftazidime_laboratory_typing_platform", + "ceftiofur_laboratory_typing_platform": { + "name": "ceftiofur_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "ceftazidime_laboratory_typing_platform", + "title": "ceftiofur_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -37938,8 +39585,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 327, - "alias": "ceftazidime_laboratory_typing_platform", + "rank": 356, + "alias": "ceftiofur_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37954,10 +39601,10 @@ } ] }, - "ceftazidime_laboratory_typing_platform_version": { - "name": "ceftazidime_laboratory_typing_platform_version", + "ceftiofur_laboratory_typing_platform_version": { + "name": "ceftiofur_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "ceftazidime_laboratory_typing_platform_version", + "title": "ceftiofur_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -37967,8 +39614,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 328, - "alias": "ceftazidime_laboratory_typing_platform_version", + "rank": 357, + "alias": "ceftiofur_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -37976,10 +39623,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime_vendor_name": { - "name": "ceftazidime_vendor_name", + "ceftiofur_vendor_name": { + "name": "ceftiofur_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "ceftazidime_vendor_name", + "title": "ceftiofur_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -37992,8 +39639,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 329, - "alias": "ceftazidime_vendor_name", + "rank": 358, + "alias": "ceftiofur_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38008,10 +39655,10 @@ } ] }, - "ceftazidime_testing_standard": { - "name": "ceftazidime_testing_standard", + "ceftiofur_testing_standard": { + "name": "ceftiofur_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "ceftazidime_testing_standard", + "title": "ceftiofur_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -38024,8 +39671,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 330, - "alias": "ceftazidime_testing_standard", + "rank": 359, + "alias": "ceftiofur_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38041,10 +39688,10 @@ } ] }, - "ceftazidime_testing_standard_version": { - "name": "ceftazidime_testing_standard_version", + "ceftiofur_testing_standard_version": { + "name": "ceftiofur_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "ceftazidime_testing_standard_version", + "title": "ceftiofur_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -38054,8 +39701,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 331, - "alias": "ceftazidime_testing_standard_version", + "rank": 360, + "alias": "ceftiofur_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38063,10 +39710,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime_testing_standard_details": { - "name": "ceftazidime_testing_standard_details", + "ceftiofur_testing_standard_details": { + "name": "ceftiofur_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "ceftazidime_testing_standard_details", + "title": "ceftiofur_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -38079,8 +39726,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 332, - "alias": "ceftazidime_testing_standard_details", + "rank": 361, + "alias": "ceftiofur_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38088,10 +39735,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime_susceptible_breakpoint": { - "name": "ceftazidime_susceptible_breakpoint", + "ceftiofur_susceptible_breakpoint": { + "name": "ceftiofur_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "ceftazidime_susceptible_breakpoint", + "title": "ceftiofur_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -38101,8 +39748,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 333, - "alias": "ceftazidime_susceptible_breakpoint", + "rank": 362, + "alias": "ceftiofur_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38110,18 +39757,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime_intermediate_breakpoint": { - "name": "ceftazidime_intermediate_breakpoint", + "ceftiofur_intermediate_breakpoint": { + "name": "ceftiofur_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "ceftazidime_intermediate_breakpoint", + "title": "ceftiofur_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 334, - "alias": "ceftazidime_intermediate_breakpoint", + "rank": 363, + "alias": "ceftiofur_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38129,10 +39776,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime_resistant_breakpoint": { - "name": "ceftazidime_resistant_breakpoint", + "ceftiofur_resistant_breakpoint": { + "name": "ceftiofur_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "ceftazidime_resistant_breakpoint", + "title": "ceftiofur_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -38142,8 +39789,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 335, - "alias": "ceftazidime_resistant_breakpoint", + "rank": 364, + "alias": "ceftiofur_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38151,10 +39798,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidimeclavulanic_acid_resistance_phenotype": { - "name": "ceftazidimeclavulanic_acid_resistance_phenotype", + "ceftriaxone_resistance_phenotype": { + "name": "ceftriaxone_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "ceftazidime-clavulanic_acid_resistance_phenotype", + "title": "ceftriaxone_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -38167,8 +39814,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 336, - "alias": "ceftazidimeclavulanic_acid_resistance_phenotype", + "rank": 365, + "alias": "ceftriaxone_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38184,10 +39831,10 @@ } ] }, - "ceftazidimeclavulanic_acid_measurement": { - "name": "ceftazidimeclavulanic_acid_measurement", - "description": "The measured value of ceftazidime-clavulanic acid resistance.", - "title": "ceftazidime-clavulanic_acid_measurement", + "ceftriaxone_measurement": { + "name": "ceftriaxone_measurement", + "description": "The measured value of ceftriaxone resistance.", + "title": "ceftriaxone_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -38200,8 +39847,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 337, - "alias": "ceftazidimeclavulanic_acid_measurement", + "rank": 366, + "alias": "ceftriaxone_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38217,10 +39864,10 @@ } ] }, - "ceftazidimeclavulanic_acid_measurement_units": { - "name": "ceftazidimeclavulanic_acid_measurement_units", + "ceftriaxone_measurement_units": { + "name": "ceftriaxone_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "ceftazidime-clavulanic_acid_measurement_units", + "title": "ceftriaxone_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -38233,8 +39880,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 338, - "alias": "ceftazidimeclavulanic_acid_measurement_units", + "rank": 367, + "alias": "ceftriaxone_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38250,10 +39897,10 @@ } ] }, - "ceftazidimeclavulanic_acid_measurement_sign": { - "name": "ceftazidimeclavulanic_acid_measurement_sign", + "ceftriaxone_measurement_sign": { + "name": "ceftriaxone_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "ceftazidime-clavulanic_acid_measurement_sign", + "title": "ceftriaxone_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -38266,8 +39913,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 339, - "alias": "ceftazidimeclavulanic_acid_measurement_sign", + "rank": 368, + "alias": "ceftriaxone_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38283,10 +39930,10 @@ } ] }, - "ceftazidimeclavulanic_acid_laboratory_typing_method": { - "name": "ceftazidimeclavulanic_acid_laboratory_typing_method", + "ceftriaxone_laboratory_typing_method": { + "name": "ceftriaxone_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "ceftazidime-clavulanic_acid_laboratory_typing_method", + "title": "ceftriaxone_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -38299,8 +39946,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 340, - "alias": "ceftazidimeclavulanic_acid_laboratory_typing_method", + "rank": 369, + "alias": "ceftriaxone_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38315,10 +39962,10 @@ } ] }, - "ceftazidimeclavulanic_acid_laboratory_typing_platform": { - "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform", + "ceftriaxone_laboratory_typing_platform": { + "name": "ceftriaxone_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform", + "title": "ceftriaxone_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -38331,8 +39978,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 341, - "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform", + "rank": 370, + "alias": "ceftriaxone_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38347,10 +39994,10 @@ } ] }, - "ceftazidimeclavulanic_acid_laboratory_typing_platform_version": { - "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", + "ceftriaxone_laboratory_typing_platform_version": { + "name": "ceftriaxone_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform_version", + "title": "ceftriaxone_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -38360,8 +40007,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 342, - "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", + "rank": 371, + "alias": "ceftriaxone_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38369,10 +40016,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidimeclavulanic_acid_vendor_name": { - "name": "ceftazidimeclavulanic_acid_vendor_name", + "ceftriaxone_vendor_name": { + "name": "ceftriaxone_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "ceftazidime-clavulanic_acid_vendor_name", + "title": "ceftriaxone_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -38385,8 +40032,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 343, - "alias": "ceftazidimeclavulanic_acid_vendor_name", + "rank": 372, + "alias": "ceftriaxone_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38401,10 +40048,10 @@ } ] }, - "ceftazidimeclavulanic_acid_testing_standard": { - "name": "ceftazidimeclavulanic_acid_testing_standard", + "ceftriaxone_testing_standard": { + "name": "ceftriaxone_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "ceftazidime-clavulanic_acid_testing_standard", + "title": "ceftriaxone_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -38417,8 +40064,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 344, - "alias": "ceftazidimeclavulanic_acid_testing_standard", + "rank": 373, + "alias": "ceftriaxone_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38434,10 +40081,10 @@ } ] }, - "ceftazidimeclavulanic_acid_testing_standard_version": { - "name": "ceftazidimeclavulanic_acid_testing_standard_version", + "ceftriaxone_testing_standard_version": { + "name": "ceftriaxone_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "ceftazidime-clavulanic_acid_testing_standard_version", + "title": "ceftriaxone_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -38447,8 +40094,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 345, - "alias": "ceftazidimeclavulanic_acid_testing_standard_version", + "rank": 374, + "alias": "ceftriaxone_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38456,10 +40103,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidimeclavulanic_acid_testing_standard_details": { - "name": "ceftazidimeclavulanic_acid_testing_standard_details", + "ceftriaxone_testing_standard_details": { + "name": "ceftriaxone_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "ceftazidime-clavulanic_acid_testing_standard_details", + "title": "ceftriaxone_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -38472,8 +40119,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 346, - "alias": "ceftazidimeclavulanic_acid_testing_standard_details", + "rank": 375, + "alias": "ceftriaxone_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38481,10 +40128,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidimeclavulanic_acid_susceptible_breakpoint": { - "name": "ceftazidimeclavulanic_acid_susceptible_breakpoint", + "ceftriaxone_susceptible_breakpoint": { + "name": "ceftriaxone_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "ceftazidime-clavulanic_acid_susceptible_breakpoint", + "title": "ceftriaxone_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -38494,8 +40141,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 347, - "alias": "ceftazidimeclavulanic_acid_susceptible_breakpoint", + "rank": 376, + "alias": "ceftriaxone_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38503,18 +40150,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidimeclavulanic_acid_intermediate_breakpoint": { - "name": "ceftazidimeclavulanic_acid_intermediate_breakpoint", + "ceftriaxone_intermediate_breakpoint": { + "name": "ceftriaxone_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "ceftazidime-clavulanic_acid_intermediate_breakpoint", + "title": "ceftriaxone_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 348, - "alias": "ceftazidimeclavulanic_acid_intermediate_breakpoint", + "rank": 377, + "alias": "ceftriaxone_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38522,10 +40169,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidimeclavulanic_acid_resistant_breakpoint": { - "name": "ceftazidimeclavulanic_acid_resistant_breakpoint", + "ceftriaxone_resistant_breakpoint": { + "name": "ceftriaxone_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "ceftazidime-clavulanic_acid_resistant_breakpoint", + "title": "ceftriaxone_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -38535,8 +40182,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 349, - "alias": "ceftazidimeclavulanic_acid_resistant_breakpoint", + "rank": 378, + "alias": "ceftriaxone_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38544,10 +40191,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftiofur_resistance_phenotype": { - "name": "ceftiofur_resistance_phenotype", + "cephalothin_resistance_phenotype": { + "name": "cephalothin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "ceftiofur_resistance_phenotype", + "title": "cephalothin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -38560,8 +40207,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 350, - "alias": "ceftiofur_resistance_phenotype", + "rank": 379, + "alias": "cephalothin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38577,10 +40224,10 @@ } ] }, - "ceftiofur_measurement": { - "name": "ceftiofur_measurement", - "description": "The measured value of ceftiofur resistance.", - "title": "ceftiofur_measurement", + "cephalothin_measurement": { + "name": "cephalothin_measurement", + "description": "The measured value of cephalothin resistance.", + "title": "cephalothin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -38593,8 +40240,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 351, - "alias": "ceftiofur_measurement", + "rank": 380, + "alias": "cephalothin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38610,10 +40257,10 @@ } ] }, - "ceftiofur_measurement_units": { - "name": "ceftiofur_measurement_units", + "cephalothin_measurement_units": { + "name": "cephalothin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "ceftiofur_measurement_units", + "title": "cephalothin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -38626,8 +40273,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 352, - "alias": "ceftiofur_measurement_units", + "rank": 381, + "alias": "cephalothin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38643,10 +40290,10 @@ } ] }, - "ceftiofur_measurement_sign": { - "name": "ceftiofur_measurement_sign", + "cephalothin_measurement_sign": { + "name": "cephalothin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "ceftiofur_measurement_sign", + "title": "cephalothin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -38659,8 +40306,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 353, - "alias": "ceftiofur_measurement_sign", + "rank": 382, + "alias": "cephalothin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38676,10 +40323,10 @@ } ] }, - "ceftiofur_laboratory_typing_method": { - "name": "ceftiofur_laboratory_typing_method", + "cephalothin_laboratory_typing_method": { + "name": "cephalothin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "ceftiofur_laboratory_typing_method", + "title": "cephalothin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -38692,8 +40339,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 354, - "alias": "ceftiofur_laboratory_typing_method", + "rank": 383, + "alias": "cephalothin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38708,10 +40355,10 @@ } ] }, - "ceftiofur_laboratory_typing_platform": { - "name": "ceftiofur_laboratory_typing_platform", + "cephalothin_laboratory_typing_platform": { + "name": "cephalothin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "ceftiofur_laboratory_typing_platform", + "title": "cephalothin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -38724,8 +40371,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 355, - "alias": "ceftiofur_laboratory_typing_platform", + "rank": 384, + "alias": "cephalothin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38740,10 +40387,10 @@ } ] }, - "ceftiofur_laboratory_typing_platform_version": { - "name": "ceftiofur_laboratory_typing_platform_version", + "cephalothin_laboratory_typing_platform_version": { + "name": "cephalothin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "ceftiofur_laboratory_typing_platform_version", + "title": "cephalothin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -38753,8 +40400,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 356, - "alias": "ceftiofur_laboratory_typing_platform_version", + "rank": 385, + "alias": "cephalothin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38762,10 +40409,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftiofur_vendor_name": { - "name": "ceftiofur_vendor_name", + "cephalothin_vendor_name": { + "name": "cephalothin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "ceftiofur_vendor_name", + "title": "cephalothin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -38778,8 +40425,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 357, - "alias": "ceftiofur_vendor_name", + "rank": 386, + "alias": "cephalothin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38794,10 +40441,10 @@ } ] }, - "ceftiofur_testing_standard": { - "name": "ceftiofur_testing_standard", + "cephalothin_testing_standard": { + "name": "cephalothin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "ceftiofur_testing_standard", + "title": "cephalothin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -38810,8 +40457,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 358, - "alias": "ceftiofur_testing_standard", + "rank": 387, + "alias": "cephalothin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38827,10 +40474,10 @@ } ] }, - "ceftiofur_testing_standard_version": { - "name": "ceftiofur_testing_standard_version", + "cephalothin_testing_standard_version": { + "name": "cephalothin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "ceftiofur_testing_standard_version", + "title": "cephalothin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -38840,8 +40487,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 359, - "alias": "ceftiofur_testing_standard_version", + "rank": 388, + "alias": "cephalothin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38849,10 +40496,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftiofur_testing_standard_details": { - "name": "ceftiofur_testing_standard_details", + "cephalothin_testing_standard_details": { + "name": "cephalothin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "ceftiofur_testing_standard_details", + "title": "cephalothin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -38865,8 +40512,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 360, - "alias": "ceftiofur_testing_standard_details", + "rank": 389, + "alias": "cephalothin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38874,10 +40521,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftiofur_susceptible_breakpoint": { - "name": "ceftiofur_susceptible_breakpoint", + "cephalothin_susceptible_breakpoint": { + "name": "cephalothin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "ceftiofur_susceptible_breakpoint", + "title": "cephalothin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -38887,8 +40534,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 361, - "alias": "ceftiofur_susceptible_breakpoint", + "rank": 390, + "alias": "cephalothin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38896,18 +40543,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftiofur_intermediate_breakpoint": { - "name": "ceftiofur_intermediate_breakpoint", + "cephalothin_intermediate_breakpoint": { + "name": "cephalothin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "ceftiofur_intermediate_breakpoint", + "title": "cephalothin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 362, - "alias": "ceftiofur_intermediate_breakpoint", + "rank": 391, + "alias": "cephalothin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38915,10 +40562,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftiofur_resistant_breakpoint": { - "name": "ceftiofur_resistant_breakpoint", + "cephalothin_resistant_breakpoint": { + "name": "cephalothin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "ceftiofur_resistant_breakpoint", + "title": "cephalothin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -38928,8 +40575,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 363, - "alias": "ceftiofur_resistant_breakpoint", + "rank": 392, + "alias": "cephalothin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38937,10 +40584,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftriaxone_resistance_phenotype": { - "name": "ceftriaxone_resistance_phenotype", + "chloramphenicol_resistance_phenotype": { + "name": "chloramphenicol_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "ceftriaxone_resistance_phenotype", + "title": "chloramphenicol_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -38953,8 +40600,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 364, - "alias": "ceftriaxone_resistance_phenotype", + "rank": 393, + "alias": "chloramphenicol_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -38970,10 +40617,10 @@ } ] }, - "ceftriaxone_measurement": { - "name": "ceftriaxone_measurement", - "description": "The measured value of ceftriaxone resistance.", - "title": "ceftriaxone_measurement", + "chloramphenicol_measurement": { + "name": "chloramphenicol_measurement", + "description": "The measured value of chloramphenicol resistance.", + "title": "chloramphenicol_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -38986,8 +40633,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 365, - "alias": "ceftriaxone_measurement", + "rank": 394, + "alias": "chloramphenicol_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39003,10 +40650,10 @@ } ] }, - "ceftriaxone_measurement_units": { - "name": "ceftriaxone_measurement_units", + "chloramphenicol_measurement_units": { + "name": "chloramphenicol_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "ceftriaxone_measurement_units", + "title": "chloramphenicol_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -39019,8 +40666,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 366, - "alias": "ceftriaxone_measurement_units", + "rank": 395, + "alias": "chloramphenicol_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39036,10 +40683,10 @@ } ] }, - "ceftriaxone_measurement_sign": { - "name": "ceftriaxone_measurement_sign", + "chloramphenicol_measurement_sign": { + "name": "chloramphenicol_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "ceftriaxone_measurement_sign", + "title": "chloramphenicol_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -39052,8 +40699,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 367, - "alias": "ceftriaxone_measurement_sign", + "rank": 396, + "alias": "chloramphenicol_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39069,10 +40716,10 @@ } ] }, - "ceftriaxone_laboratory_typing_method": { - "name": "ceftriaxone_laboratory_typing_method", + "chloramphenicol_laboratory_typing_method": { + "name": "chloramphenicol_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "ceftriaxone_laboratory_typing_method", + "title": "chloramphenicol_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -39085,8 +40732,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 368, - "alias": "ceftriaxone_laboratory_typing_method", + "rank": 397, + "alias": "chloramphenicol_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39101,10 +40748,10 @@ } ] }, - "ceftriaxone_laboratory_typing_platform": { - "name": "ceftriaxone_laboratory_typing_platform", + "chloramphenicol_laboratory_typing_platform": { + "name": "chloramphenicol_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "ceftriaxone_laboratory_typing_platform", + "title": "chloramphenicol_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -39117,8 +40764,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 369, - "alias": "ceftriaxone_laboratory_typing_platform", + "rank": 398, + "alias": "chloramphenicol_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39133,10 +40780,10 @@ } ] }, - "ceftriaxone_laboratory_typing_platform_version": { - "name": "ceftriaxone_laboratory_typing_platform_version", + "chloramphenicol_laboratory_typing_platform_version": { + "name": "chloramphenicol_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "ceftriaxone_laboratory_typing_platform_version", + "title": "chloramphenicol_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -39146,8 +40793,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 370, - "alias": "ceftriaxone_laboratory_typing_platform_version", + "rank": 399, + "alias": "chloramphenicol_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39155,10 +40802,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftriaxone_vendor_name": { - "name": "ceftriaxone_vendor_name", + "chloramphenicol_vendor_name": { + "name": "chloramphenicol_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "ceftriaxone_vendor_name", + "title": "chloramphenicol_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -39171,8 +40818,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 371, - "alias": "ceftriaxone_vendor_name", + "rank": 400, + "alias": "chloramphenicol_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39187,10 +40834,10 @@ } ] }, - "ceftriaxone_testing_standard": { - "name": "ceftriaxone_testing_standard", + "chloramphenicol_testing_standard": { + "name": "chloramphenicol_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "ceftriaxone_testing_standard", + "title": "chloramphenicol_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -39203,8 +40850,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 372, - "alias": "ceftriaxone_testing_standard", + "rank": 401, + "alias": "chloramphenicol_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39220,10 +40867,10 @@ } ] }, - "ceftriaxone_testing_standard_version": { - "name": "ceftriaxone_testing_standard_version", + "chloramphenicol_testing_standard_version": { + "name": "chloramphenicol_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "ceftriaxone_testing_standard_version", + "title": "chloramphenicol_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -39233,8 +40880,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 373, - "alias": "ceftriaxone_testing_standard_version", + "rank": 402, + "alias": "chloramphenicol_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39242,10 +40889,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftriaxone_testing_standard_details": { - "name": "ceftriaxone_testing_standard_details", + "chloramphenicol_testing_standard_details": { + "name": "chloramphenicol_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "ceftriaxone_testing_standard_details", + "title": "chloramphenicol_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -39258,8 +40905,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 374, - "alias": "ceftriaxone_testing_standard_details", + "rank": 403, + "alias": "chloramphenicol_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39267,10 +40914,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftriaxone_susceptible_breakpoint": { - "name": "ceftriaxone_susceptible_breakpoint", + "chloramphenicol_susceptible_breakpoint": { + "name": "chloramphenicol_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "ceftriaxone_susceptible_breakpoint", + "title": "chloramphenicol_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -39280,8 +40927,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 375, - "alias": "ceftriaxone_susceptible_breakpoint", + "rank": 404, + "alias": "chloramphenicol_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39289,18 +40936,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftriaxone_intermediate_breakpoint": { - "name": "ceftriaxone_intermediate_breakpoint", + "chloramphenicol_intermediate_breakpoint": { + "name": "chloramphenicol_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "ceftriaxone_intermediate_breakpoint", + "title": "chloramphenicol_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 376, - "alias": "ceftriaxone_intermediate_breakpoint", + "rank": 405, + "alias": "chloramphenicol_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39308,10 +40955,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftriaxone_resistant_breakpoint": { - "name": "ceftriaxone_resistant_breakpoint", + "chloramphenicol_resistant_breakpoint": { + "name": "chloramphenicol_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "ceftriaxone_resistant_breakpoint", + "title": "chloramphenicol_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -39321,8 +40968,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 377, - "alias": "ceftriaxone_resistant_breakpoint", + "rank": 406, + "alias": "chloramphenicol_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39330,10 +40977,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cephalothin_resistance_phenotype": { - "name": "cephalothin_resistance_phenotype", + "ciprofloxacin_resistance_phenotype": { + "name": "ciprofloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "cephalothin_resistance_phenotype", + "title": "ciprofloxacin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -39346,8 +40993,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 378, - "alias": "cephalothin_resistance_phenotype", + "rank": 407, + "alias": "ciprofloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39363,10 +41010,10 @@ } ] }, - "cephalothin_measurement": { - "name": "cephalothin_measurement", - "description": "The measured value of cephalothin resistance.", - "title": "cephalothin_measurement", + "ciprofloxacin_measurement": { + "name": "ciprofloxacin_measurement", + "description": "The measured value of ciprofloxacin resistance.", + "title": "ciprofloxacin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -39379,8 +41026,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 379, - "alias": "cephalothin_measurement", + "rank": 408, + "alias": "ciprofloxacin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39396,10 +41043,10 @@ } ] }, - "cephalothin_measurement_units": { - "name": "cephalothin_measurement_units", + "ciprofloxacin_measurement_units": { + "name": "ciprofloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "cephalothin_measurement_units", + "title": "ciprofloxacin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -39412,8 +41059,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 380, - "alias": "cephalothin_measurement_units", + "rank": 409, + "alias": "ciprofloxacin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39429,10 +41076,10 @@ } ] }, - "cephalothin_measurement_sign": { - "name": "cephalothin_measurement_sign", + "ciprofloxacin_measurement_sign": { + "name": "ciprofloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "cephalothin_measurement_sign", + "title": "ciprofloxacin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -39445,8 +41092,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 381, - "alias": "cephalothin_measurement_sign", + "rank": 410, + "alias": "ciprofloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39462,10 +41109,10 @@ } ] }, - "cephalothin_laboratory_typing_method": { - "name": "cephalothin_laboratory_typing_method", + "ciprofloxacin_laboratory_typing_method": { + "name": "ciprofloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "cephalothin_laboratory_typing_method", + "title": "ciprofloxacin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -39478,8 +41125,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 382, - "alias": "cephalothin_laboratory_typing_method", + "rank": 411, + "alias": "ciprofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39494,10 +41141,10 @@ } ] }, - "cephalothin_laboratory_typing_platform": { - "name": "cephalothin_laboratory_typing_platform", + "ciprofloxacin_laboratory_typing_platform": { + "name": "ciprofloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "cephalothin_laboratory_typing_platform", + "title": "ciprofloxacin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -39510,8 +41157,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 383, - "alias": "cephalothin_laboratory_typing_platform", + "rank": 412, + "alias": "ciprofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39526,10 +41173,10 @@ } ] }, - "cephalothin_laboratory_typing_platform_version": { - "name": "cephalothin_laboratory_typing_platform_version", + "ciprofloxacin_laboratory_typing_platform_version": { + "name": "ciprofloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "cephalothin_laboratory_typing_platform_version", + "title": "ciprofloxacin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -39539,8 +41186,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 384, - "alias": "cephalothin_laboratory_typing_platform_version", + "rank": 413, + "alias": "ciprofloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39548,10 +41195,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cephalothin_vendor_name": { - "name": "cephalothin_vendor_name", + "ciprofloxacin_vendor_name": { + "name": "ciprofloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "cephalothin_vendor_name", + "title": "ciprofloxacin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -39564,8 +41211,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 385, - "alias": "cephalothin_vendor_name", + "rank": 414, + "alias": "ciprofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39580,10 +41227,10 @@ } ] }, - "cephalothin_testing_standard": { - "name": "cephalothin_testing_standard", + "ciprofloxacin_testing_standard": { + "name": "ciprofloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "cephalothin_testing_standard", + "title": "ciprofloxacin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -39596,8 +41243,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 386, - "alias": "cephalothin_testing_standard", + "rank": 415, + "alias": "ciprofloxacin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39613,10 +41260,10 @@ } ] }, - "cephalothin_testing_standard_version": { - "name": "cephalothin_testing_standard_version", + "ciprofloxacin_testing_standard_version": { + "name": "ciprofloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "cephalothin_testing_standard_version", + "title": "ciprofloxacin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -39626,8 +41273,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 387, - "alias": "cephalothin_testing_standard_version", + "rank": 416, + "alias": "ciprofloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39635,10 +41282,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cephalothin_testing_standard_details": { - "name": "cephalothin_testing_standard_details", + "ciprofloxacin_testing_standard_details": { + "name": "ciprofloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "cephalothin_testing_standard_details", + "title": "ciprofloxacin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -39651,8 +41298,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 388, - "alias": "cephalothin_testing_standard_details", + "rank": 417, + "alias": "ciprofloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39660,10 +41307,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cephalothin_susceptible_breakpoint": { - "name": "cephalothin_susceptible_breakpoint", + "ciprofloxacin_susceptible_breakpoint": { + "name": "ciprofloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "cephalothin_susceptible_breakpoint", + "title": "ciprofloxacin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -39673,8 +41320,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 389, - "alias": "cephalothin_susceptible_breakpoint", + "rank": 418, + "alias": "ciprofloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39682,18 +41329,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cephalothin_intermediate_breakpoint": { - "name": "cephalothin_intermediate_breakpoint", + "ciprofloxacin_intermediate_breakpoint": { + "name": "ciprofloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "cephalothin_intermediate_breakpoint", + "title": "ciprofloxacin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 390, - "alias": "cephalothin_intermediate_breakpoint", + "rank": 419, + "alias": "ciprofloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39701,10 +41348,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cephalothin_resistant_breakpoint": { - "name": "cephalothin_resistant_breakpoint", + "ciprofloxacin_resistant_breakpoint": { + "name": "ciprofloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "cephalothin_resistant_breakpoint", + "title": "ciprofloxacin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -39714,8 +41361,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 391, - "alias": "cephalothin_resistant_breakpoint", + "rank": 420, + "alias": "ciprofloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39723,10 +41370,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "chloramphenicol_resistance_phenotype": { - "name": "chloramphenicol_resistance_phenotype", + "clindamycin_resistance_phenotype": { + "name": "clindamycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "chloramphenicol_resistance_phenotype", + "title": "clindamycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -39739,8 +41386,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 392, - "alias": "chloramphenicol_resistance_phenotype", + "rank": 421, + "alias": "clindamycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39756,10 +41403,10 @@ } ] }, - "chloramphenicol_measurement": { - "name": "chloramphenicol_measurement", - "description": "The measured value of chloramphenicol resistance.", - "title": "chloramphenicol_measurement", + "clindamycin_measurement": { + "name": "clindamycin_measurement", + "description": "The measured value of clindamycin resistance.", + "title": "clindamycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -39772,8 +41419,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 393, - "alias": "chloramphenicol_measurement", + "rank": 422, + "alias": "clindamycin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39789,10 +41436,10 @@ } ] }, - "chloramphenicol_measurement_units": { - "name": "chloramphenicol_measurement_units", + "clindamycin_measurement_units": { + "name": "clindamycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "chloramphenicol_measurement_units", + "title": "clindamycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -39805,8 +41452,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 394, - "alias": "chloramphenicol_measurement_units", + "rank": 423, + "alias": "clindamycin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39822,10 +41469,10 @@ } ] }, - "chloramphenicol_measurement_sign": { - "name": "chloramphenicol_measurement_sign", + "clindamycin_measurement_sign": { + "name": "clindamycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "chloramphenicol_measurement_sign", + "title": "clindamycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -39838,8 +41485,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 395, - "alias": "chloramphenicol_measurement_sign", + "rank": 424, + "alias": "clindamycin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39855,10 +41502,10 @@ } ] }, - "chloramphenicol_laboratory_typing_method": { - "name": "chloramphenicol_laboratory_typing_method", + "clindamycin_laboratory_typing_method": { + "name": "clindamycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "chloramphenicol_laboratory_typing_method", + "title": "clindamycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -39871,8 +41518,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 396, - "alias": "chloramphenicol_laboratory_typing_method", + "rank": 425, + "alias": "clindamycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39887,10 +41534,10 @@ } ] }, - "chloramphenicol_laboratory_typing_platform": { - "name": "chloramphenicol_laboratory_typing_platform", + "clindamycin_laboratory_typing_platform": { + "name": "clindamycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "chloramphenicol_laboratory_typing_platform", + "title": "clindamycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -39903,8 +41550,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 397, - "alias": "chloramphenicol_laboratory_typing_platform", + "rank": 426, + "alias": "clindamycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39919,10 +41566,10 @@ } ] }, - "chloramphenicol_laboratory_typing_platform_version": { - "name": "chloramphenicol_laboratory_typing_platform_version", + "clindamycin_laboratory_typing_platform_version": { + "name": "clindamycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "chloramphenicol_laboratory_typing_platform_version", + "title": "clindamycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -39932,8 +41579,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 398, - "alias": "chloramphenicol_laboratory_typing_platform_version", + "rank": 427, + "alias": "clindamycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39941,10 +41588,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "chloramphenicol_vendor_name": { - "name": "chloramphenicol_vendor_name", + "clindamycin_vendor_name": { + "name": "clindamycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "chloramphenicol_vendor_name", + "title": "clindamycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -39957,8 +41604,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 399, - "alias": "chloramphenicol_vendor_name", + "rank": 428, + "alias": "clindamycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -39973,10 +41620,10 @@ } ] }, - "chloramphenicol_testing_standard": { - "name": "chloramphenicol_testing_standard", + "clindamycin_testing_standard": { + "name": "clindamycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "chloramphenicol_testing_standard", + "title": "clindamycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -39989,8 +41636,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 400, - "alias": "chloramphenicol_testing_standard", + "rank": 429, + "alias": "clindamycin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40006,10 +41653,10 @@ } ] }, - "chloramphenicol_testing_standard_version": { - "name": "chloramphenicol_testing_standard_version", + "clindamycin_testing_standard_version": { + "name": "clindamycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "chloramphenicol_testing_standard_version", + "title": "clindamycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -40019,8 +41666,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 401, - "alias": "chloramphenicol_testing_standard_version", + "rank": 430, + "alias": "clindamycin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40028,10 +41675,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "chloramphenicol_testing_standard_details": { - "name": "chloramphenicol_testing_standard_details", + "clindamycin_testing_standard_details": { + "name": "clindamycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "chloramphenicol_testing_standard_details", + "title": "clindamycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -40044,8 +41691,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 402, - "alias": "chloramphenicol_testing_standard_details", + "rank": 431, + "alias": "clindamycin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40053,10 +41700,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "chloramphenicol_susceptible_breakpoint": { - "name": "chloramphenicol_susceptible_breakpoint", + "clindamycin_susceptible_breakpoint": { + "name": "clindamycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "chloramphenicol_susceptible_breakpoint", + "title": "clindamycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -40066,8 +41713,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 403, - "alias": "chloramphenicol_susceptible_breakpoint", + "rank": 432, + "alias": "clindamycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40075,18 +41722,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "chloramphenicol_intermediate_breakpoint": { - "name": "chloramphenicol_intermediate_breakpoint", + "clindamycin_intermediate_breakpoint": { + "name": "clindamycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "chloramphenicol_intermediate_breakpoint", + "title": "clindamycin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 404, - "alias": "chloramphenicol_intermediate_breakpoint", + "rank": 433, + "alias": "clindamycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40094,10 +41741,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "chloramphenicol_resistant_breakpoint": { - "name": "chloramphenicol_resistant_breakpoint", + "clindamycin_resistant_breakpoint": { + "name": "clindamycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "chloramphenicol_resistant_breakpoint", + "title": "clindamycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -40107,8 +41754,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 405, - "alias": "chloramphenicol_resistant_breakpoint", + "rank": 434, + "alias": "clindamycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40116,10 +41763,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ciprofloxacin_resistance_phenotype": { - "name": "ciprofloxacin_resistance_phenotype", + "doxycycline_resistance_phenotype": { + "name": "doxycycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "ciprofloxacin_resistance_phenotype", + "title": "doxycycline_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -40132,8 +41779,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 406, - "alias": "ciprofloxacin_resistance_phenotype", + "rank": 435, + "alias": "doxycycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40149,10 +41796,10 @@ } ] }, - "ciprofloxacin_measurement": { - "name": "ciprofloxacin_measurement", - "description": "The measured value of ciprofloxacin resistance.", - "title": "ciprofloxacin_measurement", + "doxycycline_measurement": { + "name": "doxycycline_measurement", + "description": "The measured value of doxycycline resistance.", + "title": "doxycycline_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -40165,8 +41812,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 407, - "alias": "ciprofloxacin_measurement", + "rank": 436, + "alias": "doxycycline_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40182,10 +41829,10 @@ } ] }, - "ciprofloxacin_measurement_units": { - "name": "ciprofloxacin_measurement_units", + "doxycycline_measurement_units": { + "name": "doxycycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "ciprofloxacin_measurement_units", + "title": "doxycycline_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -40198,8 +41845,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 408, - "alias": "ciprofloxacin_measurement_units", + "rank": 437, + "alias": "doxycycline_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40215,10 +41862,10 @@ } ] }, - "ciprofloxacin_measurement_sign": { - "name": "ciprofloxacin_measurement_sign", + "doxycycline_measurement_sign": { + "name": "doxycycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "ciprofloxacin_measurement_sign", + "title": "doxycycline_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -40231,8 +41878,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 409, - "alias": "ciprofloxacin_measurement_sign", + "rank": 438, + "alias": "doxycycline_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40248,10 +41895,10 @@ } ] }, - "ciprofloxacin_laboratory_typing_method": { - "name": "ciprofloxacin_laboratory_typing_method", + "doxycycline_laboratory_typing_method": { + "name": "doxycycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "ciprofloxacin_laboratory_typing_method", + "title": "doxycycline_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -40264,8 +41911,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 410, - "alias": "ciprofloxacin_laboratory_typing_method", + "rank": 439, + "alias": "doxycycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40280,10 +41927,10 @@ } ] }, - "ciprofloxacin_laboratory_typing_platform": { - "name": "ciprofloxacin_laboratory_typing_platform", + "doxycycline_laboratory_typing_platform": { + "name": "doxycycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "ciprofloxacin_laboratory_typing_platform", + "title": "doxycycline_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -40296,8 +41943,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 411, - "alias": "ciprofloxacin_laboratory_typing_platform", + "rank": 440, + "alias": "doxycycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40312,10 +41959,10 @@ } ] }, - "ciprofloxacin_laboratory_typing_platform_version": { - "name": "ciprofloxacin_laboratory_typing_platform_version", + "doxycycline_laboratory_typing_platform_version": { + "name": "doxycycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "ciprofloxacin_laboratory_typing_platform_version", + "title": "doxycycline_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -40325,8 +41972,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 412, - "alias": "ciprofloxacin_laboratory_typing_platform_version", + "rank": 441, + "alias": "doxycycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40334,10 +41981,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ciprofloxacin_vendor_name": { - "name": "ciprofloxacin_vendor_name", + "doxycycline_vendor_name": { + "name": "doxycycline_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "ciprofloxacin_vendor_name", + "title": "doxycycline_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -40350,8 +41997,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 413, - "alias": "ciprofloxacin_vendor_name", + "rank": 442, + "alias": "doxycycline_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40366,10 +42013,10 @@ } ] }, - "ciprofloxacin_testing_standard": { - "name": "ciprofloxacin_testing_standard", + "doxycycline_testing_standard": { + "name": "doxycycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "ciprofloxacin_testing_standard", + "title": "doxycycline_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -40382,8 +42029,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 414, - "alias": "ciprofloxacin_testing_standard", + "rank": 443, + "alias": "doxycycline_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40399,10 +42046,10 @@ } ] }, - "ciprofloxacin_testing_standard_version": { - "name": "ciprofloxacin_testing_standard_version", + "doxycycline_testing_standard_version": { + "name": "doxycycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "ciprofloxacin_testing_standard_version", + "title": "doxycycline_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -40412,8 +42059,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 415, - "alias": "ciprofloxacin_testing_standard_version", + "rank": 444, + "alias": "doxycycline_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40421,10 +42068,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ciprofloxacin_testing_standard_details": { - "name": "ciprofloxacin_testing_standard_details", + "doxycycline_testing_standard_details": { + "name": "doxycycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "ciprofloxacin_testing_standard_details", + "title": "doxycycline_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -40437,8 +42084,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 416, - "alias": "ciprofloxacin_testing_standard_details", + "rank": 445, + "alias": "doxycycline_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40446,10 +42093,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ciprofloxacin_susceptible_breakpoint": { - "name": "ciprofloxacin_susceptible_breakpoint", + "doxycycline_susceptible_breakpoint": { + "name": "doxycycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "ciprofloxacin_susceptible_breakpoint", + "title": "doxycycline_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -40459,8 +42106,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 417, - "alias": "ciprofloxacin_susceptible_breakpoint", + "rank": 446, + "alias": "doxycycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40468,18 +42115,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ciprofloxacin_intermediate_breakpoint": { - "name": "ciprofloxacin_intermediate_breakpoint", + "doxycycline_intermediate_breakpoint": { + "name": "doxycycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "ciprofloxacin_intermediate_breakpoint", + "title": "doxycycline_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 418, - "alias": "ciprofloxacin_intermediate_breakpoint", + "rank": 447, + "alias": "doxycycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40487,10 +42134,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ciprofloxacin_resistant_breakpoint": { - "name": "ciprofloxacin_resistant_breakpoint", + "doxycycline_resistant_breakpoint": { + "name": "doxycycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "ciprofloxacin_resistant_breakpoint", + "title": "doxycycline_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -40500,8 +42147,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 419, - "alias": "ciprofloxacin_resistant_breakpoint", + "rank": 448, + "alias": "doxycycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40509,10 +42156,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "clindamycin_resistance_phenotype": { - "name": "clindamycin_resistance_phenotype", + "enrofloxacin_resistance_phenotype": { + "name": "enrofloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "clindamycin_resistance_phenotype", + "title": "enrofloxacin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -40525,8 +42172,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 420, - "alias": "clindamycin_resistance_phenotype", + "rank": 449, + "alias": "enrofloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40542,10 +42189,10 @@ } ] }, - "clindamycin_measurement": { - "name": "clindamycin_measurement", - "description": "The measured value of clindamycin resistance.", - "title": "clindamycin_measurement", + "enrofloxacin_measurement": { + "name": "enrofloxacin_measurement", + "description": "The measured value of enrofloxacin resistance.", + "title": "enrofloxacin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -40558,8 +42205,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 421, - "alias": "clindamycin_measurement", + "rank": 450, + "alias": "enrofloxacin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40575,10 +42222,10 @@ } ] }, - "clindamycin_measurement_units": { - "name": "clindamycin_measurement_units", + "enrofloxacin_measurement_units": { + "name": "enrofloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "clindamycin_measurement_units", + "title": "enrofloxacin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -40591,8 +42238,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 422, - "alias": "clindamycin_measurement_units", + "rank": 451, + "alias": "enrofloxacin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40608,10 +42255,10 @@ } ] }, - "clindamycin_measurement_sign": { - "name": "clindamycin_measurement_sign", + "enrofloxacin_measurement_sign": { + "name": "enrofloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "clindamycin_measurement_sign", + "title": "enrofloxacin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -40624,8 +42271,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 423, - "alias": "clindamycin_measurement_sign", + "rank": 452, + "alias": "enrofloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40641,10 +42288,10 @@ } ] }, - "clindamycin_laboratory_typing_method": { - "name": "clindamycin_laboratory_typing_method", + "enrofloxacin_laboratory_typing_method": { + "name": "enrofloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "clindamycin_laboratory_typing_method", + "title": "enrofloxacin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -40657,8 +42304,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 424, - "alias": "clindamycin_laboratory_typing_method", + "rank": 453, + "alias": "enrofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40673,10 +42320,10 @@ } ] }, - "clindamycin_laboratory_typing_platform": { - "name": "clindamycin_laboratory_typing_platform", + "enrofloxacin_laboratory_typing_platform": { + "name": "enrofloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "clindamycin_laboratory_typing_platform", + "title": "enrofloxacin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -40689,8 +42336,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 425, - "alias": "clindamycin_laboratory_typing_platform", + "rank": 454, + "alias": "enrofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40705,10 +42352,10 @@ } ] }, - "clindamycin_laboratory_typing_platform_version": { - "name": "clindamycin_laboratory_typing_platform_version", + "enrofloxacin_laboratory_typing_platform_version": { + "name": "enrofloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "clindamycin_laboratory_typing_platform_version", + "title": "enrofloxacin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -40718,8 +42365,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 426, - "alias": "clindamycin_laboratory_typing_platform_version", + "rank": 455, + "alias": "enrofloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40727,10 +42374,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "clindamycin_vendor_name": { - "name": "clindamycin_vendor_name", + "enrofloxacin_vendor_name": { + "name": "enrofloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "clindamycin_vendor_name", + "title": "enrofloxacin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -40743,8 +42390,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 427, - "alias": "clindamycin_vendor_name", + "rank": 456, + "alias": "enrofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40759,10 +42406,10 @@ } ] }, - "clindamycin_testing_standard": { - "name": "clindamycin_testing_standard", + "enrofloxacin_testing_standard": { + "name": "enrofloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "clindamycin_testing_standard", + "title": "enrofloxacin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -40775,8 +42422,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 428, - "alias": "clindamycin_testing_standard", + "rank": 457, + "alias": "enrofloxacin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40792,10 +42439,10 @@ } ] }, - "clindamycin_testing_standard_version": { - "name": "clindamycin_testing_standard_version", + "enrofloxacin_testing_standard_version": { + "name": "enrofloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "clindamycin_testing_standard_version", + "title": "enrofloxacin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -40805,8 +42452,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 429, - "alias": "clindamycin_testing_standard_version", + "rank": 458, + "alias": "enrofloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40814,10 +42461,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "clindamycin_testing_standard_details": { - "name": "clindamycin_testing_standard_details", + "enrofloxacin_testing_standard_details": { + "name": "enrofloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "clindamycin_testing_standard_details", + "title": "enrofloxacin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -40830,8 +42477,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 430, - "alias": "clindamycin_testing_standard_details", + "rank": 459, + "alias": "enrofloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40839,10 +42486,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "clindamycin_susceptible_breakpoint": { - "name": "clindamycin_susceptible_breakpoint", + "enrofloxacin_susceptible_breakpoint": { + "name": "enrofloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "clindamycin_susceptible_breakpoint", + "title": "enrofloxacin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -40852,8 +42499,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 431, - "alias": "clindamycin_susceptible_breakpoint", + "rank": 460, + "alias": "enrofloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40861,18 +42508,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "clindamycin_intermediate_breakpoint": { - "name": "clindamycin_intermediate_breakpoint", + "enrofloxacin_intermediate_breakpoint": { + "name": "enrofloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "clindamycin_intermediate_breakpoint", + "title": "enrofloxacin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 432, - "alias": "clindamycin_intermediate_breakpoint", + "rank": 461, + "alias": "enrofloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40880,10 +42527,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "clindamycin_resistant_breakpoint": { - "name": "clindamycin_resistant_breakpoint", + "enrofloxacin_resistant_breakpoint": { + "name": "enrofloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "clindamycin_resistant_breakpoint", + "title": "enrofloxacin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -40893,8 +42540,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 433, - "alias": "clindamycin_resistant_breakpoint", + "rank": 462, + "alias": "enrofloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40902,10 +42549,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "doxycycline_resistance_phenotype": { - "name": "doxycycline_resistance_phenotype", + "erythromycin_resistance_phenotype": { + "name": "erythromycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "doxycycline_resistance_phenotype", + "title": "erythromycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -40918,8 +42565,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 434, - "alias": "doxycycline_resistance_phenotype", + "rank": 463, + "alias": "erythromycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40935,10 +42582,10 @@ } ] }, - "doxycycline_measurement": { - "name": "doxycycline_measurement", - "description": "The measured value of doxycycline resistance.", - "title": "doxycycline_measurement", + "erythromycin_measurement": { + "name": "erythromycin_measurement", + "description": "The measured value of erythromycin resistance.", + "title": "erythromycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -40951,8 +42598,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 435, - "alias": "doxycycline_measurement", + "rank": 464, + "alias": "erythromycin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -40968,10 +42615,10 @@ } ] }, - "doxycycline_measurement_units": { - "name": "doxycycline_measurement_units", + "erythromycin_measurement_units": { + "name": "erythromycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "doxycycline_measurement_units", + "title": "erythromycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -40984,8 +42631,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 436, - "alias": "doxycycline_measurement_units", + "rank": 465, + "alias": "erythromycin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41001,10 +42648,10 @@ } ] }, - "doxycycline_measurement_sign": { - "name": "doxycycline_measurement_sign", + "erythromycin_measurement_sign": { + "name": "erythromycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "doxycycline_measurement_sign", + "title": "erythromycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -41017,8 +42664,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 437, - "alias": "doxycycline_measurement_sign", + "rank": 466, + "alias": "erythromycin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41034,10 +42681,10 @@ } ] }, - "doxycycline_laboratory_typing_method": { - "name": "doxycycline_laboratory_typing_method", + "erythromycin_laboratory_typing_method": { + "name": "erythromycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "doxycycline_laboratory_typing_method", + "title": "erythromycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -41050,8 +42697,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 438, - "alias": "doxycycline_laboratory_typing_method", + "rank": 467, + "alias": "erythromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41066,10 +42713,10 @@ } ] }, - "doxycycline_laboratory_typing_platform": { - "name": "doxycycline_laboratory_typing_platform", + "erythromycin_laboratory_typing_platform": { + "name": "erythromycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "doxycycline_laboratory_typing_platform", + "title": "erythromycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -41082,8 +42729,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 439, - "alias": "doxycycline_laboratory_typing_platform", + "rank": 468, + "alias": "erythromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41098,10 +42745,10 @@ } ] }, - "doxycycline_laboratory_typing_platform_version": { - "name": "doxycycline_laboratory_typing_platform_version", + "erythromycin_laboratory_typing_platform_version": { + "name": "erythromycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "doxycycline_laboratory_typing_platform_version", + "title": "erythromycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -41111,8 +42758,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 440, - "alias": "doxycycline_laboratory_typing_platform_version", + "rank": 469, + "alias": "erythromycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41120,10 +42767,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "doxycycline_vendor_name": { - "name": "doxycycline_vendor_name", + "erythromycin_vendor_name": { + "name": "erythromycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "doxycycline_vendor_name", + "title": "erythromycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -41136,8 +42783,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 441, - "alias": "doxycycline_vendor_name", + "rank": 470, + "alias": "erythromycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41152,10 +42799,10 @@ } ] }, - "doxycycline_testing_standard": { - "name": "doxycycline_testing_standard", + "erythromycin_testing_standard": { + "name": "erythromycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "doxycycline_testing_standard", + "title": "erythromycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -41168,8 +42815,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 442, - "alias": "doxycycline_testing_standard", + "rank": 471, + "alias": "erythromycin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41185,10 +42832,10 @@ } ] }, - "doxycycline_testing_standard_version": { - "name": "doxycycline_testing_standard_version", + "erythromycin_testing_standard_version": { + "name": "erythromycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "doxycycline_testing_standard_version", + "title": "erythromycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -41198,8 +42845,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 443, - "alias": "doxycycline_testing_standard_version", + "rank": 472, + "alias": "erythromycin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41207,10 +42854,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "doxycycline_testing_standard_details": { - "name": "doxycycline_testing_standard_details", + "erythromycin_testing_standard_details": { + "name": "erythromycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "doxycycline_testing_standard_details", + "title": "erythromycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -41223,8 +42870,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 444, - "alias": "doxycycline_testing_standard_details", + "rank": 473, + "alias": "erythromycin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41232,10 +42879,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "doxycycline_susceptible_breakpoint": { - "name": "doxycycline_susceptible_breakpoint", + "erythromycin_susceptible_breakpoint": { + "name": "erythromycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "doxycycline_susceptible_breakpoint", + "title": "erythromycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -41245,8 +42892,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 445, - "alias": "doxycycline_susceptible_breakpoint", + "rank": 474, + "alias": "erythromycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41254,18 +42901,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "doxycycline_intermediate_breakpoint": { - "name": "doxycycline_intermediate_breakpoint", + "erythromycin_intermediate_breakpoint": { + "name": "erythromycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "doxycycline_intermediate_breakpoint", + "title": "erythromycin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 446, - "alias": "doxycycline_intermediate_breakpoint", + "rank": 475, + "alias": "erythromycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41273,10 +42920,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "doxycycline_resistant_breakpoint": { - "name": "doxycycline_resistant_breakpoint", + "erythromycin_resistant_breakpoint": { + "name": "erythromycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "doxycycline_resistant_breakpoint", + "title": "erythromycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -41286,8 +42933,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 447, - "alias": "doxycycline_resistant_breakpoint", + "rank": 476, + "alias": "erythromycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41295,10 +42942,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "enrofloxacin_resistance_phenotype": { - "name": "enrofloxacin_resistance_phenotype", + "florfenicol_resistance_phenotype": { + "name": "florfenicol_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "enrofloxacin_resistance_phenotype", + "title": "florfenicol_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -41311,8 +42958,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 448, - "alias": "enrofloxacin_resistance_phenotype", + "rank": 477, + "alias": "florfenicol_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41328,10 +42975,10 @@ } ] }, - "enrofloxacin_measurement": { - "name": "enrofloxacin_measurement", - "description": "The measured value of enrofloxacin resistance.", - "title": "enrofloxacin_measurement", + "florfenicol_measurement": { + "name": "florfenicol_measurement", + "description": "The measured value of florfenicol resistance.", + "title": "florfenicol_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -41344,8 +42991,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 449, - "alias": "enrofloxacin_measurement", + "rank": 478, + "alias": "florfenicol_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41361,10 +43008,10 @@ } ] }, - "enrofloxacin_measurement_units": { - "name": "enrofloxacin_measurement_units", + "florfenicol_measurement_units": { + "name": "florfenicol_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "enrofloxacin_measurement_units", + "title": "florfenicol_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -41377,8 +43024,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 450, - "alias": "enrofloxacin_measurement_units", + "rank": 479, + "alias": "florfenicol_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41394,10 +43041,10 @@ } ] }, - "enrofloxacin_measurement_sign": { - "name": "enrofloxacin_measurement_sign", + "florfenicol_measurement_sign": { + "name": "florfenicol_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "enrofloxacin_measurement_sign", + "title": "florfenicol_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -41410,8 +43057,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 451, - "alias": "enrofloxacin_measurement_sign", + "rank": 480, + "alias": "florfenicol_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41427,10 +43074,10 @@ } ] }, - "enrofloxacin_laboratory_typing_method": { - "name": "enrofloxacin_laboratory_typing_method", + "florfenicol_laboratory_typing_method": { + "name": "florfenicol_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "enrofloxacin_laboratory_typing_method", + "title": "florfenicol_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -41443,8 +43090,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 452, - "alias": "enrofloxacin_laboratory_typing_method", + "rank": 481, + "alias": "florfenicol_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41459,10 +43106,10 @@ } ] }, - "enrofloxacin_laboratory_typing_platform": { - "name": "enrofloxacin_laboratory_typing_platform", + "florfenicol_laboratory_typing_platform": { + "name": "florfenicol_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "enrofloxacin_laboratory_typing_platform", + "title": "florfenicol_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -41475,8 +43122,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 453, - "alias": "enrofloxacin_laboratory_typing_platform", + "rank": 482, + "alias": "florfenicol_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41491,10 +43138,10 @@ } ] }, - "enrofloxacin_laboratory_typing_platform_version": { - "name": "enrofloxacin_laboratory_typing_platform_version", + "florfenicol_laboratory_typing_platform_version": { + "name": "florfenicol_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "enrofloxacin_laboratory_typing_platform_version", + "title": "florfenicol_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -41504,8 +43151,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 454, - "alias": "enrofloxacin_laboratory_typing_platform_version", + "rank": 483, + "alias": "florfenicol_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41513,10 +43160,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "enrofloxacin_vendor_name": { - "name": "enrofloxacin_vendor_name", + "florfenicol_vendor_name": { + "name": "florfenicol_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "enrofloxacin_vendor_name", + "title": "florfenicol_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -41529,8 +43176,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 455, - "alias": "enrofloxacin_vendor_name", + "rank": 484, + "alias": "florfenicol_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41545,10 +43192,10 @@ } ] }, - "enrofloxacin_testing_standard": { - "name": "enrofloxacin_testing_standard", + "florfenicol_testing_standard": { + "name": "florfenicol_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "enrofloxacin_testing_standard", + "title": "florfenicol_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -41561,8 +43208,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 456, - "alias": "enrofloxacin_testing_standard", + "rank": 485, + "alias": "florfenicol_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41578,10 +43225,10 @@ } ] }, - "enrofloxacin_testing_standard_version": { - "name": "enrofloxacin_testing_standard_version", + "florfenicol_testing_standard_version": { + "name": "florfenicol_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "enrofloxacin_testing_standard_version", + "title": "florfenicol_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -41591,8 +43238,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 457, - "alias": "enrofloxacin_testing_standard_version", + "rank": 486, + "alias": "florfenicol_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41600,10 +43247,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "enrofloxacin_testing_standard_details": { - "name": "enrofloxacin_testing_standard_details", + "florfenicol_testing_standard_details": { + "name": "florfenicol_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "enrofloxacin_testing_standard_details", + "title": "florfenicol_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -41616,8 +43263,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 458, - "alias": "enrofloxacin_testing_standard_details", + "rank": 487, + "alias": "florfenicol_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41625,10 +43272,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "enrofloxacin_susceptible_breakpoint": { - "name": "enrofloxacin_susceptible_breakpoint", + "florfenicol_susceptible_breakpoint": { + "name": "florfenicol_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "enrofloxacin_susceptible_breakpoint", + "title": "florfenicol_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -41638,8 +43285,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 459, - "alias": "enrofloxacin_susceptible_breakpoint", + "rank": 488, + "alias": "florfenicol_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41647,18 +43294,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "enrofloxacin_intermediate_breakpoint": { - "name": "enrofloxacin_intermediate_breakpoint", + "florfenicol_intermediate_breakpoint": { + "name": "florfenicol_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "enrofloxacin_intermediate_breakpoint", + "title": "florfenicol_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 460, - "alias": "enrofloxacin_intermediate_breakpoint", + "rank": 489, + "alias": "florfenicol_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41666,10 +43313,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "enrofloxacin_resistant_breakpoint": { - "name": "enrofloxacin_resistant_breakpoint", + "florfenicol_resistant_breakpoint": { + "name": "florfenicol_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "enrofloxacin_resistant_breakpoint", + "title": "florfenicol_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -41679,8 +43326,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 461, - "alias": "enrofloxacin_resistant_breakpoint", + "rank": 490, + "alias": "florfenicol_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41688,10 +43335,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "erythromycin_resistance_phenotype": { - "name": "erythromycin_resistance_phenotype", + "gentamicin_resistance_phenotype": { + "name": "gentamicin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "erythromycin_resistance_phenotype", + "title": "gentamicin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -41704,8 +43351,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 462, - "alias": "erythromycin_resistance_phenotype", + "rank": 491, + "alias": "gentamicin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41721,10 +43368,10 @@ } ] }, - "erythromycin_measurement": { - "name": "erythromycin_measurement", - "description": "The measured value of erythromycin resistance.", - "title": "erythromycin_measurement", + "gentamicin_measurement": { + "name": "gentamicin_measurement", + "description": "The measured value of gentamicin resistance.", + "title": "gentamicin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -41737,8 +43384,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 463, - "alias": "erythromycin_measurement", + "rank": 492, + "alias": "gentamicin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41754,10 +43401,10 @@ } ] }, - "erythromycin_measurement_units": { - "name": "erythromycin_measurement_units", + "gentamicin_measurement_units": { + "name": "gentamicin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "erythromycin_measurement_units", + "title": "gentamicin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -41770,8 +43417,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 464, - "alias": "erythromycin_measurement_units", + "rank": 493, + "alias": "gentamicin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41787,10 +43434,10 @@ } ] }, - "erythromycin_measurement_sign": { - "name": "erythromycin_measurement_sign", + "gentamicin_measurement_sign": { + "name": "gentamicin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "erythromycin_measurement_sign", + "title": "gentamicin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -41803,8 +43450,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 465, - "alias": "erythromycin_measurement_sign", + "rank": 494, + "alias": "gentamicin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41820,10 +43467,10 @@ } ] }, - "erythromycin_laboratory_typing_method": { - "name": "erythromycin_laboratory_typing_method", + "gentamicin_laboratory_typing_method": { + "name": "gentamicin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "erythromycin_laboratory_typing_method", + "title": "gentamicin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -41836,8 +43483,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 466, - "alias": "erythromycin_laboratory_typing_method", + "rank": 495, + "alias": "gentamicin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41852,10 +43499,10 @@ } ] }, - "erythromycin_laboratory_typing_platform": { - "name": "erythromycin_laboratory_typing_platform", + "gentamicin_laboratory_typing_platform": { + "name": "gentamicin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "erythromycin_laboratory_typing_platform", + "title": "gentamicin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -41868,8 +43515,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 467, - "alias": "erythromycin_laboratory_typing_platform", + "rank": 496, + "alias": "gentamicin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41884,10 +43531,10 @@ } ] }, - "erythromycin_laboratory_typing_platform_version": { - "name": "erythromycin_laboratory_typing_platform_version", + "gentamicin_laboratory_typing_platform_version": { + "name": "gentamicin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "erythromycin_laboratory_typing_platform_version", + "title": "gentamicin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -41897,8 +43544,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 468, - "alias": "erythromycin_laboratory_typing_platform_version", + "rank": 497, + "alias": "gentamicin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41906,10 +43553,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "erythromycin_vendor_name": { - "name": "erythromycin_vendor_name", + "gentamicin_vendor_name": { + "name": "gentamicin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "erythromycin_vendor_name", + "title": "gentamicin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -41922,8 +43569,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 469, - "alias": "erythromycin_vendor_name", + "rank": 498, + "alias": "gentamicin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41938,10 +43585,10 @@ } ] }, - "erythromycin_testing_standard": { - "name": "erythromycin_testing_standard", + "gentamicin_testing_standard": { + "name": "gentamicin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "erythromycin_testing_standard", + "title": "gentamicin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -41954,8 +43601,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 470, - "alias": "erythromycin_testing_standard", + "rank": 499, + "alias": "gentamicin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41971,10 +43618,10 @@ } ] }, - "erythromycin_testing_standard_version": { - "name": "erythromycin_testing_standard_version", + "gentamicin_testing_standard_version": { + "name": "gentamicin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "erythromycin_testing_standard_version", + "title": "gentamicin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -41984,8 +43631,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 471, - "alias": "erythromycin_testing_standard_version", + "rank": 500, + "alias": "gentamicin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -41993,10 +43640,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "erythromycin_testing_standard_details": { - "name": "erythromycin_testing_standard_details", + "gentamicin_testing_standard_details": { + "name": "gentamicin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "erythromycin_testing_standard_details", + "title": "gentamicin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -42009,8 +43656,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 472, - "alias": "erythromycin_testing_standard_details", + "rank": 501, + "alias": "gentamicin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42018,10 +43665,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "erythromycin_susceptible_breakpoint": { - "name": "erythromycin_susceptible_breakpoint", + "gentamicin_susceptible_breakpoint": { + "name": "gentamicin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "erythromycin_susceptible_breakpoint", + "title": "gentamicin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -42031,8 +43678,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 473, - "alias": "erythromycin_susceptible_breakpoint", + "rank": 502, + "alias": "gentamicin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42040,18 +43687,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "erythromycin_intermediate_breakpoint": { - "name": "erythromycin_intermediate_breakpoint", + "gentamicin_intermediate_breakpoint": { + "name": "gentamicin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "erythromycin_intermediate_breakpoint", + "title": "gentamicin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 474, - "alias": "erythromycin_intermediate_breakpoint", + "rank": 503, + "alias": "gentamicin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42059,10 +43706,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "erythromycin_resistant_breakpoint": { - "name": "erythromycin_resistant_breakpoint", + "gentamicin_resistant_breakpoint": { + "name": "gentamicin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "erythromycin_resistant_breakpoint", + "title": "gentamicin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -42072,8 +43719,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 475, - "alias": "erythromycin_resistant_breakpoint", + "rank": 504, + "alias": "gentamicin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42081,10 +43728,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "florfenicol_resistance_phenotype": { - "name": "florfenicol_resistance_phenotype", + "imipenem_resistance_phenotype": { + "name": "imipenem_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "florfenicol_resistance_phenotype", + "title": "imipenem_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -42097,8 +43744,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 476, - "alias": "florfenicol_resistance_phenotype", + "rank": 505, + "alias": "imipenem_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42114,10 +43761,10 @@ } ] }, - "florfenicol_measurement": { - "name": "florfenicol_measurement", - "description": "The measured value of florfenicol resistance.", - "title": "florfenicol_measurement", + "imipenem_measurement": { + "name": "imipenem_measurement", + "description": "The measured value of imipenem resistance.", + "title": "imipenem_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -42130,8 +43777,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 477, - "alias": "florfenicol_measurement", + "rank": 506, + "alias": "imipenem_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42147,10 +43794,10 @@ } ] }, - "florfenicol_measurement_units": { - "name": "florfenicol_measurement_units", + "imipenem_measurement_units": { + "name": "imipenem_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "florfenicol_measurement_units", + "title": "imipenem_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -42163,8 +43810,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 478, - "alias": "florfenicol_measurement_units", + "rank": 507, + "alias": "imipenem_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42180,10 +43827,10 @@ } ] }, - "florfenicol_measurement_sign": { - "name": "florfenicol_measurement_sign", + "imipenem_measurement_sign": { + "name": "imipenem_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "florfenicol_measurement_sign", + "title": "imipenem_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -42196,8 +43843,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 479, - "alias": "florfenicol_measurement_sign", + "rank": 508, + "alias": "imipenem_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42213,10 +43860,10 @@ } ] }, - "florfenicol_laboratory_typing_method": { - "name": "florfenicol_laboratory_typing_method", + "imipenem_laboratory_typing_method": { + "name": "imipenem_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "florfenicol_laboratory_typing_method", + "title": "imipenem_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -42229,8 +43876,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 480, - "alias": "florfenicol_laboratory_typing_method", + "rank": 509, + "alias": "imipenem_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42245,10 +43892,10 @@ } ] }, - "florfenicol_laboratory_typing_platform": { - "name": "florfenicol_laboratory_typing_platform", + "imipenem_laboratory_typing_platform": { + "name": "imipenem_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "florfenicol_laboratory_typing_platform", + "title": "imipenem_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -42261,8 +43908,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 481, - "alias": "florfenicol_laboratory_typing_platform", + "rank": 510, + "alias": "imipenem_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42277,10 +43924,10 @@ } ] }, - "florfenicol_laboratory_typing_platform_version": { - "name": "florfenicol_laboratory_typing_platform_version", + "imipenem_laboratory_typing_platform_version": { + "name": "imipenem_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "florfenicol_laboratory_typing_platform_version", + "title": "imipenem_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -42290,8 +43937,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 482, - "alias": "florfenicol_laboratory_typing_platform_version", + "rank": 511, + "alias": "imipenem_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42299,10 +43946,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "florfenicol_vendor_name": { - "name": "florfenicol_vendor_name", + "imipenem_vendor_name": { + "name": "imipenem_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "florfenicol_vendor_name", + "title": "imipenem_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -42315,8 +43962,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 483, - "alias": "florfenicol_vendor_name", + "rank": 512, + "alias": "imipenem_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42331,10 +43978,10 @@ } ] }, - "florfenicol_testing_standard": { - "name": "florfenicol_testing_standard", + "imipenem_testing_standard": { + "name": "imipenem_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "florfenicol_testing_standard", + "title": "imipenem_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -42347,8 +43994,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 484, - "alias": "florfenicol_testing_standard", + "rank": 513, + "alias": "imipenem_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42364,10 +44011,10 @@ } ] }, - "florfenicol_testing_standard_version": { - "name": "florfenicol_testing_standard_version", + "imipenem_testing_standard_version": { + "name": "imipenem_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "florfenicol_testing_standard_version", + "title": "imipenem_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -42377,8 +44024,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 485, - "alias": "florfenicol_testing_standard_version", + "rank": 514, + "alias": "imipenem_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42386,10 +44033,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "florfenicol_testing_standard_details": { - "name": "florfenicol_testing_standard_details", + "imipenem_testing_standard_details": { + "name": "imipenem_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "florfenicol_testing_standard_details", + "title": "imipenem_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -42402,8 +44049,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 486, - "alias": "florfenicol_testing_standard_details", + "rank": 515, + "alias": "imipenem_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42411,10 +44058,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "florfenicol_susceptible_breakpoint": { - "name": "florfenicol_susceptible_breakpoint", + "imipenem_susceptible_breakpoint": { + "name": "imipenem_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "florfenicol_susceptible_breakpoint", + "title": "imipenem_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -42424,8 +44071,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 487, - "alias": "florfenicol_susceptible_breakpoint", + "rank": 516, + "alias": "imipenem_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42433,18 +44080,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "florfenicol_intermediate_breakpoint": { - "name": "florfenicol_intermediate_breakpoint", + "imipenem_intermediate_breakpoint": { + "name": "imipenem_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "florfenicol_intermediate_breakpoint", + "title": "imipenem_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 488, - "alias": "florfenicol_intermediate_breakpoint", + "rank": 517, + "alias": "imipenem_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42452,10 +44099,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "florfenicol_resistant_breakpoint": { - "name": "florfenicol_resistant_breakpoint", + "imipenem_resistant_breakpoint": { + "name": "imipenem_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "florfenicol_resistant_breakpoint", + "title": "imipenem_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -42465,8 +44112,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 489, - "alias": "florfenicol_resistant_breakpoint", + "rank": 518, + "alias": "imipenem_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42474,10 +44121,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "gentamicin_resistance_phenotype": { - "name": "gentamicin_resistance_phenotype", + "kanamycin_resistance_phenotype": { + "name": "kanamycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "gentamicin_resistance_phenotype", + "title": "kanamycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -42490,8 +44137,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 490, - "alias": "gentamicin_resistance_phenotype", + "rank": 519, + "alias": "kanamycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42507,10 +44154,10 @@ } ] }, - "gentamicin_measurement": { - "name": "gentamicin_measurement", - "description": "The measured value of gentamicin resistance.", - "title": "gentamicin_measurement", + "kanamycin_measurement": { + "name": "kanamycin_measurement", + "description": "The measured value of kanamycin resistance.", + "title": "kanamycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -42523,8 +44170,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 491, - "alias": "gentamicin_measurement", + "rank": 520, + "alias": "kanamycin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42540,10 +44187,10 @@ } ] }, - "gentamicin_measurement_units": { - "name": "gentamicin_measurement_units", + "kanamycin_measurement_units": { + "name": "kanamycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "gentamicin_measurement_units", + "title": "kanamycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -42556,8 +44203,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 492, - "alias": "gentamicin_measurement_units", + "rank": 521, + "alias": "kanamycin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42573,10 +44220,10 @@ } ] }, - "gentamicin_measurement_sign": { - "name": "gentamicin_measurement_sign", + "kanamycin_measurement_sign": { + "name": "kanamycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "gentamicin_measurement_sign", + "title": "kanamycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -42589,8 +44236,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 493, - "alias": "gentamicin_measurement_sign", + "rank": 522, + "alias": "kanamycin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42606,10 +44253,10 @@ } ] }, - "gentamicin_laboratory_typing_method": { - "name": "gentamicin_laboratory_typing_method", + "kanamycin_laboratory_typing_method": { + "name": "kanamycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "gentamicin_laboratory_typing_method", + "title": "kanamycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -42622,8 +44269,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 494, - "alias": "gentamicin_laboratory_typing_method", + "rank": 523, + "alias": "kanamycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42638,10 +44285,10 @@ } ] }, - "gentamicin_laboratory_typing_platform": { - "name": "gentamicin_laboratory_typing_platform", + "kanamycin_laboratory_typing_platform": { + "name": "kanamycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "gentamicin_laboratory_typing_platform", + "title": "kanamycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -42654,8 +44301,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 495, - "alias": "gentamicin_laboratory_typing_platform", + "rank": 524, + "alias": "kanamycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42670,10 +44317,10 @@ } ] }, - "gentamicin_laboratory_typing_platform_version": { - "name": "gentamicin_laboratory_typing_platform_version", + "kanamycin_laboratory_typing_platform_version": { + "name": "kanamycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "gentamicin_laboratory_typing_platform_version", + "title": "kanamycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -42683,8 +44330,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 496, - "alias": "gentamicin_laboratory_typing_platform_version", + "rank": 525, + "alias": "kanamycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42692,10 +44339,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "gentamicin_vendor_name": { - "name": "gentamicin_vendor_name", + "kanamycin_vendor_name": { + "name": "kanamycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "gentamicin_vendor_name", + "title": "kanamycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -42708,8 +44355,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 497, - "alias": "gentamicin_vendor_name", + "rank": 526, + "alias": "kanamycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42724,10 +44371,10 @@ } ] }, - "gentamicin_testing_standard": { - "name": "gentamicin_testing_standard", + "kanamycin_testing_standard": { + "name": "kanamycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "gentamicin_testing_standard", + "title": "kanamycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -42740,8 +44387,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 498, - "alias": "gentamicin_testing_standard", + "rank": 527, + "alias": "kanamycin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42757,10 +44404,10 @@ } ] }, - "gentamicin_testing_standard_version": { - "name": "gentamicin_testing_standard_version", + "kanamycin_testing_standard_version": { + "name": "kanamycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "gentamicin_testing_standard_version", + "title": "kanamycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -42770,8 +44417,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 499, - "alias": "gentamicin_testing_standard_version", + "rank": 528, + "alias": "kanamycin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42779,10 +44426,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "gentamicin_testing_standard_details": { - "name": "gentamicin_testing_standard_details", + "kanamycin_testing_standard_details": { + "name": "kanamycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "gentamicin_testing_standard_details", + "title": "kanamycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -42795,8 +44442,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 500, - "alias": "gentamicin_testing_standard_details", + "rank": 529, + "alias": "kanamycin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42804,10 +44451,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "gentamicin_susceptible_breakpoint": { - "name": "gentamicin_susceptible_breakpoint", + "kanamycin_susceptible_breakpoint": { + "name": "kanamycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "gentamicin_susceptible_breakpoint", + "title": "kanamycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -42817,8 +44464,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 501, - "alias": "gentamicin_susceptible_breakpoint", + "rank": 530, + "alias": "kanamycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42826,18 +44473,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "gentamicin_intermediate_breakpoint": { - "name": "gentamicin_intermediate_breakpoint", + "kanamycin_intermediate_breakpoint": { + "name": "kanamycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "gentamicin_intermediate_breakpoint", + "title": "kanamycin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 502, - "alias": "gentamicin_intermediate_breakpoint", + "rank": 531, + "alias": "kanamycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42845,10 +44492,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "gentamicin_resistant_breakpoint": { - "name": "gentamicin_resistant_breakpoint", + "kanamycin_resistant_breakpoint": { + "name": "kanamycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "gentamicin_resistant_breakpoint", + "title": "kanamycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -42858,8 +44505,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 503, - "alias": "gentamicin_resistant_breakpoint", + "rank": 532, + "alias": "kanamycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42867,10 +44514,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "imipenem_resistance_phenotype": { - "name": "imipenem_resistance_phenotype", + "levofloxacin_resistance_phenotype": { + "name": "levofloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "imipenem_resistance_phenotype", + "title": "levofloxacin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -42883,8 +44530,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 504, - "alias": "imipenem_resistance_phenotype", + "rank": 533, + "alias": "levofloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42900,10 +44547,10 @@ } ] }, - "imipenem_measurement": { - "name": "imipenem_measurement", - "description": "The measured value of imipenem resistance.", - "title": "imipenem_measurement", + "levofloxacin_measurement": { + "name": "levofloxacin_measurement", + "description": "The measured value of levofloxacin resistance.", + "title": "levofloxacin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -42916,8 +44563,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 505, - "alias": "imipenem_measurement", + "rank": 534, + "alias": "levofloxacin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42933,10 +44580,10 @@ } ] }, - "imipenem_measurement_units": { - "name": "imipenem_measurement_units", + "levofloxacin_measurement_units": { + "name": "levofloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "imipenem_measurement_units", + "title": "levofloxacin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -42949,8 +44596,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 506, - "alias": "imipenem_measurement_units", + "rank": 535, + "alias": "levofloxacin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42966,10 +44613,10 @@ } ] }, - "imipenem_measurement_sign": { - "name": "imipenem_measurement_sign", + "levofloxacin_measurement_sign": { + "name": "levofloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "imipenem_measurement_sign", + "title": "levofloxacin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -42982,8 +44629,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 507, - "alias": "imipenem_measurement_sign", + "rank": 536, + "alias": "levofloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -42999,10 +44646,10 @@ } ] }, - "imipenem_laboratory_typing_method": { - "name": "imipenem_laboratory_typing_method", + "levofloxacin_laboratory_typing_method": { + "name": "levofloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "imipenem_laboratory_typing_method", + "title": "levofloxacin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -43015,8 +44662,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 508, - "alias": "imipenem_laboratory_typing_method", + "rank": 537, + "alias": "levofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43031,10 +44678,10 @@ } ] }, - "imipenem_laboratory_typing_platform": { - "name": "imipenem_laboratory_typing_platform", + "levofloxacin_laboratory_typing_platform": { + "name": "levofloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "imipenem_laboratory_typing_platform", + "title": "levofloxacin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -43047,8 +44694,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 509, - "alias": "imipenem_laboratory_typing_platform", + "rank": 538, + "alias": "levofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43063,10 +44710,10 @@ } ] }, - "imipenem_laboratory_typing_platform_version": { - "name": "imipenem_laboratory_typing_platform_version", + "levofloxacin_laboratory_typing_platform_version": { + "name": "levofloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "imipenem_laboratory_typing_platform_version", + "title": "levofloxacin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -43076,8 +44723,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 510, - "alias": "imipenem_laboratory_typing_platform_version", + "rank": 539, + "alias": "levofloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43085,10 +44732,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "imipenem_vendor_name": { - "name": "imipenem_vendor_name", + "levofloxacin_vendor_name": { + "name": "levofloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "imipenem_vendor_name", + "title": "levofloxacin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -43101,8 +44748,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 511, - "alias": "imipenem_vendor_name", + "rank": 540, + "alias": "levofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43117,10 +44764,10 @@ } ] }, - "imipenem_testing_standard": { - "name": "imipenem_testing_standard", + "levofloxacin_testing_standard": { + "name": "levofloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "imipenem_testing_standard", + "title": "levofloxacin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -43133,8 +44780,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 512, - "alias": "imipenem_testing_standard", + "rank": 541, + "alias": "levofloxacin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43150,10 +44797,10 @@ } ] }, - "imipenem_testing_standard_version": { - "name": "imipenem_testing_standard_version", + "levofloxacin_testing_standard_version": { + "name": "levofloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "imipenem_testing_standard_version", + "title": "levofloxacin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -43163,8 +44810,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 513, - "alias": "imipenem_testing_standard_version", + "rank": 542, + "alias": "levofloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43172,10 +44819,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "imipenem_testing_standard_details": { - "name": "imipenem_testing_standard_details", + "levofloxacin_testing_standard_details": { + "name": "levofloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "imipenem_testing_standard_details", + "title": "levofloxacin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -43188,8 +44835,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 514, - "alias": "imipenem_testing_standard_details", + "rank": 543, + "alias": "levofloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43197,10 +44844,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "imipenem_susceptible_breakpoint": { - "name": "imipenem_susceptible_breakpoint", + "levofloxacin_susceptible_breakpoint": { + "name": "levofloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "imipenem_susceptible_breakpoint", + "title": "levofloxacin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -43210,8 +44857,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 515, - "alias": "imipenem_susceptible_breakpoint", + "rank": 544, + "alias": "levofloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43219,18 +44866,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "imipenem_intermediate_breakpoint": { - "name": "imipenem_intermediate_breakpoint", + "levofloxacin_intermediate_breakpoint": { + "name": "levofloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "imipenem_intermediate_breakpoint", + "title": "levofloxacin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 516, - "alias": "imipenem_intermediate_breakpoint", + "rank": 545, + "alias": "levofloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43238,10 +44885,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "imipenem_resistant_breakpoint": { - "name": "imipenem_resistant_breakpoint", + "levofloxacin_resistant_breakpoint": { + "name": "levofloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "imipenem_resistant_breakpoint", + "title": "levofloxacin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -43251,8 +44898,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 517, - "alias": "imipenem_resistant_breakpoint", + "rank": 546, + "alias": "levofloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43260,10 +44907,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "kanamycin_resistance_phenotype": { - "name": "kanamycin_resistance_phenotype", + "linezolid_resistance_phenotype": { + "name": "linezolid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "kanamycin_resistance_phenotype", + "title": "linezolid_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -43276,8 +44923,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 518, - "alias": "kanamycin_resistance_phenotype", + "rank": 547, + "alias": "linezolid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43293,10 +44940,10 @@ } ] }, - "kanamycin_measurement": { - "name": "kanamycin_measurement", - "description": "The measured value of kanamycin resistance.", - "title": "kanamycin_measurement", + "linezolid_measurement": { + "name": "linezolid_measurement", + "description": "The measured value of linezolid resistance.", + "title": "linezolid_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -43309,8 +44956,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 519, - "alias": "kanamycin_measurement", + "rank": 548, + "alias": "linezolid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43326,10 +44973,10 @@ } ] }, - "kanamycin_measurement_units": { - "name": "kanamycin_measurement_units", + "linezolid_measurement_units": { + "name": "linezolid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "kanamycin_measurement_units", + "title": "linezolid_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -43342,8 +44989,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 520, - "alias": "kanamycin_measurement_units", + "rank": 549, + "alias": "linezolid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43359,10 +45006,10 @@ } ] }, - "kanamycin_measurement_sign": { - "name": "kanamycin_measurement_sign", + "linezolid_measurement_sign": { + "name": "linezolid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "kanamycin_measurement_sign", + "title": "linezolid_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -43375,8 +45022,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 521, - "alias": "kanamycin_measurement_sign", + "rank": 550, + "alias": "linezolid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43392,10 +45039,10 @@ } ] }, - "kanamycin_laboratory_typing_method": { - "name": "kanamycin_laboratory_typing_method", + "linezolid_laboratory_typing_method": { + "name": "linezolid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "kanamycin_laboratory_typing_method", + "title": "linezolid_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -43408,8 +45055,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 522, - "alias": "kanamycin_laboratory_typing_method", + "rank": 551, + "alias": "linezolid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43424,10 +45071,10 @@ } ] }, - "kanamycin_laboratory_typing_platform": { - "name": "kanamycin_laboratory_typing_platform", + "linezolid_laboratory_typing_platform": { + "name": "linezolid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "kanamycin_laboratory_typing_platform", + "title": "linezolid_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -43440,8 +45087,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 523, - "alias": "kanamycin_laboratory_typing_platform", + "rank": 552, + "alias": "linezolid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43456,10 +45103,10 @@ } ] }, - "kanamycin_laboratory_typing_platform_version": { - "name": "kanamycin_laboratory_typing_platform_version", + "linezolid_laboratory_typing_platform_version": { + "name": "linezolid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "kanamycin_laboratory_typing_platform_version", + "title": "linezolid_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -43469,8 +45116,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 524, - "alias": "kanamycin_laboratory_typing_platform_version", + "rank": 553, + "alias": "linezolid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43478,10 +45125,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "kanamycin_vendor_name": { - "name": "kanamycin_vendor_name", + "linezolid_vendor_name": { + "name": "linezolid_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "kanamycin_vendor_name", + "title": "linezolid_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -43494,8 +45141,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 525, - "alias": "kanamycin_vendor_name", + "rank": 554, + "alias": "linezolid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43510,10 +45157,10 @@ } ] }, - "kanamycin_testing_standard": { - "name": "kanamycin_testing_standard", + "linezolid_testing_standard": { + "name": "linezolid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "kanamycin_testing_standard", + "title": "linezolid_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -43526,8 +45173,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 526, - "alias": "kanamycin_testing_standard", + "rank": 555, + "alias": "linezolid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43543,10 +45190,10 @@ } ] }, - "kanamycin_testing_standard_version": { - "name": "kanamycin_testing_standard_version", + "linezolid_testing_standard_version": { + "name": "linezolid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "kanamycin_testing_standard_version", + "title": "linezolid_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -43556,8 +45203,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 527, - "alias": "kanamycin_testing_standard_version", + "rank": 556, + "alias": "linezolid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43565,10 +45212,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "kanamycin_testing_standard_details": { - "name": "kanamycin_testing_standard_details", + "linezolid_testing_standard_details": { + "name": "linezolid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "kanamycin_testing_standard_details", + "title": "linezolid_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -43581,8 +45228,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 528, - "alias": "kanamycin_testing_standard_details", + "rank": 557, + "alias": "linezolid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43590,10 +45237,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "kanamycin_susceptible_breakpoint": { - "name": "kanamycin_susceptible_breakpoint", + "linezolid_susceptible_breakpoint": { + "name": "linezolid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "kanamycin_susceptible_breakpoint", + "title": "linezolid_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -43603,8 +45250,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 529, - "alias": "kanamycin_susceptible_breakpoint", + "rank": 558, + "alias": "linezolid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43612,18 +45259,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "kanamycin_intermediate_breakpoint": { - "name": "kanamycin_intermediate_breakpoint", + "linezolid_intermediate_breakpoint": { + "name": "linezolid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "kanamycin_intermediate_breakpoint", + "title": "linezolid_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 530, - "alias": "kanamycin_intermediate_breakpoint", + "rank": 559, + "alias": "linezolid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43631,10 +45278,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "kanamycin_resistant_breakpoint": { - "name": "kanamycin_resistant_breakpoint", + "linezolid_resistant_breakpoint": { + "name": "linezolid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "kanamycin_resistant_breakpoint", + "title": "linezolid_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -43644,8 +45291,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 531, - "alias": "kanamycin_resistant_breakpoint", + "rank": 560, + "alias": "linezolid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43653,10 +45300,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "levofloxacin_resistance_phenotype": { - "name": "levofloxacin_resistance_phenotype", + "meropenem_resistance_phenotype": { + "name": "meropenem_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "levofloxacin_resistance_phenotype", + "title": "meropenem_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -43669,8 +45316,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 532, - "alias": "levofloxacin_resistance_phenotype", + "rank": 561, + "alias": "meropenem_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43686,10 +45333,10 @@ } ] }, - "levofloxacin_measurement": { - "name": "levofloxacin_measurement", - "description": "The measured value of levofloxacin resistance.", - "title": "levofloxacin_measurement", + "meropenem_measurement": { + "name": "meropenem_measurement", + "description": "The measured value of meropenem resistance.", + "title": "meropenem_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -43702,8 +45349,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 533, - "alias": "levofloxacin_measurement", + "rank": 562, + "alias": "meropenem_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43719,10 +45366,10 @@ } ] }, - "levofloxacin_measurement_units": { - "name": "levofloxacin_measurement_units", + "meropenem_measurement_units": { + "name": "meropenem_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "levofloxacin_measurement_units", + "title": "meropenem_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -43735,8 +45382,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 534, - "alias": "levofloxacin_measurement_units", + "rank": 563, + "alias": "meropenem_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43752,10 +45399,10 @@ } ] }, - "levofloxacin_measurement_sign": { - "name": "levofloxacin_measurement_sign", + "meropenem_measurement_sign": { + "name": "meropenem_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "levofloxacin_measurement_sign", + "title": "meropenem_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -43768,8 +45415,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 535, - "alias": "levofloxacin_measurement_sign", + "rank": 564, + "alias": "meropenem_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43785,10 +45432,10 @@ } ] }, - "levofloxacin_laboratory_typing_method": { - "name": "levofloxacin_laboratory_typing_method", + "meropenem_laboratory_typing_method": { + "name": "meropenem_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "levofloxacin_laboratory_typing_method", + "title": "meropenem_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -43801,8 +45448,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 536, - "alias": "levofloxacin_laboratory_typing_method", + "rank": 565, + "alias": "meropenem_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43817,10 +45464,10 @@ } ] }, - "levofloxacin_laboratory_typing_platform": { - "name": "levofloxacin_laboratory_typing_platform", + "meropenem_laboratory_typing_platform": { + "name": "meropenem_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "levofloxacin_laboratory_typing_platform", + "title": "meropenem_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -43833,8 +45480,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 537, - "alias": "levofloxacin_laboratory_typing_platform", + "rank": 566, + "alias": "meropenem_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43849,10 +45496,10 @@ } ] }, - "levofloxacin_laboratory_typing_platform_version": { - "name": "levofloxacin_laboratory_typing_platform_version", + "meropenem_laboratory_typing_platform_version": { + "name": "meropenem_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "levofloxacin_laboratory_typing_platform_version", + "title": "meropenem_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -43862,8 +45509,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 538, - "alias": "levofloxacin_laboratory_typing_platform_version", + "rank": 567, + "alias": "meropenem_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43871,10 +45518,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "levofloxacin_vendor_name": { - "name": "levofloxacin_vendor_name", + "meropenem_vendor_name": { + "name": "meropenem_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "levofloxacin_vendor_name", + "title": "meropenem_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -43887,8 +45534,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 539, - "alias": "levofloxacin_vendor_name", + "rank": 568, + "alias": "meropenem_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43903,10 +45550,10 @@ } ] }, - "levofloxacin_testing_standard": { - "name": "levofloxacin_testing_standard", + "meropenem_testing_standard": { + "name": "meropenem_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "levofloxacin_testing_standard", + "title": "meropenem_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -43919,8 +45566,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 540, - "alias": "levofloxacin_testing_standard", + "rank": 569, + "alias": "meropenem_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43936,10 +45583,10 @@ } ] }, - "levofloxacin_testing_standard_version": { - "name": "levofloxacin_testing_standard_version", + "meropenem_testing_standard_version": { + "name": "meropenem_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "levofloxacin_testing_standard_version", + "title": "meropenem_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -43949,8 +45596,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 541, - "alias": "levofloxacin_testing_standard_version", + "rank": 570, + "alias": "meropenem_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43958,10 +45605,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "levofloxacin_testing_standard_details": { - "name": "levofloxacin_testing_standard_details", + "meropenem_testing_standard_details": { + "name": "meropenem_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "levofloxacin_testing_standard_details", + "title": "meropenem_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -43974,8 +45621,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 542, - "alias": "levofloxacin_testing_standard_details", + "rank": 571, + "alias": "meropenem_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -43983,10 +45630,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "levofloxacin_susceptible_breakpoint": { - "name": "levofloxacin_susceptible_breakpoint", + "meropenem_susceptible_breakpoint": { + "name": "meropenem_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "levofloxacin_susceptible_breakpoint", + "title": "meropenem_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -43996,8 +45643,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 543, - "alias": "levofloxacin_susceptible_breakpoint", + "rank": 572, + "alias": "meropenem_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44005,18 +45652,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "levofloxacin_intermediate_breakpoint": { - "name": "levofloxacin_intermediate_breakpoint", + "meropenem_intermediate_breakpoint": { + "name": "meropenem_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "levofloxacin_intermediate_breakpoint", + "title": "meropenem_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 544, - "alias": "levofloxacin_intermediate_breakpoint", + "rank": 573, + "alias": "meropenem_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44024,10 +45671,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "levofloxacin_resistant_breakpoint": { - "name": "levofloxacin_resistant_breakpoint", + "meropenem_resistant_breakpoint": { + "name": "meropenem_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "levofloxacin_resistant_breakpoint", + "title": "meropenem_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -44037,8 +45684,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 545, - "alias": "levofloxacin_resistant_breakpoint", + "rank": 574, + "alias": "meropenem_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44046,10 +45693,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "linezolid_resistance_phenotype": { - "name": "linezolid_resistance_phenotype", + "nalidixic_acid_resistance_phenotype": { + "name": "nalidixic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "linezolid_resistance_phenotype", + "title": "nalidixic_acid_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -44062,8 +45709,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 546, - "alias": "linezolid_resistance_phenotype", + "rank": 575, + "alias": "nalidixic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44079,10 +45726,10 @@ } ] }, - "linezolid_measurement": { - "name": "linezolid_measurement", - "description": "The measured value of linezolid resistance.", - "title": "linezolid_measurement", + "nalidixic_acid_measurement": { + "name": "nalidixic_acid_measurement", + "description": "The measured value of nalidixic-acid resistance.", + "title": "nalidixic_acid_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -44095,8 +45742,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 547, - "alias": "linezolid_measurement", + "rank": 576, + "alias": "nalidixic_acid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44112,10 +45759,10 @@ } ] }, - "linezolid_measurement_units": { - "name": "linezolid_measurement_units", + "nalidixic_acid_measurement_units": { + "name": "nalidixic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "linezolid_measurement_units", + "title": "nalidixic_acid_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -44128,8 +45775,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 548, - "alias": "linezolid_measurement_units", + "rank": 577, + "alias": "nalidixic_acid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44145,10 +45792,10 @@ } ] }, - "linezolid_measurement_sign": { - "name": "linezolid_measurement_sign", + "nalidixic_acid_measurement_sign": { + "name": "nalidixic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "linezolid_measurement_sign", + "title": "nalidixic_acid_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -44161,8 +45808,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 549, - "alias": "linezolid_measurement_sign", + "rank": 578, + "alias": "nalidixic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44178,10 +45825,10 @@ } ] }, - "linezolid_laboratory_typing_method": { - "name": "linezolid_laboratory_typing_method", + "nalidixic_acid_laboratory_typing_method": { + "name": "nalidixic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "linezolid_laboratory_typing_method", + "title": "nalidixic_acid_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -44194,8 +45841,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 550, - "alias": "linezolid_laboratory_typing_method", + "rank": 579, + "alias": "nalidixic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44210,10 +45857,10 @@ } ] }, - "linezolid_laboratory_typing_platform": { - "name": "linezolid_laboratory_typing_platform", + "nalidixic_acid_laboratory_typing_platform": { + "name": "nalidixic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "linezolid_laboratory_typing_platform", + "title": "nalidixic_acid_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -44226,8 +45873,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 551, - "alias": "linezolid_laboratory_typing_platform", + "rank": 580, + "alias": "nalidixic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44242,10 +45889,10 @@ } ] }, - "linezolid_laboratory_typing_platform_version": { - "name": "linezolid_laboratory_typing_platform_version", + "nalidixic_acid_laboratory_typing_platform_version": { + "name": "nalidixic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "linezolid_laboratory_typing_platform_version", + "title": "nalidixic_acid_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -44255,8 +45902,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 552, - "alias": "linezolid_laboratory_typing_platform_version", + "rank": 581, + "alias": "nalidixic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44264,10 +45911,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "linezolid_vendor_name": { - "name": "linezolid_vendor_name", + "nalidixic_acid_vendor_name": { + "name": "nalidixic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "linezolid_vendor_name", + "title": "nalidixic_acid_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -44280,8 +45927,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 553, - "alias": "linezolid_vendor_name", + "rank": 582, + "alias": "nalidixic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44296,10 +45943,10 @@ } ] }, - "linezolid_testing_standard": { - "name": "linezolid_testing_standard", + "nalidixic_acid_testing_standard": { + "name": "nalidixic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "linezolid_testing_standard", + "title": "nalidixic_acid_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -44312,8 +45959,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 554, - "alias": "linezolid_testing_standard", + "rank": 583, + "alias": "nalidixic_acid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44329,10 +45976,10 @@ } ] }, - "linezolid_testing_standard_version": { - "name": "linezolid_testing_standard_version", + "nalidixic_acid_testing_standard_version": { + "name": "nalidixic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "linezolid_testing_standard_version", + "title": "nalidixic_acid_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -44342,8 +45989,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 555, - "alias": "linezolid_testing_standard_version", + "rank": 584, + "alias": "nalidixic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44351,10 +45998,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "linezolid_testing_standard_details": { - "name": "linezolid_testing_standard_details", + "nalidixic_acid_testing_standard_details": { + "name": "nalidixic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "linezolid_testing_standard_details", + "title": "nalidixic_acid_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -44367,8 +46014,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 556, - "alias": "linezolid_testing_standard_details", + "rank": 585, + "alias": "nalidixic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44376,10 +46023,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "linezolid_susceptible_breakpoint": { - "name": "linezolid_susceptible_breakpoint", + "nalidixic_acid_susceptible_breakpoint": { + "name": "nalidixic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "linezolid_susceptible_breakpoint", + "title": "nalidixic_acid_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -44389,8 +46036,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 557, - "alias": "linezolid_susceptible_breakpoint", + "rank": 586, + "alias": "nalidixic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44398,18 +46045,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "linezolid_intermediate_breakpoint": { - "name": "linezolid_intermediate_breakpoint", + "nalidixic_acid_intermediate_breakpoint": { + "name": "nalidixic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "linezolid_intermediate_breakpoint", + "title": "nalidixic_acid_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 558, - "alias": "linezolid_intermediate_breakpoint", + "rank": 587, + "alias": "nalidixic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44417,10 +46064,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "linezolid_resistant_breakpoint": { - "name": "linezolid_resistant_breakpoint", + "nalidixic_acid_resistant_breakpoint": { + "name": "nalidixic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "linezolid_resistant_breakpoint", + "title": "nalidixic_acid_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -44430,8 +46077,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 559, - "alias": "linezolid_resistant_breakpoint", + "rank": 588, + "alias": "nalidixic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44439,10 +46086,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "meropenem_resistance_phenotype": { - "name": "meropenem_resistance_phenotype", + "neomycin_resistance_phenotype": { + "name": "neomycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "meropenem_resistance_phenotype", + "title": "neomycin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -44452,11 +46099,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:resistance_phenotype" - ], - "rank": 560, - "alias": "meropenem_resistance_phenotype", + "rank": 589, + "alias": "neomycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44472,10 +46116,10 @@ } ] }, - "meropenem_measurement": { - "name": "meropenem_measurement", - "description": "The measured value of meropenem resistance.", - "title": "meropenem_measurement", + "neomycin_measurement": { + "name": "neomycin_measurement", + "description": "The measured value of neomycin resistance.", + "title": "neomycin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -44484,12 +46128,9 @@ "value": "4" } ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement" - ], - "rank": 561, - "alias": "meropenem_measurement", + "from_schema": "https://example.com/GRDI", + "rank": 590, + "alias": "neomycin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44505,10 +46146,10 @@ } ] }, - "meropenem_measurement_units": { - "name": "meropenem_measurement_units", + "neomycin_measurement_units": { + "name": "neomycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "meropenem_measurement_units", + "title": "neomycin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -44518,11 +46159,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_units" - ], - "rank": 562, - "alias": "meropenem_measurement_units", + "rank": 591, + "alias": "neomycin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44538,10 +46176,10 @@ } ] }, - "meropenem_measurement_sign": { - "name": "meropenem_measurement_sign", + "neomycin_measurement_sign": { + "name": "neomycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "meropenem_measurement_sign", + "title": "neomycin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -44551,11 +46189,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_sign" - ], - "rank": 563, - "alias": "meropenem_measurement_sign", + "rank": 592, + "alias": "neomycin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44571,10 +46206,10 @@ } ] }, - "meropenem_laboratory_typing_method": { - "name": "meropenem_laboratory_typing_method", + "neomycin_laboratory_typing_method": { + "name": "neomycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "meropenem_laboratory_typing_method", + "title": "neomycin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -44584,11 +46219,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_method" - ], - "rank": 564, - "alias": "meropenem_laboratory_typing_method", + "rank": 593, + "alias": "neomycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44603,10 +46235,10 @@ } ] }, - "meropenem_laboratory_typing_platform": { - "name": "meropenem_laboratory_typing_platform", + "neomycin_laboratory_typing_platform": { + "name": "neomycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "meropenem_laboratory_typing_platform", + "title": "neomycin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -44616,11 +46248,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_platform" - ], - "rank": 565, - "alias": "meropenem_laboratory_typing_platform", + "rank": 594, + "alias": "neomycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44635,10 +46264,10 @@ } ] }, - "meropenem_laboratory_typing_platform_version": { - "name": "meropenem_laboratory_typing_platform_version", + "neomycin_laboratory_typing_platform_version": { + "name": "neomycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "meropenem_laboratory_typing_platform_version", + "title": "neomycin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -44648,8 +46277,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 566, - "alias": "meropenem_laboratory_typing_platform_version", + "rank": 595, + "alias": "neomycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44657,10 +46286,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "meropenem_vendor_name": { - "name": "meropenem_vendor_name", + "neomycin_vendor_name": { + "name": "neomycin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "meropenem_vendor_name", + "title": "neomycin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -44670,11 +46299,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:vendor" - ], - "rank": 567, - "alias": "meropenem_vendor_name", + "rank": 596, + "alias": "neomycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44689,10 +46315,10 @@ } ] }, - "meropenem_testing_standard": { - "name": "meropenem_testing_standard", + "neomycin_testing_standard": { + "name": "neomycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "meropenem_testing_standard", + "title": "neomycin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -44702,11 +46328,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:testing_standard" - ], - "rank": 568, - "alias": "meropenem_testing_standard", + "rank": 597, + "alias": "neomycin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44722,10 +46345,10 @@ } ] }, - "meropenem_testing_standard_version": { - "name": "meropenem_testing_standard_version", + "neomycin_testing_standard_version": { + "name": "neomycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "meropenem_testing_standard_version", + "title": "neomycin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -44735,8 +46358,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 569, - "alias": "meropenem_testing_standard_version", + "rank": 598, + "alias": "neomycin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44744,10 +46367,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "meropenem_testing_standard_details": { - "name": "meropenem_testing_standard_details", + "neomycin_testing_standard_details": { + "name": "neomycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "meropenem_testing_standard_details", + "title": "neomycin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -44760,8 +46383,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 570, - "alias": "meropenem_testing_standard_details", + "rank": 599, + "alias": "neomycin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44769,10 +46392,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "meropenem_susceptible_breakpoint": { - "name": "meropenem_susceptible_breakpoint", + "neomycin_susceptible_breakpoint": { + "name": "neomycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "meropenem_susceptible_breakpoint", + "title": "neomycin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -44782,8 +46405,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 571, - "alias": "meropenem_susceptible_breakpoint", + "rank": 600, + "alias": "neomycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44791,18 +46414,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "meropenem_intermediate_breakpoint": { - "name": "meropenem_intermediate_breakpoint", + "neomycin_intermediate_breakpoint": { + "name": "neomycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "meropenem_intermediate_breakpoint", + "title": "neomycin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 572, - "alias": "meropenem_intermediate_breakpoint", + "rank": 601, + "alias": "neomycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44810,10 +46433,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "meropenem_resistant_breakpoint": { - "name": "meropenem_resistant_breakpoint", + "neomycin_resistant_breakpoint": { + "name": "neomycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "meropenem_resistant_breakpoint", + "title": "neomycin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -44823,8 +46446,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 573, - "alias": "meropenem_resistant_breakpoint", + "rank": 602, + "alias": "neomycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44832,10 +46455,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nalidixic_acid_resistance_phenotype": { - "name": "nalidixic_acid_resistance_phenotype", + "nitrofurantoin_resistance_phenotype": { + "name": "nitrofurantoin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "nalidixic_acid_resistance_phenotype", + "title": "nitrofurantoin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -44848,8 +46471,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 574, - "alias": "nalidixic_acid_resistance_phenotype", + "rank": 603, + "alias": "nitrofurantoin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44865,10 +46488,10 @@ } ] }, - "nalidixic_acid_measurement": { - "name": "nalidixic_acid_measurement", - "description": "The measured value of nalidixic-acid resistance.", - "title": "nalidixic_acid_measurement", + "nitrofurantoin_measurement": { + "name": "nitrofurantoin_measurement", + "description": "The measured value of nitrofurantoin resistance.", + "title": "nitrofurantoin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -44881,8 +46504,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 575, - "alias": "nalidixic_acid_measurement", + "rank": 604, + "alias": "nitrofurantoin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44898,10 +46521,10 @@ } ] }, - "nalidixic_acid_measurement_units": { - "name": "nalidixic_acid_measurement_units", + "nitrofurantoin_measurement_units": { + "name": "nitrofurantoin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "nalidixic_acid_measurement_units", + "title": "nitrofurantoin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -44914,8 +46537,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 576, - "alias": "nalidixic_acid_measurement_units", + "rank": 605, + "alias": "nitrofurantoin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44931,10 +46554,10 @@ } ] }, - "nalidixic_acid_measurement_sign": { - "name": "nalidixic_acid_measurement_sign", + "nitrofurantoin_measurement_sign": { + "name": "nitrofurantoin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "nalidixic_acid_measurement_sign", + "title": "nitrofurantoin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -44947,8 +46570,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 577, - "alias": "nalidixic_acid_measurement_sign", + "rank": 606, + "alias": "nitrofurantoin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44964,10 +46587,10 @@ } ] }, - "nalidixic_acid_laboratory_typing_method": { - "name": "nalidixic_acid_laboratory_typing_method", + "nitrofurantoin_laboratory_typing_method": { + "name": "nitrofurantoin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "nalidixic_acid_laboratory_typing_method", + "title": "nitrofurantoin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -44980,8 +46603,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 578, - "alias": "nalidixic_acid_laboratory_typing_method", + "rank": 607, + "alias": "nitrofurantoin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -44996,10 +46619,10 @@ } ] }, - "nalidixic_acid_laboratory_typing_platform": { - "name": "nalidixic_acid_laboratory_typing_platform", + "nitrofurantoin_laboratory_typing_platform": { + "name": "nitrofurantoin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "nalidixic_acid_laboratory_typing_platform", + "title": "nitrofurantoin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -45012,8 +46635,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 579, - "alias": "nalidixic_acid_laboratory_typing_platform", + "rank": 608, + "alias": "nitrofurantoin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45028,10 +46651,10 @@ } ] }, - "nalidixic_acid_laboratory_typing_platform_version": { - "name": "nalidixic_acid_laboratory_typing_platform_version", + "nitrofurantoin_laboratory_typing_platform_version": { + "name": "nitrofurantoin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "nalidixic_acid_laboratory_typing_platform_version", + "title": "nitrofurantoin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -45041,8 +46664,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 580, - "alias": "nalidixic_acid_laboratory_typing_platform_version", + "rank": 609, + "alias": "nitrofurantoin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45050,10 +46673,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nalidixic_acid_vendor_name": { - "name": "nalidixic_acid_vendor_name", + "nitrofurantoin_vendor_name": { + "name": "nitrofurantoin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "nalidixic_acid_vendor_name", + "title": "nitrofurantoin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -45066,8 +46689,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 581, - "alias": "nalidixic_acid_vendor_name", + "rank": 610, + "alias": "nitrofurantoin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45082,10 +46705,10 @@ } ] }, - "nalidixic_acid_testing_standard": { - "name": "nalidixic_acid_testing_standard", + "nitrofurantoin_testing_standard": { + "name": "nitrofurantoin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "nalidixic_acid_testing_standard", + "title": "nitrofurantoin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -45098,8 +46721,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 582, - "alias": "nalidixic_acid_testing_standard", + "rank": 611, + "alias": "nitrofurantoin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45115,10 +46738,10 @@ } ] }, - "nalidixic_acid_testing_standard_version": { - "name": "nalidixic_acid_testing_standard_version", + "nitrofurantoin_testing_standard_version": { + "name": "nitrofurantoin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "nalidixic_acid_testing_standard_version", + "title": "nitrofurantoin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -45128,8 +46751,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 583, - "alias": "nalidixic_acid_testing_standard_version", + "rank": 612, + "alias": "nitrofurantoin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45137,10 +46760,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nalidixic_acid_testing_standard_details": { - "name": "nalidixic_acid_testing_standard_details", + "nitrofurantoin_testing_standard_details": { + "name": "nitrofurantoin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "nalidixic_acid_testing_standard_details", + "title": "nitrofurantoin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -45153,8 +46776,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 584, - "alias": "nalidixic_acid_testing_standard_details", + "rank": 613, + "alias": "nitrofurantoin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45162,10 +46785,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nalidixic_acid_susceptible_breakpoint": { - "name": "nalidixic_acid_susceptible_breakpoint", + "nitrofurantoin_susceptible_breakpoint": { + "name": "nitrofurantoin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "nalidixic_acid_susceptible_breakpoint", + "title": "nitrofurantoin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -45175,8 +46798,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 585, - "alias": "nalidixic_acid_susceptible_breakpoint", + "rank": 614, + "alias": "nitrofurantoin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45184,18 +46807,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nalidixic_acid_intermediate_breakpoint": { - "name": "nalidixic_acid_intermediate_breakpoint", + "nitrofurantoin_intermediate_breakpoint": { + "name": "nitrofurantoin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "nalidixic_acid_intermediate_breakpoint", + "title": "nitrofurantoin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 586, - "alias": "nalidixic_acid_intermediate_breakpoint", + "rank": 615, + "alias": "nitrofurantoin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45203,10 +46826,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nalidixic_acid_resistant_breakpoint": { - "name": "nalidixic_acid_resistant_breakpoint", + "nitrofurantoin_resistant_breakpoint": { + "name": "nitrofurantoin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "nalidixic_acid_resistant_breakpoint", + "title": "nitrofurantoin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -45216,8 +46839,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 587, - "alias": "nalidixic_acid_resistant_breakpoint", + "rank": 616, + "alias": "nitrofurantoin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45225,10 +46848,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_resistance_phenotype": { - "name": "nitrofurantoin_resistance_phenotype", + "norfloxacin_resistance_phenotype": { + "name": "norfloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "nitrofurantoin_resistance_phenotype", + "title": "norfloxacin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -45241,8 +46864,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 588, - "alias": "nitrofurantoin_resistance_phenotype", + "rank": 617, + "alias": "norfloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45258,10 +46881,10 @@ } ] }, - "nitrofurantoin_measurement": { - "name": "nitrofurantoin_measurement", - "description": "The measured value of nitrofurantoin resistance.", - "title": "nitrofurantoin_measurement", + "norfloxacin_measurement": { + "name": "norfloxacin_measurement", + "description": "The measured value of norfloxacin resistance.", + "title": "norfloxacin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -45274,8 +46897,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 589, - "alias": "nitrofurantoin_measurement", + "rank": 618, + "alias": "norfloxacin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45291,10 +46914,10 @@ } ] }, - "nitrofurantoin_measurement_units": { - "name": "nitrofurantoin_measurement_units", + "norfloxacin_measurement_units": { + "name": "norfloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "nitrofurantoin_measurement_units", + "title": "norfloxacin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -45307,8 +46930,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 590, - "alias": "nitrofurantoin_measurement_units", + "rank": 619, + "alias": "norfloxacin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45324,10 +46947,10 @@ } ] }, - "nitrofurantoin_measurement_sign": { - "name": "nitrofurantoin_measurement_sign", + "norfloxacin_measurement_sign": { + "name": "norfloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "nitrofurantoin_measurement_sign", + "title": "norfloxacin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -45340,8 +46963,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 591, - "alias": "nitrofurantoin_measurement_sign", + "rank": 620, + "alias": "norfloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45357,10 +46980,10 @@ } ] }, - "nitrofurantoin_laboratory_typing_method": { - "name": "nitrofurantoin_laboratory_typing_method", + "norfloxacin_laboratory_typing_method": { + "name": "norfloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "nitrofurantoin_laboratory_typing_method", + "title": "norfloxacin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -45373,8 +46996,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 592, - "alias": "nitrofurantoin_laboratory_typing_method", + "rank": 621, + "alias": "norfloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45389,10 +47012,10 @@ } ] }, - "nitrofurantoin_laboratory_typing_platform": { - "name": "nitrofurantoin_laboratory_typing_platform", + "norfloxacin_laboratory_typing_platform": { + "name": "norfloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "nitrofurantoin_laboratory_typing_platform", + "title": "norfloxacin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -45405,8 +47028,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 593, - "alias": "nitrofurantoin_laboratory_typing_platform", + "rank": 622, + "alias": "norfloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45421,10 +47044,10 @@ } ] }, - "nitrofurantoin_laboratory_typing_platform_version": { - "name": "nitrofurantoin_laboratory_typing_platform_version", + "norfloxacin_laboratory_typing_platform_version": { + "name": "norfloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "nitrofurantoin_laboratory_typing_platform_version", + "title": "norfloxacin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -45434,8 +47057,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 594, - "alias": "nitrofurantoin_laboratory_typing_platform_version", + "rank": 623, + "alias": "norfloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45443,10 +47066,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_vendor_name": { - "name": "nitrofurantoin_vendor_name", + "norfloxacin_vendor_name": { + "name": "norfloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "nitrofurantoin_vendor_name", + "title": "norfloxacin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -45459,8 +47082,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 595, - "alias": "nitrofurantoin_vendor_name", + "rank": 624, + "alias": "norfloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45475,10 +47098,10 @@ } ] }, - "nitrofurantoin_testing_standard": { - "name": "nitrofurantoin_testing_standard", + "norfloxacin_testing_standard": { + "name": "norfloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "nitrofurantoin_testing_standard", + "title": "norfloxacin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -45491,8 +47114,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 596, - "alias": "nitrofurantoin_testing_standard", + "rank": 625, + "alias": "norfloxacin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45508,10 +47131,10 @@ } ] }, - "nitrofurantoin_testing_standard_version": { - "name": "nitrofurantoin_testing_standard_version", + "norfloxacin_testing_standard_version": { + "name": "norfloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "nitrofurantoin_testing_standard_version", + "title": "norfloxacin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -45521,8 +47144,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 597, - "alias": "nitrofurantoin_testing_standard_version", + "rank": 626, + "alias": "norfloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45530,10 +47153,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_testing_standard_details": { - "name": "nitrofurantoin_testing_standard_details", + "norfloxacin_testing_standard_details": { + "name": "norfloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "nitrofurantoin_testing_standard_details", + "title": "norfloxacin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -45546,8 +47169,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 598, - "alias": "nitrofurantoin_testing_standard_details", + "rank": 627, + "alias": "norfloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45555,10 +47178,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_susceptible_breakpoint": { - "name": "nitrofurantoin_susceptible_breakpoint", + "norfloxacin_susceptible_breakpoint": { + "name": "norfloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "nitrofurantoin_susceptible_breakpoint", + "title": "norfloxacin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -45568,8 +47191,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 599, - "alias": "nitrofurantoin_susceptible_breakpoint", + "rank": 628, + "alias": "norfloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45577,18 +47200,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_intermediate_breakpoint": { - "name": "nitrofurantoin_intermediate_breakpoint", + "norfloxacin_intermediate_breakpoint": { + "name": "norfloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "nitrofurantoin_intermediate_breakpoint", + "title": "norfloxacin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 600, - "alias": "nitrofurantoin_intermediate_breakpoint", + "rank": 629, + "alias": "norfloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45596,10 +47219,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "nitrofurantoin_resistant_breakpoint": { - "name": "nitrofurantoin_resistant_breakpoint", + "norfloxacin_resistant_breakpoint": { + "name": "norfloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "nitrofurantoin_resistant_breakpoint", + "title": "norfloxacin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -45609,8 +47232,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 601, - "alias": "nitrofurantoin_resistant_breakpoint", + "rank": 630, + "alias": "norfloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45618,10 +47241,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "norfloxacin_resistance_phenotype": { - "name": "norfloxacin_resistance_phenotype", + "oxolinicacid_resistance_phenotype": { + "name": "oxolinicacid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "norfloxacin_resistance_phenotype", + "title": "oxolinic-acid_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -45634,8 +47257,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 602, - "alias": "norfloxacin_resistance_phenotype", + "rank": 631, + "alias": "oxolinicacid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45651,10 +47274,10 @@ } ] }, - "norfloxacin_measurement": { - "name": "norfloxacin_measurement", - "description": "The measured value of norfloxacin resistance.", - "title": "norfloxacin_measurement", + "oxolinicacid_measurement": { + "name": "oxolinicacid_measurement", + "description": "The measured value of oxolinic-acid resistance.", + "title": "oxolinic-acid_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -45667,8 +47290,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 603, - "alias": "norfloxacin_measurement", + "rank": 632, + "alias": "oxolinicacid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45684,10 +47307,10 @@ } ] }, - "norfloxacin_measurement_units": { - "name": "norfloxacin_measurement_units", + "oxolinicacid_measurement_units": { + "name": "oxolinicacid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "norfloxacin_measurement_units", + "title": "oxolinic-acid_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -45700,8 +47323,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 604, - "alias": "norfloxacin_measurement_units", + "rank": 633, + "alias": "oxolinicacid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45717,10 +47340,10 @@ } ] }, - "norfloxacin_measurement_sign": { - "name": "norfloxacin_measurement_sign", + "oxolinicacid_measurement_sign": { + "name": "oxolinicacid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "norfloxacin_measurement_sign", + "title": "oxolinic-acid_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -45733,8 +47356,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 605, - "alias": "norfloxacin_measurement_sign", + "rank": 634, + "alias": "oxolinicacid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45750,10 +47373,10 @@ } ] }, - "norfloxacin_laboratory_typing_method": { - "name": "norfloxacin_laboratory_typing_method", + "oxolinicacid_laboratory_typing_method": { + "name": "oxolinicacid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "norfloxacin_laboratory_typing_method", + "title": "oxolinic-acid_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -45766,8 +47389,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 606, - "alias": "norfloxacin_laboratory_typing_method", + "rank": 635, + "alias": "oxolinicacid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45782,10 +47405,10 @@ } ] }, - "norfloxacin_laboratory_typing_platform": { - "name": "norfloxacin_laboratory_typing_platform", + "oxolinicacid_laboratory_typing_platform": { + "name": "oxolinicacid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "norfloxacin_laboratory_typing_platform", + "title": "oxolinic-acid_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -45798,8 +47421,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 607, - "alias": "norfloxacin_laboratory_typing_platform", + "rank": 636, + "alias": "oxolinicacid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45814,10 +47437,10 @@ } ] }, - "norfloxacin_laboratory_typing_platform_version": { - "name": "norfloxacin_laboratory_typing_platform_version", + "oxolinicacid_laboratory_typing_platform_version": { + "name": "oxolinicacid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "norfloxacin_laboratory_typing_platform_version", + "title": "oxolinic-acid_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -45827,8 +47450,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 608, - "alias": "norfloxacin_laboratory_typing_platform_version", + "rank": 637, + "alias": "oxolinicacid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45836,10 +47459,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "norfloxacin_vendor_name": { - "name": "norfloxacin_vendor_name", + "oxolinicacid_vendor_name": { + "name": "oxolinicacid_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "norfloxacin_vendor_name", + "title": "oxolinic-acid_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -45852,8 +47475,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 609, - "alias": "norfloxacin_vendor_name", + "rank": 638, + "alias": "oxolinicacid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45868,10 +47491,10 @@ } ] }, - "norfloxacin_testing_standard": { - "name": "norfloxacin_testing_standard", + "oxolinicacid_testing_standard": { + "name": "oxolinicacid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "norfloxacin_testing_standard", + "title": "oxolinic-acid_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -45884,8 +47507,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 610, - "alias": "norfloxacin_testing_standard", + "rank": 639, + "alias": "oxolinicacid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45901,10 +47524,10 @@ } ] }, - "norfloxacin_testing_standard_version": { - "name": "norfloxacin_testing_standard_version", + "oxolinicacid_testing_standard_version": { + "name": "oxolinicacid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "norfloxacin_testing_standard_version", + "title": "oxolinic-acid_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -45914,8 +47537,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 611, - "alias": "norfloxacin_testing_standard_version", + "rank": 640, + "alias": "oxolinicacid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45923,10 +47546,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "norfloxacin_testing_standard_details": { - "name": "norfloxacin_testing_standard_details", + "oxolinicacid_testing_standard_details": { + "name": "oxolinicacid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "norfloxacin_testing_standard_details", + "title": "oxolinic-acid_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -45939,8 +47562,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 612, - "alias": "norfloxacin_testing_standard_details", + "rank": 641, + "alias": "oxolinicacid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45948,10 +47571,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "norfloxacin_susceptible_breakpoint": { - "name": "norfloxacin_susceptible_breakpoint", + "oxolinicacid_susceptible_breakpoint": { + "name": "oxolinicacid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "norfloxacin_susceptible_breakpoint", + "title": "oxolinic-acid_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -45961,8 +47584,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 613, - "alias": "norfloxacin_susceptible_breakpoint", + "rank": 642, + "alias": "oxolinicacid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45970,18 +47593,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "norfloxacin_intermediate_breakpoint": { - "name": "norfloxacin_intermediate_breakpoint", + "oxolinicacid_intermediate_breakpoint": { + "name": "oxolinicacid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "norfloxacin_intermediate_breakpoint", + "title": "oxolinic-acid_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 614, - "alias": "norfloxacin_intermediate_breakpoint", + "rank": 643, + "alias": "oxolinicacid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -45989,10 +47612,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "norfloxacin_resistant_breakpoint": { - "name": "norfloxacin_resistant_breakpoint", + "oxolinicacid_resistant_breakpoint": { + "name": "oxolinicacid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "norfloxacin_resistant_breakpoint", + "title": "oxolinic-acid_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -46002,8 +47625,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 615, - "alias": "norfloxacin_resistant_breakpoint", + "rank": 644, + "alias": "oxolinicacid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46011,10 +47634,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinicacid_resistance_phenotype": { - "name": "oxolinicacid_resistance_phenotype", + "oxytetracycline_resistance_phenotype": { + "name": "oxytetracycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "oxolinic-acid_resistance_phenotype", + "title": "oxytetracycline_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -46027,8 +47650,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 616, - "alias": "oxolinicacid_resistance_phenotype", + "rank": 645, + "alias": "oxytetracycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46044,10 +47667,10 @@ } ] }, - "oxolinicacid_measurement": { - "name": "oxolinicacid_measurement", - "description": "The measured value of oxolinic-acid resistance.", - "title": "oxolinic-acid_measurement", + "oxytetracycline_measurement": { + "name": "oxytetracycline_measurement", + "description": "The measured value of oxytetracycline resistance.", + "title": "oxytetracycline_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -46060,8 +47683,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 617, - "alias": "oxolinicacid_measurement", + "rank": 646, + "alias": "oxytetracycline_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46077,10 +47700,10 @@ } ] }, - "oxolinicacid_measurement_units": { - "name": "oxolinicacid_measurement_units", + "oxytetracycline_measurement_units": { + "name": "oxytetracycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "oxolinic-acid_measurement_units", + "title": "oxytetracycline_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -46093,8 +47716,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 618, - "alias": "oxolinicacid_measurement_units", + "rank": 647, + "alias": "oxytetracycline_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46110,10 +47733,10 @@ } ] }, - "oxolinicacid_measurement_sign": { - "name": "oxolinicacid_measurement_sign", + "oxytetracycline_measurement_sign": { + "name": "oxytetracycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "oxolinic-acid_measurement_sign", + "title": "oxytetracycline_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -46126,8 +47749,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 619, - "alias": "oxolinicacid_measurement_sign", + "rank": 648, + "alias": "oxytetracycline_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46143,10 +47766,10 @@ } ] }, - "oxolinicacid_laboratory_typing_method": { - "name": "oxolinicacid_laboratory_typing_method", + "oxytetracycline_laboratory_typing_method": { + "name": "oxytetracycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "oxolinic-acid_laboratory_typing_method", + "title": "oxytetracycline_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -46159,8 +47782,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 620, - "alias": "oxolinicacid_laboratory_typing_method", + "rank": 649, + "alias": "oxytetracycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46175,10 +47798,10 @@ } ] }, - "oxolinicacid_laboratory_typing_platform": { - "name": "oxolinicacid_laboratory_typing_platform", + "oxytetracycline_laboratory_typing_platform": { + "name": "oxytetracycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "oxolinic-acid_laboratory_typing_platform", + "title": "oxytetracycline_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -46191,8 +47814,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 621, - "alias": "oxolinicacid_laboratory_typing_platform", + "rank": 650, + "alias": "oxytetracycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46207,10 +47830,10 @@ } ] }, - "oxolinicacid_laboratory_typing_platform_version": { - "name": "oxolinicacid_laboratory_typing_platform_version", + "oxytetracycline_laboratory_typing_platform_version": { + "name": "oxytetracycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "oxolinic-acid_laboratory_typing_platform_version", + "title": "oxytetracycline_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -46220,8 +47843,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 622, - "alias": "oxolinicacid_laboratory_typing_platform_version", + "rank": 651, + "alias": "oxytetracycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46229,10 +47852,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinicacid_vendor_name": { - "name": "oxolinicacid_vendor_name", + "oxytetracycline_vendor_name": { + "name": "oxytetracycline_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "oxolinic-acid_vendor_name", + "title": "oxytetracycline_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -46245,8 +47868,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 623, - "alias": "oxolinicacid_vendor_name", + "rank": 652, + "alias": "oxytetracycline_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46261,10 +47884,10 @@ } ] }, - "oxolinicacid_testing_standard": { - "name": "oxolinicacid_testing_standard", + "oxytetracycline_testing_standard": { + "name": "oxytetracycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "oxolinic-acid_testing_standard", + "title": "oxytetracycline_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -46277,8 +47900,8 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 624, - "alias": "oxolinicacid_testing_standard", + "rank": 653, + "alias": "oxytetracycline_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46294,10 +47917,10 @@ } ] }, - "oxolinicacid_testing_standard_version": { - "name": "oxolinicacid_testing_standard_version", + "oxytetracycline_testing_standard_version": { + "name": "oxytetracycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "oxolinic-acid_testing_standard_version", + "title": "oxytetracycline_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -46307,8 +47930,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 625, - "alias": "oxolinicacid_testing_standard_version", + "rank": 654, + "alias": "oxytetracycline_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46316,10 +47939,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinicacid_testing_standard_details": { - "name": "oxolinicacid_testing_standard_details", + "oxytetracycline_testing_standard_details": { + "name": "oxytetracycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "oxolinic-acid_testing_standard_details", + "title": "oxytetracycline_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -46332,8 +47955,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 626, - "alias": "oxolinicacid_testing_standard_details", + "rank": 655, + "alias": "oxytetracycline_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46341,10 +47964,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinicacid_susceptible_breakpoint": { - "name": "oxolinicacid_susceptible_breakpoint", + "oxytetracycline_susceptible_breakpoint": { + "name": "oxytetracycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "oxolinic-acid_susceptible_breakpoint", + "title": "oxytetracycline_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -46354,8 +47977,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 627, - "alias": "oxolinicacid_susceptible_breakpoint", + "rank": 656, + "alias": "oxytetracycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46363,18 +47986,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinicacid_intermediate_breakpoint": { - "name": "oxolinicacid_intermediate_breakpoint", + "oxytetracycline_intermediate_breakpoint": { + "name": "oxytetracycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "oxolinic-acid_intermediate_breakpoint", + "title": "oxytetracycline_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 628, - "alias": "oxolinicacid_intermediate_breakpoint", + "rank": 657, + "alias": "oxytetracycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46382,10 +48005,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinicacid_resistant_breakpoint": { - "name": "oxolinicacid_resistant_breakpoint", + "oxytetracycline_resistant_breakpoint": { + "name": "oxytetracycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "oxolinic-acid_resistant_breakpoint", + "title": "oxytetracycline_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -46395,8 +48018,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 629, - "alias": "oxolinicacid_resistant_breakpoint", + "rank": 658, + "alias": "oxytetracycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46404,10 +48027,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxytetracycline_resistance_phenotype": { - "name": "oxytetracycline_resistance_phenotype", + "penicillin_resistance_phenotype": { + "name": "penicillin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "oxytetracycline_resistance_phenotype", + "title": "penicillin_resistance_phenotype", "comments": [ "Select a phenotype from the pick list provided." ], @@ -46417,11 +48040,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:resistance_phenotype" - ], - "rank": 630, - "alias": "oxytetracycline_resistance_phenotype", + "rank": 659, + "alias": "penicillin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46437,10 +48057,10 @@ } ] }, - "oxytetracycline_measurement": { - "name": "oxytetracycline_measurement", - "description": "The measured value of oxytetracycline resistance.", - "title": "oxytetracycline_measurement", + "penicillin_measurement": { + "name": "penicillin_measurement", + "description": "The measured value of penicillin resistance.", + "title": "penicillin_measurement", "comments": [ "This field should only contain a number (either an integer or a number with decimals)." ], @@ -46450,11 +48070,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement" - ], - "rank": 631, - "alias": "oxytetracycline_measurement", + "rank": 660, + "alias": "penicillin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46470,10 +48087,10 @@ } ] }, - "oxytetracycline_measurement_units": { - "name": "oxytetracycline_measurement_units", + "penicillin_measurement_units": { + "name": "penicillin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", - "title": "oxytetracycline_measurement_units", + "title": "penicillin_measurement_units", "comments": [ "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." ], @@ -46483,11 +48100,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_units" - ], - "rank": 632, - "alias": "oxytetracycline_measurement_units", + "rank": 661, + "alias": "penicillin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46503,10 +48117,10 @@ } ] }, - "oxytetracycline_measurement_sign": { - "name": "oxytetracycline_measurement_sign", + "penicillin_measurement_sign": { + "name": "penicillin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "oxytetracycline_measurement_sign", + "title": "penicillin_measurement_sign", "comments": [ "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." ], @@ -46516,11 +48130,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:measurement_sign" - ], - "rank": 633, - "alias": "oxytetracycline_measurement_sign", + "rank": 662, + "alias": "penicillin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46536,10 +48147,10 @@ } ] }, - "oxytetracycline_laboratory_typing_method": { - "name": "oxytetracycline_laboratory_typing_method", + "penicillin_laboratory_typing_method": { + "name": "penicillin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", - "title": "oxytetracycline_laboratory_typing_method", + "title": "penicillin_laboratory_typing_method", "comments": [ "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." ], @@ -46549,11 +48160,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_method" - ], - "rank": 634, - "alias": "oxytetracycline_laboratory_typing_method", + "rank": 663, + "alias": "penicillin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46568,10 +48176,10 @@ } ] }, - "oxytetracycline_laboratory_typing_platform": { - "name": "oxytetracycline_laboratory_typing_platform", + "penicillin_laboratory_typing_platform": { + "name": "penicillin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "oxytetracycline_laboratory_typing_platform", + "title": "penicillin_laboratory_typing_platform", "comments": [ "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." ], @@ -46581,11 +48189,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:laboratory_typing_platform" - ], - "rank": 635, - "alias": "oxytetracycline_laboratory_typing_platform", + "rank": 664, + "alias": "penicillin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46600,10 +48205,10 @@ } ] }, - "oxytetracycline_laboratory_typing_platform_version": { - "name": "oxytetracycline_laboratory_typing_platform_version", + "penicillin_laboratory_typing_platform_version": { + "name": "penicillin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "oxytetracycline_laboratory_typing_platform_version", + "title": "penicillin_laboratory_typing_platform_version", "comments": [ "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." ], @@ -46613,8 +48218,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 636, - "alias": "oxytetracycline_laboratory_typing_platform_version", + "rank": 665, + "alias": "penicillin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46622,10 +48227,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxytetracycline_vendor_name": { - "name": "oxytetracycline_vendor_name", + "penicillin_vendor_name": { + "name": "penicillin_vendor_name", "description": "The name of the vendor of the testing platform used.", - "title": "oxytetracycline_vendor_name", + "title": "penicillin_vendor_name", "comments": [ "Provide the full name of the company (avoid abbreviations)." ], @@ -46635,11 +48240,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:vendor" - ], - "rank": 637, - "alias": "oxytetracycline_vendor_name", + "rank": 666, + "alias": "penicillin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46654,10 +48256,10 @@ } ] }, - "oxytetracycline_testing_standard": { - "name": "oxytetracycline_testing_standard", + "penicillin_testing_standard": { + "name": "penicillin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", - "title": "oxytetracycline_testing_standard", + "title": "penicillin_testing_standard", "comments": [ "Select a testing standard from the pick list provided." ], @@ -46667,11 +48269,8 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:testing_standard" - ], - "rank": 638, - "alias": "oxytetracycline_testing_standard", + "rank": 667, + "alias": "penicillin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46687,10 +48286,10 @@ } ] }, - "oxytetracycline_testing_standard_version": { - "name": "oxytetracycline_testing_standard_version", + "penicillin_testing_standard_version": { + "name": "penicillin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", - "title": "oxytetracycline_testing_standard_version", + "title": "penicillin_testing_standard_version", "comments": [ "If applicable, include a version number for the testing standard used." ], @@ -46700,8 +48299,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 639, - "alias": "oxytetracycline_testing_standard_version", + "rank": 668, + "alias": "penicillin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46709,10 +48308,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxytetracycline_testing_standard_details": { - "name": "oxytetracycline_testing_standard_details", + "penicillin_testing_standard_details": { + "name": "penicillin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "oxytetracycline_testing_standard_details", + "title": "penicillin_testing_standard_details", "comments": [ "This information may include the year or location where the testing standard was published. If not applicable, leave blank." ], @@ -46725,8 +48324,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 640, - "alias": "oxytetracycline_testing_standard_details", + "rank": 669, + "alias": "penicillin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46734,10 +48333,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxytetracycline_susceptible_breakpoint": { - "name": "oxytetracycline_susceptible_breakpoint", + "penicillin_susceptible_breakpoint": { + "name": "penicillin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", - "title": "oxytetracycline_susceptible_breakpoint", + "title": "penicillin_susceptible_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." ], @@ -46747,8 +48346,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 641, - "alias": "oxytetracycline_susceptible_breakpoint", + "rank": 670, + "alias": "penicillin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46756,18 +48355,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxytetracycline_intermediate_breakpoint": { - "name": "oxytetracycline_intermediate_breakpoint", + "penicillin_intermediate_breakpoint": { + "name": "penicillin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", - "title": "oxytetracycline_intermediate_breakpoint", + "title": "penicillin_intermediate_breakpoint", "examples": [ { "value": "16" } ], "from_schema": "https://example.com/GRDI", - "rank": 642, - "alias": "oxytetracycline_intermediate_breakpoint", + "rank": 671, + "alias": "penicillin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46775,10 +48374,10 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxytetracycline_resistant_breakpoint": { - "name": "oxytetracycline_resistant_breakpoint", + "penicillin_resistant_breakpoint": { + "name": "penicillin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", - "title": "oxytetracycline_resistant_breakpoint", + "title": "penicillin_resistant_breakpoint", "comments": [ "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." ], @@ -46788,8 +48387,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 643, - "alias": "oxytetracycline_resistant_breakpoint", + "rank": 672, + "alias": "penicillin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -46813,7 +48412,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 644, + "rank": 673, "alias": "piperacillin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -46846,7 +48445,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 645, + "rank": 674, "alias": "piperacillin_measurement", "owner": "GRDI", "domain_of": [ @@ -46879,7 +48478,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 646, + "rank": 675, "alias": "piperacillin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -46912,7 +48511,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 647, + "rank": 676, "alias": "piperacillin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -46945,7 +48544,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 648, + "rank": 677, "alias": "piperacillin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -46977,7 +48576,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 649, + "rank": 678, "alias": "piperacillin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -47006,7 +48605,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 650, + "rank": 679, "alias": "piperacillin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -47031,7 +48630,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 651, + "rank": 680, "alias": "piperacillin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -47063,7 +48662,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 652, + "rank": 681, "alias": "piperacillin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -47093,7 +48692,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 653, + "rank": 682, "alias": "piperacillin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -47118,7 +48717,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 654, + "rank": 683, "alias": "piperacillin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -47140,7 +48739,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 655, + "rank": 684, "alias": "piperacillin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47159,7 +48758,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 656, + "rank": 685, "alias": "piperacillin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47181,7 +48780,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 657, + "rank": 686, "alias": "piperacillin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47206,7 +48805,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 658, + "rank": 687, "alias": "piperacillintazobactam_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -47239,7 +48838,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 659, + "rank": 688, "alias": "piperacillintazobactam_measurement", "owner": "GRDI", "domain_of": [ @@ -47272,7 +48871,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 660, + "rank": 689, "alias": "piperacillintazobactam_measurement_units", "owner": "GRDI", "domain_of": [ @@ -47305,7 +48904,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 661, + "rank": 690, "alias": "piperacillintazobactam_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -47338,7 +48937,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 662, + "rank": 691, "alias": "piperacillintazobactam_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -47370,7 +48969,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 663, + "rank": 692, "alias": "piperacillintazobactam_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -47399,7 +48998,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 664, + "rank": 693, "alias": "piperacillintazobactam_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -47424,7 +49023,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 665, + "rank": 694, "alias": "piperacillintazobactam_vendor_name", "owner": "GRDI", "domain_of": [ @@ -47456,7 +49055,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 666, + "rank": 695, "alias": "piperacillintazobactam_testing_standard", "owner": "GRDI", "domain_of": [ @@ -47486,7 +49085,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 667, + "rank": 696, "alias": "piperacillintazobactam_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -47511,7 +49110,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 668, + "rank": 697, "alias": "piperacillintazobactam_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -47533,7 +49132,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 669, + "rank": 698, "alias": "piperacillintazobactam_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47552,7 +49151,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 670, + "rank": 699, "alias": "piperacillintazobactam_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47574,7 +49173,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 671, + "rank": 700, "alias": "piperacillintazobactam_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47599,7 +49198,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 672, + "rank": 701, "alias": "polymyxinb_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -47632,7 +49231,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 673, + "rank": 702, "alias": "polymyxinb_measurement", "owner": "GRDI", "domain_of": [ @@ -47665,7 +49264,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 674, + "rank": 703, "alias": "polymyxinb_measurement_units", "owner": "GRDI", "domain_of": [ @@ -47698,7 +49297,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 675, + "rank": 704, "alias": "polymyxinb_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -47731,7 +49330,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 676, + "rank": 705, "alias": "polymyxinb_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -47763,7 +49362,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 677, + "rank": 706, "alias": "polymyxinb_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -47792,7 +49391,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 678, + "rank": 707, "alias": "polymyxinb_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -47817,7 +49416,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 679, + "rank": 708, "alias": "polymyxinb_vendor_name", "owner": "GRDI", "domain_of": [ @@ -47849,7 +49448,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 680, + "rank": 709, "alias": "polymyxinb_testing_standard", "owner": "GRDI", "domain_of": [ @@ -47879,7 +49478,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 681, + "rank": 710, "alias": "polymyxinb_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -47904,7 +49503,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 682, + "rank": 711, "alias": "polymyxinb_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -47926,7 +49525,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 683, + "rank": 712, "alias": "polymyxinb_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47945,7 +49544,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 684, + "rank": 713, "alias": "polymyxinb_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47967,7 +49566,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 685, + "rank": 714, "alias": "polymyxinb_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47992,7 +49591,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 686, + "rank": 715, "alias": "quinupristindalfopristin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -48025,7 +49624,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 687, + "rank": 716, "alias": "quinupristindalfopristin_measurement", "owner": "GRDI", "domain_of": [ @@ -48058,7 +49657,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 688, + "rank": 717, "alias": "quinupristindalfopristin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -48091,7 +49690,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 689, + "rank": 718, "alias": "quinupristindalfopristin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -48124,7 +49723,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 690, + "rank": 719, "alias": "quinupristindalfopristin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -48156,7 +49755,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 691, + "rank": 720, "alias": "quinupristindalfopristin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -48185,7 +49784,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 692, + "rank": 721, "alias": "quinupristindalfopristin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -48210,7 +49809,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 693, + "rank": 722, "alias": "quinupristindalfopristin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -48242,7 +49841,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 694, + "rank": 723, "alias": "quinupristindalfopristin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -48272,7 +49871,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 695, + "rank": 724, "alias": "quinupristindalfopristin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -48297,7 +49896,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 696, + "rank": 725, "alias": "quinupristindalfopristin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -48319,7 +49918,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 697, + "rank": 726, "alias": "quinupristindalfopristin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48338,7 +49937,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 698, + "rank": 727, "alias": "quinupristindalfopristin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48360,7 +49959,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 699, + "rank": 728, "alias": "quinupristindalfopristin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48385,7 +49984,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 700, + "rank": 729, "alias": "streptomycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -48418,7 +50017,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 701, + "rank": 730, "alias": "streptomycin_measurement", "owner": "GRDI", "domain_of": [ @@ -48451,7 +50050,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 702, + "rank": 731, "alias": "streptomycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -48484,7 +50083,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 703, + "rank": 732, "alias": "streptomycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -48517,7 +50116,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 704, + "rank": 733, "alias": "streptomycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -48549,7 +50148,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 705, + "rank": 734, "alias": "streptomycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -48578,7 +50177,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 706, + "rank": 735, "alias": "streptomycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -48603,7 +50202,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 707, + "rank": 736, "alias": "streptomycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -48635,7 +50234,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 708, + "rank": 737, "alias": "streptomycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -48665,7 +50264,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 709, + "rank": 738, "alias": "streptomycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -48690,7 +50289,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 710, + "rank": 739, "alias": "streptomycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -48712,7 +50311,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 711, + "rank": 740, "alias": "streptomycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48731,7 +50330,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 712, + "rank": 741, "alias": "streptomycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48753,7 +50352,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 713, + "rank": 742, "alias": "streptomycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48778,7 +50377,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 714, + "rank": 743, "alias": "sulfisoxazole_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -48811,7 +50410,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 715, + "rank": 744, "alias": "sulfisoxazole_measurement", "owner": "GRDI", "domain_of": [ @@ -48844,7 +50443,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 716, + "rank": 745, "alias": "sulfisoxazole_measurement_units", "owner": "GRDI", "domain_of": [ @@ -48877,7 +50476,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 717, + "rank": 746, "alias": "sulfisoxazole_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -48910,7 +50509,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 718, + "rank": 747, "alias": "sulfisoxazole_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -48942,7 +50541,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 719, + "rank": 748, "alias": "sulfisoxazole_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -48971,7 +50570,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 720, + "rank": 749, "alias": "sulfisoxazole_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -48996,7 +50595,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 721, + "rank": 750, "alias": "sulfisoxazole_vendor_name", "owner": "GRDI", "domain_of": [ @@ -49028,7 +50627,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 722, + "rank": 751, "alias": "sulfisoxazole_testing_standard", "owner": "GRDI", "domain_of": [ @@ -49058,7 +50657,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 723, + "rank": 752, "alias": "sulfisoxazole_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -49083,7 +50682,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 724, + "rank": 753, "alias": "sulfisoxazole_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -49105,7 +50704,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 725, + "rank": 754, "alias": "sulfisoxazole_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49124,7 +50723,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 726, + "rank": 755, "alias": "sulfisoxazole_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49146,7 +50745,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 727, + "rank": 756, "alias": "sulfisoxazole_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49171,7 +50770,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 728, + "rank": 757, "alias": "telithromycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -49204,7 +50803,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 729, + "rank": 758, "alias": "telithromycin_measurement", "owner": "GRDI", "domain_of": [ @@ -49237,7 +50836,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 730, + "rank": 759, "alias": "telithromycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -49270,7 +50869,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 731, + "rank": 760, "alias": "telithromycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -49303,7 +50902,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 732, + "rank": 761, "alias": "telithromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -49335,7 +50934,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 733, + "rank": 762, "alias": "telithromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -49364,7 +50963,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 734, + "rank": 763, "alias": "telithromycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -49389,7 +50988,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 735, + "rank": 764, "alias": "telithromycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -49421,7 +51020,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 736, + "rank": 765, "alias": "telithromycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -49451,7 +51050,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 737, + "rank": 766, "alias": "telithromycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -49476,7 +51075,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 738, + "rank": 767, "alias": "telithromycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -49498,7 +51097,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 739, + "rank": 768, "alias": "telithromycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49517,7 +51116,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 740, + "rank": 769, "alias": "telithromycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49539,7 +51138,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 741, + "rank": 770, "alias": "telithromycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49564,7 +51163,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 742, + "rank": 771, "alias": "tetracycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -49597,7 +51196,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 743, + "rank": 772, "alias": "tetracycline_measurement", "owner": "GRDI", "domain_of": [ @@ -49630,7 +51229,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 744, + "rank": 773, "alias": "tetracycline_measurement_units", "owner": "GRDI", "domain_of": [ @@ -49663,7 +51262,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 745, + "rank": 774, "alias": "tetracycline_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -49696,7 +51295,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 746, + "rank": 775, "alias": "tetracycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -49728,7 +51327,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 747, + "rank": 776, "alias": "tetracycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -49757,7 +51356,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 748, + "rank": 777, "alias": "tetracycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -49782,7 +51381,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 749, + "rank": 778, "alias": "tetracycline_vendor_name", "owner": "GRDI", "domain_of": [ @@ -49814,7 +51413,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 750, + "rank": 779, "alias": "tetracycline_testing_standard", "owner": "GRDI", "domain_of": [ @@ -49844,7 +51443,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 751, + "rank": 780, "alias": "tetracycline_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -49869,7 +51468,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 752, + "rank": 781, "alias": "tetracycline_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -49891,7 +51490,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 753, + "rank": 782, "alias": "tetracycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49910,7 +51509,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 754, + "rank": 783, "alias": "tetracycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49932,7 +51531,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 755, + "rank": 784, "alias": "tetracycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49957,7 +51556,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 756, + "rank": 785, "alias": "tigecycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -49990,7 +51589,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 757, + "rank": 786, "alias": "tigecycline_measurement", "owner": "GRDI", "domain_of": [ @@ -50023,7 +51622,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 758, + "rank": 787, "alias": "tigecycline_measurement_units", "owner": "GRDI", "domain_of": [ @@ -50056,7 +51655,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 759, + "rank": 788, "alias": "tigecycline_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -50089,7 +51688,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 760, + "rank": 789, "alias": "tigecycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -50121,7 +51720,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 761, + "rank": 790, "alias": "tigecycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -50150,7 +51749,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 762, + "rank": 791, "alias": "tigecycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -50175,7 +51774,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 763, + "rank": 792, "alias": "tigecycline_vendor_name", "owner": "GRDI", "domain_of": [ @@ -50207,7 +51806,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 764, + "rank": 793, "alias": "tigecycline_testing_standard", "owner": "GRDI", "domain_of": [ @@ -50237,7 +51836,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 765, + "rank": 794, "alias": "tigecycline_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -50262,7 +51861,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 766, + "rank": 795, "alias": "tigecycline_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -50284,7 +51883,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 767, + "rank": 796, "alias": "tigecycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -50303,7 +51902,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 768, + "rank": 797, "alias": "tigecycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -50325,7 +51924,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 769, + "rank": 798, "alias": "tigecycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -50350,7 +51949,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 770, + "rank": 799, "alias": "trimethoprimsulfamethoxazole_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -50383,7 +51982,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 771, + "rank": 800, "alias": "trimethoprimsulfamethoxazole_measurement", "owner": "GRDI", "domain_of": [ @@ -50416,7 +52015,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 772, + "rank": 801, "alias": "trimethoprimsulfamethoxazole_measurement_units", "owner": "GRDI", "domain_of": [ @@ -50449,7 +52048,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 773, + "rank": 802, "alias": "trimethoprimsulfamethoxazole_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -50482,7 +52081,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 774, + "rank": 803, "alias": "trimethoprimsulfamethoxazole_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -50514,7 +52113,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 775, + "rank": 804, "alias": "trimethoprimsulfamethoxazole_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -50543,7 +52142,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 776, + "rank": 805, "alias": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -50568,7 +52167,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 777, + "rank": 806, "alias": "trimethoprimsulfamethoxazole_vendor_name", "owner": "GRDI", "domain_of": [ @@ -50600,7 +52199,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 778, + "rank": 807, "alias": "trimethoprimsulfamethoxazole_testing_standard", "owner": "GRDI", "domain_of": [ @@ -50630,7 +52229,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 779, + "rank": 808, "alias": "trimethoprimsulfamethoxazole_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -50655,7 +52254,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 780, + "rank": 809, "alias": "trimethoprimsulfamethoxazole_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -50677,7 +52276,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 781, + "rank": 810, "alias": "trimethoprimsulfamethoxazole_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -50696,7 +52295,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 782, + "rank": 811, "alias": "trimethoprimsulfamethoxazole_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -50718,7 +52317,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 783, + "rank": 812, "alias": "trimethoprimsulfamethoxazole_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -50740,7 +52339,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 784, + "rank": 813, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "GRDI", @@ -50764,7 +52363,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 785, + "rank": 814, "slot_uri": "GENEPIO:0001518", "alias": "dataharmonizer_provenance", "owner": "GRDI", diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index e957906b..ada9d532 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -127,6 +127,7 @@ classes: - sequenced_by_contact_name - sequenced_by_contact_email - purpose_of_sequencing + - sequencing_date - sequencing_project_name - sequencing_platform - sequencing_instrument @@ -604,6 +605,20 @@ classes: - nalidixic_acid_susceptible_breakpoint - nalidixic_acid_intermediate_breakpoint - nalidixic_acid_resistant_breakpoint + - neomycin_resistance_phenotype + - neomycin_measurement + - neomycin_measurement_units + - neomycin_measurement_sign + - neomycin_laboratory_typing_method + - neomycin_laboratory_typing_platform + - neomycin_laboratory_typing_platform_version + - neomycin_vendor_name + - neomycin_testing_standard + - neomycin_testing_standard_version + - neomycin_testing_standard_details + - neomycin_susceptible_breakpoint + - neomycin_intermediate_breakpoint + - neomycin_resistant_breakpoint - nitrofurantoin_resistance_phenotype - nitrofurantoin_measurement - nitrofurantoin_measurement_units @@ -660,6 +675,20 @@ classes: - oxytetracycline_susceptible_breakpoint - oxytetracycline_intermediate_breakpoint - oxytetracycline_resistant_breakpoint + - penicillin_resistance_phenotype + - penicillin_measurement + - penicillin_measurement_units + - penicillin_measurement_sign + - penicillin_laboratory_typing_method + - penicillin_laboratory_typing_platform + - penicillin_laboratory_typing_platform_version + - penicillin_vendor_name + - penicillin_testing_standard + - penicillin_testing_standard_version + - penicillin_testing_standard_details + - penicillin_susceptible_breakpoint + - penicillin_intermediate_breakpoint + - penicillin_resistant_breakpoint - piperacillin_resistance_phenotype - piperacillin_measurement - piperacillin_measurement_units @@ -1133,2030 +1162,2117 @@ classes: purpose_of_sequencing: rank: 110 slot_group: Sequence information - sequencing_project_name: + sequencing_date: rank: 111 slot_group: Sequence information - sequencing_platform: + sequencing_project_name: rank: 112 slot_group: Sequence information - sequencing_instrument: + sequencing_platform: rank: 113 slot_group: Sequence information - sequencing_assay_type: + sequencing_instrument: rank: 114 slot_group: Sequence information - library_preparation_kit: + sequencing_assay_type: rank: 115 slot_group: Sequence information - dna_fragment_length: + library_preparation_kit: rank: 116 slot_group: Sequence information - genomic_target_enrichment_method: + dna_fragment_length: rank: 117 slot_group: Sequence information - genomic_target_enrichment_method_details: + genomic_target_enrichment_method: rank: 118 slot_group: Sequence information - amplicon_pcr_primer_scheme: + genomic_target_enrichment_method_details: rank: 119 slot_group: Sequence information - amplicon_size: + amplicon_pcr_primer_scheme: rank: 120 slot_group: Sequence information - sequencing_flow_cell_version: + amplicon_size: rank: 121 slot_group: Sequence information - sequencing_protocol: + sequencing_flow_cell_version: rank: 122 slot_group: Sequence information - r1_fastq_filename: + sequencing_protocol: rank: 123 slot_group: Sequence information - r2_fastq_filename: + r1_fastq_filename: rank: 124 slot_group: Sequence information - fast5_filename: + r2_fastq_filename: rank: 125 slot_group: Sequence information - genome_sequence_filename: + fast5_filename: rank: 126 slot_group: Sequence information - quality_control_method_name: + genome_sequence_filename: rank: 127 + slot_group: Sequence information + quality_control_method_name: + rank: 128 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 128 + rank: 129 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 129 + rank: 130 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 130 + rank: 131 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 131 + rank: 132 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 132 + rank: 133 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 133 + rank: 134 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 134 + rank: 135 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 135 + rank: 136 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 136 + rank: 137 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 137 + rank: 138 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 138 + rank: 139 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 139 + rank: 140 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 140 + rank: 141 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 141 + rank: 142 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 142 + rank: 143 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 143 + rank: 144 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 144 + rank: 145 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 145 + rank: 146 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 146 + rank: 147 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 147 + rank: 148 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 148 + rank: 149 slot_group: Bioinformatics and QC metrics n50: - rank: 149 + rank: 150 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 150 + rank: 151 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 151 + rank: 152 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 152 + rank: 153 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 153 + rank: 154 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 154 + rank: 155 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 155 + rank: 156 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 156 + rank: 157 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 157 + rank: 158 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 158 + rank: 159 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 159 + rank: 160 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 160 + rank: 161 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 161 + rank: 162 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 162 + rank: 163 slot_group: Taxonomic identification information sequence_submitted_by: - rank: 163 + rank: 164 slot_group: Public repository information sequence_submitted_by_contact_name: - rank: 164 + rank: 165 slot_group: Public repository information sequence_submitted_by_contact_email: - rank: 165 + rank: 166 slot_group: Public repository information publication_id: - rank: 166 + rank: 167 slot_group: Public repository information attribute_package: - rank: 167 + rank: 168 slot_group: Public repository information bioproject_accession: - rank: 168 + rank: 169 slot_group: Public repository information biosample_accession: - rank: 169 + rank: 170 slot_group: Public repository information sra_accession: - rank: 170 + rank: 171 slot_group: Public repository information genbank_accession: - rank: 171 + rank: 172 slot_group: Public repository information prevalence_metrics: - rank: 172 + rank: 173 slot_group: Risk assessment information prevalence_metrics_details: - rank: 173 + rank: 174 slot_group: Risk assessment information stage_of_production: - rank: 174 + rank: 175 slot_group: Risk assessment information experimental_intervention: - rank: 175 + rank: 176 slot_group: Risk assessment information experiment_intervention_details: - rank: 176 + rank: 177 slot_group: Risk assessment information amr_testing_by: - rank: 177 + rank: 178 slot_group: Antimicrobial resistance amr_testing_by_laboratory_name: - rank: 178 + rank: 179 slot_group: Antimicrobial resistance amr_testing_by_contact_name: - rank: 179 + rank: 180 slot_group: Antimicrobial resistance amr_testing_by_contact_email: - rank: 180 + rank: 181 slot_group: Antimicrobial resistance amr_testing_date: - rank: 181 + rank: 182 slot_group: Antimicrobial resistance amikacin_resistance_phenotype: - rank: 182 + rank: 183 slot_group: Antimicrobial resistance amikacin_measurement: - rank: 183 + rank: 184 slot_group: Antimicrobial resistance amikacin_measurement_units: - rank: 184 + rank: 185 slot_group: Antimicrobial resistance amikacin_measurement_sign: - rank: 185 + rank: 186 slot_group: Antimicrobial resistance amikacin_laboratory_typing_method: - rank: 186 + rank: 187 slot_group: Antimicrobial resistance amikacin_laboratory_typing_platform: - rank: 187 + rank: 188 slot_group: Antimicrobial resistance amikacin_laboratory_typing_platform_version: - rank: 188 + rank: 189 slot_group: Antimicrobial resistance amikacin_vendor_name: - rank: 189 + rank: 190 slot_group: Antimicrobial resistance amikacin_testing_standard: - rank: 190 + rank: 191 slot_group: Antimicrobial resistance amikacin_testing_standard_version: - rank: 191 + rank: 192 slot_group: Antimicrobial resistance amikacin_testing_standard_details: - rank: 192 + rank: 193 slot_group: Antimicrobial resistance amikacin_susceptible_breakpoint: - rank: 193 + rank: 194 slot_group: Antimicrobial resistance amikacin_intermediate_breakpoint: - rank: 194 + rank: 195 slot_group: Antimicrobial resistance amikacin_resistant_breakpoint: - rank: 195 + rank: 196 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_resistance_phenotype: - rank: 196 + rank: 197 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_measurement: - rank: 197 + rank: 198 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_measurement_units: - rank: 198 + rank: 199 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_measurement_sign: - rank: 199 + rank: 200 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_laboratory_typing_method: - rank: 200 + rank: 201 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_laboratory_typing_platform: - rank: 201 + rank: 202 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_laboratory_typing_platform_version: - rank: 202 + rank: 203 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_vendor_name: - rank: 203 + rank: 204 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_testing_standard: - rank: 204 + rank: 205 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_testing_standard_version: - rank: 205 + rank: 206 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_testing_standard_details: - rank: 206 + rank: 207 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_susceptible_breakpoint: - rank: 207 + rank: 208 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_intermediate_breakpoint: - rank: 208 + rank: 209 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_resistant_breakpoint: - rank: 209 + rank: 210 slot_group: Antimicrobial resistance ampicillin_resistance_phenotype: - rank: 210 + rank: 211 slot_group: Antimicrobial resistance ampicillin_measurement: - rank: 211 + rank: 212 slot_group: Antimicrobial resistance ampicillin_measurement_units: - rank: 212 + rank: 213 slot_group: Antimicrobial resistance ampicillin_measurement_sign: - rank: 213 + rank: 214 slot_group: Antimicrobial resistance ampicillin_laboratory_typing_method: - rank: 214 + rank: 215 slot_group: Antimicrobial resistance ampicillin_laboratory_typing_platform: - rank: 215 + rank: 216 slot_group: Antimicrobial resistance ampicillin_laboratory_typing_platform_version: - rank: 216 + rank: 217 slot_group: Antimicrobial resistance ampicillin_vendor_name: - rank: 217 + rank: 218 slot_group: Antimicrobial resistance ampicillin_testing_standard: - rank: 218 + rank: 219 slot_group: Antimicrobial resistance ampicillin_testing_standard_version: - rank: 219 + rank: 220 slot_group: Antimicrobial resistance ampicillin_testing_standard_details: - rank: 220 + rank: 221 slot_group: Antimicrobial resistance ampicillin_susceptible_breakpoint: - rank: 221 + rank: 222 slot_group: Antimicrobial resistance ampicillin_intermediate_breakpoint: - rank: 222 + rank: 223 slot_group: Antimicrobial resistance ampicillin_resistant_breakpoint: - rank: 223 + rank: 224 slot_group: Antimicrobial resistance azithromycin_resistance_phenotype: - rank: 224 + rank: 225 slot_group: Antimicrobial resistance azithromycin_measurement: - rank: 225 + rank: 226 slot_group: Antimicrobial resistance azithromycin_measurement_units: - rank: 226 + rank: 227 slot_group: Antimicrobial resistance azithromycin_measurement_sign: - rank: 227 + rank: 228 slot_group: Antimicrobial resistance azithromycin_laboratory_typing_method: - rank: 228 + rank: 229 slot_group: Antimicrobial resistance azithromycin_laboratory_typing_platform: - rank: 229 + rank: 230 slot_group: Antimicrobial resistance azithromycin_laboratory_typing_platform_version: - rank: 230 + rank: 231 slot_group: Antimicrobial resistance azithromycin_vendor_name: - rank: 231 + rank: 232 slot_group: Antimicrobial resistance azithromycin_testing_standard: - rank: 232 + rank: 233 slot_group: Antimicrobial resistance azithromycin_testing_standard_version: - rank: 233 + rank: 234 slot_group: Antimicrobial resistance azithromycin_testing_standard_details: - rank: 234 + rank: 235 slot_group: Antimicrobial resistance azithromycin_susceptible_breakpoint: - rank: 235 + rank: 236 slot_group: Antimicrobial resistance azithromycin_intermediate_breakpoint: - rank: 236 + rank: 237 slot_group: Antimicrobial resistance azithromycin_resistant_breakpoint: - rank: 237 + rank: 238 slot_group: Antimicrobial resistance cefazolin_resistance_phenotype: - rank: 238 + rank: 239 slot_group: Antimicrobial resistance cefazolin_measurement: - rank: 239 + rank: 240 slot_group: Antimicrobial resistance cefazolin_measurement_units: - rank: 240 + rank: 241 slot_group: Antimicrobial resistance cefazolin_measurement_sign: - rank: 241 + rank: 242 slot_group: Antimicrobial resistance cefazolin_laboratory_typing_method: - rank: 242 + rank: 243 slot_group: Antimicrobial resistance cefazolin_laboratory_typing_platform: - rank: 243 + rank: 244 slot_group: Antimicrobial resistance cefazolin_laboratory_typing_platform_version: - rank: 244 + rank: 245 slot_group: Antimicrobial resistance cefazolin_vendor_name: - rank: 245 + rank: 246 slot_group: Antimicrobial resistance cefazolin_testing_standard: - rank: 246 + rank: 247 slot_group: Antimicrobial resistance cefazolin_testing_standard_version: - rank: 247 + rank: 248 slot_group: Antimicrobial resistance cefazolin_testing_standard_details: - rank: 248 + rank: 249 slot_group: Antimicrobial resistance cefazolin_susceptible_breakpoint: - rank: 249 + rank: 250 slot_group: Antimicrobial resistance cefazolin_intermediate_breakpoint: - rank: 250 + rank: 251 slot_group: Antimicrobial resistance cefazolin_resistant_breakpoint: - rank: 251 + rank: 252 slot_group: Antimicrobial resistance cefepime_resistance_phenotype: - rank: 252 + rank: 253 slot_group: Antimicrobial resistance cefepime_measurement: - rank: 253 + rank: 254 slot_group: Antimicrobial resistance cefepime_measurement_units: - rank: 254 + rank: 255 slot_group: Antimicrobial resistance cefepime_measurement_sign: - rank: 255 + rank: 256 slot_group: Antimicrobial resistance cefepime_laboratory_typing_method: - rank: 256 + rank: 257 slot_group: Antimicrobial resistance cefepime_laboratory_typing_platform: - rank: 257 + rank: 258 slot_group: Antimicrobial resistance cefepime_laboratory_typing_platform_version: - rank: 258 + rank: 259 slot_group: Antimicrobial resistance cefepime_vendor_name: - rank: 259 + rank: 260 slot_group: Antimicrobial resistance cefepime_testing_standard: - rank: 260 + rank: 261 slot_group: Antimicrobial resistance cefepime_testing_standard_version: - rank: 261 + rank: 262 slot_group: Antimicrobial resistance cefepime_testing_standard_details: - rank: 262 + rank: 263 slot_group: Antimicrobial resistance cefepime_susceptible_breakpoint: - rank: 263 + rank: 264 slot_group: Antimicrobial resistance cefepime_intermediate_breakpoint: - rank: 264 + rank: 265 slot_group: Antimicrobial resistance cefepime_resistant_breakpoint: - rank: 265 + rank: 266 slot_group: Antimicrobial resistance cefotaxime_resistance_phenotype: - rank: 266 + rank: 267 slot_group: Antimicrobial resistance cefotaxime_measurement: - rank: 267 + rank: 268 slot_group: Antimicrobial resistance cefotaxime_measurement_units: - rank: 268 + rank: 269 slot_group: Antimicrobial resistance cefotaxime_measurement_sign: - rank: 269 + rank: 270 slot_group: Antimicrobial resistance cefotaxime_laboratory_typing_method: - rank: 270 + rank: 271 slot_group: Antimicrobial resistance cefotaxime_laboratory_typing_platform: - rank: 271 + rank: 272 slot_group: Antimicrobial resistance cefotaxime_laboratory_typing_platform_version: - rank: 272 + rank: 273 slot_group: Antimicrobial resistance cefotaxime_vendor_name: - rank: 273 + rank: 274 slot_group: Antimicrobial resistance cefotaxime_testing_standard: - rank: 274 + rank: 275 slot_group: Antimicrobial resistance cefotaxime_testing_standard_version: - rank: 275 + rank: 276 slot_group: Antimicrobial resistance cefotaxime_testing_standard_details: - rank: 276 + rank: 277 slot_group: Antimicrobial resistance cefotaxime_susceptible_breakpoint: - rank: 277 + rank: 278 slot_group: Antimicrobial resistance cefotaxime_intermediate_breakpoint: - rank: 278 + rank: 279 slot_group: Antimicrobial resistance cefotaxime_resistant_breakpoint: - rank: 279 + rank: 280 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_resistance_phenotype: - rank: 280 + rank: 281 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_measurement: - rank: 281 + rank: 282 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_measurement_units: - rank: 282 + rank: 283 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_measurement_sign: - rank: 283 + rank: 284 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_laboratory_typing_method: - rank: 284 + rank: 285 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_laboratory_typing_platform: - rank: 285 + rank: 286 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_laboratory_typing_platform_version: - rank: 286 + rank: 287 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_vendor_name: - rank: 287 + rank: 288 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_testing_standard: - rank: 288 + rank: 289 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_testing_standard_version: - rank: 289 + rank: 290 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_testing_standard_details: - rank: 290 + rank: 291 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_susceptible_breakpoint: - rank: 291 + rank: 292 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_intermediate_breakpoint: - rank: 292 + rank: 293 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_resistant_breakpoint: - rank: 293 + rank: 294 slot_group: Antimicrobial resistance cefoxitin_resistance_phenotype: - rank: 294 + rank: 295 slot_group: Antimicrobial resistance cefoxitin_measurement: - rank: 295 + rank: 296 slot_group: Antimicrobial resistance cefoxitin_measurement_units: - rank: 296 + rank: 297 slot_group: Antimicrobial resistance cefoxitin_measurement_sign: - rank: 297 + rank: 298 slot_group: Antimicrobial resistance cefoxitin_laboratory_typing_method: - rank: 298 + rank: 299 slot_group: Antimicrobial resistance cefoxitin_laboratory_typing_platform: - rank: 299 + rank: 300 slot_group: Antimicrobial resistance cefoxitin_laboratory_typing_platform_version: - rank: 300 + rank: 301 slot_group: Antimicrobial resistance cefoxitin_vendor_name: - rank: 301 + rank: 302 slot_group: Antimicrobial resistance cefoxitin_testing_standard: - rank: 302 + rank: 303 slot_group: Antimicrobial resistance cefoxitin_testing_standard_version: - rank: 303 + rank: 304 slot_group: Antimicrobial resistance cefoxitin_testing_standard_details: - rank: 304 + rank: 305 slot_group: Antimicrobial resistance cefoxitin_susceptible_breakpoint: - rank: 305 + rank: 306 slot_group: Antimicrobial resistance cefoxitin_intermediate_breakpoint: - rank: 306 + rank: 307 slot_group: Antimicrobial resistance cefoxitin_resistant_breakpoint: - rank: 307 + rank: 308 slot_group: Antimicrobial resistance cefpodoxime_resistance_phenotype: - rank: 308 + rank: 309 slot_group: Antimicrobial resistance cefpodoxime_measurement: - rank: 309 + rank: 310 slot_group: Antimicrobial resistance cefpodoxime_measurement_units: - rank: 310 + rank: 311 slot_group: Antimicrobial resistance cefpodoxime_measurement_sign: - rank: 311 + rank: 312 slot_group: Antimicrobial resistance cefpodoxime_laboratory_typing_method: - rank: 312 + rank: 313 slot_group: Antimicrobial resistance cefpodoxime_laboratory_typing_platform: - rank: 313 + rank: 314 slot_group: Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version: - rank: 314 + rank: 315 slot_group: Antimicrobial resistance cefpodoxime_vendor_name: - rank: 315 + rank: 316 slot_group: Antimicrobial resistance cefpodoxime_testing_standard: - rank: 316 + rank: 317 slot_group: Antimicrobial resistance cefpodoxime_testing_standard_version: - rank: 317 + rank: 318 slot_group: Antimicrobial resistance cefpodoxime_testing_standard_details: - rank: 318 + rank: 319 slot_group: Antimicrobial resistance cefpodoxime_susceptible_breakpoint: - rank: 319 + rank: 320 slot_group: Antimicrobial resistance cefpodoxime_intermediate_breakpoint: - rank: 320 + rank: 321 slot_group: Antimicrobial resistance cefpodoxime_resistant_breakpoint: - rank: 321 + rank: 322 slot_group: Antimicrobial resistance ceftazidime_resistance_phenotype: - rank: 322 + rank: 323 slot_group: Antimicrobial resistance ceftazidime_measurement: - rank: 323 + rank: 324 slot_group: Antimicrobial resistance ceftazidime_measurement_units: - rank: 324 + rank: 325 slot_group: Antimicrobial resistance ceftazidime_measurement_sign: - rank: 325 + rank: 326 slot_group: Antimicrobial resistance ceftazidime_laboratory_typing_method: - rank: 326 + rank: 327 slot_group: Antimicrobial resistance ceftazidime_laboratory_typing_platform: - rank: 327 + rank: 328 slot_group: Antimicrobial resistance ceftazidime_laboratory_typing_platform_version: - rank: 328 + rank: 329 slot_group: Antimicrobial resistance ceftazidime_vendor_name: - rank: 329 + rank: 330 slot_group: Antimicrobial resistance ceftazidime_testing_standard: - rank: 330 + rank: 331 slot_group: Antimicrobial resistance ceftazidime_testing_standard_version: - rank: 331 + rank: 332 slot_group: Antimicrobial resistance ceftazidime_testing_standard_details: - rank: 332 + rank: 333 slot_group: Antimicrobial resistance ceftazidime_susceptible_breakpoint: - rank: 333 + rank: 334 slot_group: Antimicrobial resistance ceftazidime_intermediate_breakpoint: - rank: 334 + rank: 335 slot_group: Antimicrobial resistance ceftazidime_resistant_breakpoint: - rank: 335 + rank: 336 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_resistance_phenotype: - rank: 336 + rank: 337 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_measurement: - rank: 337 + rank: 338 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_measurement_units: - rank: 338 + rank: 339 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_measurement_sign: - rank: 339 + rank: 340 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_laboratory_typing_method: - rank: 340 + rank: 341 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_laboratory_typing_platform: - rank: 341 + rank: 342 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_laboratory_typing_platform_version: - rank: 342 + rank: 343 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_vendor_name: - rank: 343 + rank: 344 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_testing_standard: - rank: 344 + rank: 345 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_testing_standard_version: - rank: 345 + rank: 346 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_testing_standard_details: - rank: 346 + rank: 347 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_susceptible_breakpoint: - rank: 347 + rank: 348 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_intermediate_breakpoint: - rank: 348 + rank: 349 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_resistant_breakpoint: - rank: 349 + rank: 350 slot_group: Antimicrobial resistance ceftiofur_resistance_phenotype: - rank: 350 + rank: 351 slot_group: Antimicrobial resistance ceftiofur_measurement: - rank: 351 + rank: 352 slot_group: Antimicrobial resistance ceftiofur_measurement_units: - rank: 352 + rank: 353 slot_group: Antimicrobial resistance ceftiofur_measurement_sign: - rank: 353 + rank: 354 slot_group: Antimicrobial resistance ceftiofur_laboratory_typing_method: - rank: 354 + rank: 355 slot_group: Antimicrobial resistance ceftiofur_laboratory_typing_platform: - rank: 355 + rank: 356 slot_group: Antimicrobial resistance ceftiofur_laboratory_typing_platform_version: - rank: 356 + rank: 357 slot_group: Antimicrobial resistance ceftiofur_vendor_name: - rank: 357 + rank: 358 slot_group: Antimicrobial resistance ceftiofur_testing_standard: - rank: 358 + rank: 359 slot_group: Antimicrobial resistance ceftiofur_testing_standard_version: - rank: 359 + rank: 360 slot_group: Antimicrobial resistance ceftiofur_testing_standard_details: - rank: 360 + rank: 361 slot_group: Antimicrobial resistance ceftiofur_susceptible_breakpoint: - rank: 361 + rank: 362 slot_group: Antimicrobial resistance ceftiofur_intermediate_breakpoint: - rank: 362 + rank: 363 slot_group: Antimicrobial resistance ceftiofur_resistant_breakpoint: - rank: 363 + rank: 364 slot_group: Antimicrobial resistance ceftriaxone_resistance_phenotype: - rank: 364 + rank: 365 slot_group: Antimicrobial resistance ceftriaxone_measurement: - rank: 365 + rank: 366 slot_group: Antimicrobial resistance ceftriaxone_measurement_units: - rank: 366 + rank: 367 slot_group: Antimicrobial resistance ceftriaxone_measurement_sign: - rank: 367 + rank: 368 slot_group: Antimicrobial resistance ceftriaxone_laboratory_typing_method: - rank: 368 + rank: 369 slot_group: Antimicrobial resistance ceftriaxone_laboratory_typing_platform: - rank: 369 + rank: 370 slot_group: Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version: - rank: 370 + rank: 371 slot_group: Antimicrobial resistance ceftriaxone_vendor_name: - rank: 371 + rank: 372 slot_group: Antimicrobial resistance ceftriaxone_testing_standard: - rank: 372 + rank: 373 slot_group: Antimicrobial resistance ceftriaxone_testing_standard_version: - rank: 373 + rank: 374 slot_group: Antimicrobial resistance ceftriaxone_testing_standard_details: - rank: 374 + rank: 375 slot_group: Antimicrobial resistance ceftriaxone_susceptible_breakpoint: - rank: 375 + rank: 376 slot_group: Antimicrobial resistance ceftriaxone_intermediate_breakpoint: - rank: 376 + rank: 377 slot_group: Antimicrobial resistance ceftriaxone_resistant_breakpoint: - rank: 377 + rank: 378 slot_group: Antimicrobial resistance cephalothin_resistance_phenotype: - rank: 378 + rank: 379 slot_group: Antimicrobial resistance cephalothin_measurement: - rank: 379 + rank: 380 slot_group: Antimicrobial resistance cephalothin_measurement_units: - rank: 380 + rank: 381 slot_group: Antimicrobial resistance cephalothin_measurement_sign: - rank: 381 + rank: 382 slot_group: Antimicrobial resistance cephalothin_laboratory_typing_method: - rank: 382 + rank: 383 slot_group: Antimicrobial resistance cephalothin_laboratory_typing_platform: - rank: 383 + rank: 384 slot_group: Antimicrobial resistance cephalothin_laboratory_typing_platform_version: - rank: 384 + rank: 385 slot_group: Antimicrobial resistance cephalothin_vendor_name: - rank: 385 + rank: 386 slot_group: Antimicrobial resistance cephalothin_testing_standard: - rank: 386 + rank: 387 slot_group: Antimicrobial resistance cephalothin_testing_standard_version: - rank: 387 + rank: 388 slot_group: Antimicrobial resistance cephalothin_testing_standard_details: - rank: 388 + rank: 389 slot_group: Antimicrobial resistance cephalothin_susceptible_breakpoint: - rank: 389 + rank: 390 slot_group: Antimicrobial resistance cephalothin_intermediate_breakpoint: - rank: 390 + rank: 391 slot_group: Antimicrobial resistance cephalothin_resistant_breakpoint: - rank: 391 + rank: 392 slot_group: Antimicrobial resistance chloramphenicol_resistance_phenotype: - rank: 392 + rank: 393 slot_group: Antimicrobial resistance chloramphenicol_measurement: - rank: 393 + rank: 394 slot_group: Antimicrobial resistance chloramphenicol_measurement_units: - rank: 394 + rank: 395 slot_group: Antimicrobial resistance chloramphenicol_measurement_sign: - rank: 395 + rank: 396 slot_group: Antimicrobial resistance chloramphenicol_laboratory_typing_method: - rank: 396 + rank: 397 slot_group: Antimicrobial resistance chloramphenicol_laboratory_typing_platform: - rank: 397 + rank: 398 slot_group: Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version: - rank: 398 + rank: 399 slot_group: Antimicrobial resistance chloramphenicol_vendor_name: - rank: 399 + rank: 400 slot_group: Antimicrobial resistance chloramphenicol_testing_standard: - rank: 400 + rank: 401 slot_group: Antimicrobial resistance chloramphenicol_testing_standard_version: - rank: 401 + rank: 402 slot_group: Antimicrobial resistance chloramphenicol_testing_standard_details: - rank: 402 + rank: 403 slot_group: Antimicrobial resistance chloramphenicol_susceptible_breakpoint: - rank: 403 + rank: 404 slot_group: Antimicrobial resistance chloramphenicol_intermediate_breakpoint: - rank: 404 + rank: 405 slot_group: Antimicrobial resistance chloramphenicol_resistant_breakpoint: - rank: 405 + rank: 406 slot_group: Antimicrobial resistance ciprofloxacin_resistance_phenotype: - rank: 406 + rank: 407 slot_group: Antimicrobial resistance ciprofloxacin_measurement: - rank: 407 + rank: 408 slot_group: Antimicrobial resistance ciprofloxacin_measurement_units: - rank: 408 + rank: 409 slot_group: Antimicrobial resistance ciprofloxacin_measurement_sign: - rank: 409 + rank: 410 slot_group: Antimicrobial resistance ciprofloxacin_laboratory_typing_method: - rank: 410 + rank: 411 slot_group: Antimicrobial resistance ciprofloxacin_laboratory_typing_platform: - rank: 411 + rank: 412 slot_group: Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version: - rank: 412 + rank: 413 slot_group: Antimicrobial resistance ciprofloxacin_vendor_name: - rank: 413 + rank: 414 slot_group: Antimicrobial resistance ciprofloxacin_testing_standard: - rank: 414 + rank: 415 slot_group: Antimicrobial resistance ciprofloxacin_testing_standard_version: - rank: 415 + rank: 416 slot_group: Antimicrobial resistance ciprofloxacin_testing_standard_details: - rank: 416 + rank: 417 slot_group: Antimicrobial resistance ciprofloxacin_susceptible_breakpoint: - rank: 417 + rank: 418 slot_group: Antimicrobial resistance ciprofloxacin_intermediate_breakpoint: - rank: 418 + rank: 419 slot_group: Antimicrobial resistance ciprofloxacin_resistant_breakpoint: - rank: 419 + rank: 420 slot_group: Antimicrobial resistance clindamycin_resistance_phenotype: - rank: 420 + rank: 421 slot_group: Antimicrobial resistance clindamycin_measurement: - rank: 421 + rank: 422 slot_group: Antimicrobial resistance clindamycin_measurement_units: - rank: 422 + rank: 423 slot_group: Antimicrobial resistance clindamycin_measurement_sign: - rank: 423 + rank: 424 slot_group: Antimicrobial resistance clindamycin_laboratory_typing_method: - rank: 424 + rank: 425 slot_group: Antimicrobial resistance clindamycin_laboratory_typing_platform: - rank: 425 + rank: 426 slot_group: Antimicrobial resistance clindamycin_laboratory_typing_platform_version: - rank: 426 + rank: 427 slot_group: Antimicrobial resistance clindamycin_vendor_name: - rank: 427 + rank: 428 slot_group: Antimicrobial resistance clindamycin_testing_standard: - rank: 428 + rank: 429 slot_group: Antimicrobial resistance clindamycin_testing_standard_version: - rank: 429 + rank: 430 slot_group: Antimicrobial resistance clindamycin_testing_standard_details: - rank: 430 + rank: 431 slot_group: Antimicrobial resistance clindamycin_susceptible_breakpoint: - rank: 431 + rank: 432 slot_group: Antimicrobial resistance clindamycin_intermediate_breakpoint: - rank: 432 + rank: 433 slot_group: Antimicrobial resistance clindamycin_resistant_breakpoint: - rank: 433 + rank: 434 slot_group: Antimicrobial resistance doxycycline_resistance_phenotype: - rank: 434 + rank: 435 slot_group: Antimicrobial resistance doxycycline_measurement: - rank: 435 + rank: 436 slot_group: Antimicrobial resistance doxycycline_measurement_units: - rank: 436 + rank: 437 slot_group: Antimicrobial resistance doxycycline_measurement_sign: - rank: 437 + rank: 438 slot_group: Antimicrobial resistance doxycycline_laboratory_typing_method: - rank: 438 + rank: 439 slot_group: Antimicrobial resistance doxycycline_laboratory_typing_platform: - rank: 439 + rank: 440 slot_group: Antimicrobial resistance doxycycline_laboratory_typing_platform_version: - rank: 440 + rank: 441 slot_group: Antimicrobial resistance doxycycline_vendor_name: - rank: 441 + rank: 442 slot_group: Antimicrobial resistance doxycycline_testing_standard: - rank: 442 + rank: 443 slot_group: Antimicrobial resistance doxycycline_testing_standard_version: - rank: 443 + rank: 444 slot_group: Antimicrobial resistance doxycycline_testing_standard_details: - rank: 444 + rank: 445 slot_group: Antimicrobial resistance doxycycline_susceptible_breakpoint: - rank: 445 + rank: 446 slot_group: Antimicrobial resistance doxycycline_intermediate_breakpoint: - rank: 446 + rank: 447 slot_group: Antimicrobial resistance doxycycline_resistant_breakpoint: - rank: 447 + rank: 448 slot_group: Antimicrobial resistance enrofloxacin_resistance_phenotype: - rank: 448 + rank: 449 slot_group: Antimicrobial resistance enrofloxacin_measurement: - rank: 449 + rank: 450 slot_group: Antimicrobial resistance enrofloxacin_measurement_units: - rank: 450 + rank: 451 slot_group: Antimicrobial resistance enrofloxacin_measurement_sign: - rank: 451 + rank: 452 slot_group: Antimicrobial resistance enrofloxacin_laboratory_typing_method: - rank: 452 + rank: 453 slot_group: Antimicrobial resistance enrofloxacin_laboratory_typing_platform: - rank: 453 + rank: 454 slot_group: Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version: - rank: 454 + rank: 455 slot_group: Antimicrobial resistance enrofloxacin_vendor_name: - rank: 455 + rank: 456 slot_group: Antimicrobial resistance enrofloxacin_testing_standard: - rank: 456 + rank: 457 slot_group: Antimicrobial resistance enrofloxacin_testing_standard_version: - rank: 457 + rank: 458 slot_group: Antimicrobial resistance enrofloxacin_testing_standard_details: - rank: 458 + rank: 459 slot_group: Antimicrobial resistance enrofloxacin_susceptible_breakpoint: - rank: 459 + rank: 460 slot_group: Antimicrobial resistance enrofloxacin_intermediate_breakpoint: - rank: 460 + rank: 461 slot_group: Antimicrobial resistance enrofloxacin_resistant_breakpoint: - rank: 461 + rank: 462 slot_group: Antimicrobial resistance erythromycin_resistance_phenotype: - rank: 462 + rank: 463 slot_group: Antimicrobial resistance erythromycin_measurement: - rank: 463 + rank: 464 slot_group: Antimicrobial resistance erythromycin_measurement_units: - rank: 464 + rank: 465 slot_group: Antimicrobial resistance erythromycin_measurement_sign: - rank: 465 + rank: 466 slot_group: Antimicrobial resistance erythromycin_laboratory_typing_method: - rank: 466 + rank: 467 slot_group: Antimicrobial resistance erythromycin_laboratory_typing_platform: - rank: 467 + rank: 468 slot_group: Antimicrobial resistance erythromycin_laboratory_typing_platform_version: - rank: 468 + rank: 469 slot_group: Antimicrobial resistance erythromycin_vendor_name: - rank: 469 + rank: 470 slot_group: Antimicrobial resistance erythromycin_testing_standard: - rank: 470 + rank: 471 slot_group: Antimicrobial resistance erythromycin_testing_standard_version: - rank: 471 + rank: 472 slot_group: Antimicrobial resistance erythromycin_testing_standard_details: - rank: 472 + rank: 473 slot_group: Antimicrobial resistance erythromycin_susceptible_breakpoint: - rank: 473 + rank: 474 slot_group: Antimicrobial resistance erythromycin_intermediate_breakpoint: - rank: 474 + rank: 475 slot_group: Antimicrobial resistance erythromycin_resistant_breakpoint: - rank: 475 + rank: 476 slot_group: Antimicrobial resistance florfenicol_resistance_phenotype: - rank: 476 + rank: 477 slot_group: Antimicrobial resistance florfenicol_measurement: - rank: 477 + rank: 478 slot_group: Antimicrobial resistance florfenicol_measurement_units: - rank: 478 + rank: 479 slot_group: Antimicrobial resistance florfenicol_measurement_sign: - rank: 479 + rank: 480 slot_group: Antimicrobial resistance florfenicol_laboratory_typing_method: - rank: 480 + rank: 481 slot_group: Antimicrobial resistance florfenicol_laboratory_typing_platform: - rank: 481 + rank: 482 slot_group: Antimicrobial resistance florfenicol_laboratory_typing_platform_version: - rank: 482 + rank: 483 slot_group: Antimicrobial resistance florfenicol_vendor_name: - rank: 483 + rank: 484 slot_group: Antimicrobial resistance florfenicol_testing_standard: - rank: 484 + rank: 485 slot_group: Antimicrobial resistance florfenicol_testing_standard_version: - rank: 485 + rank: 486 slot_group: Antimicrobial resistance florfenicol_testing_standard_details: - rank: 486 + rank: 487 slot_group: Antimicrobial resistance florfenicol_susceptible_breakpoint: - rank: 487 + rank: 488 slot_group: Antimicrobial resistance florfenicol_intermediate_breakpoint: - rank: 488 + rank: 489 slot_group: Antimicrobial resistance florfenicol_resistant_breakpoint: - rank: 489 + rank: 490 slot_group: Antimicrobial resistance gentamicin_resistance_phenotype: - rank: 490 + rank: 491 slot_group: Antimicrobial resistance gentamicin_measurement: - rank: 491 + rank: 492 slot_group: Antimicrobial resistance gentamicin_measurement_units: - rank: 492 + rank: 493 slot_group: Antimicrobial resistance gentamicin_measurement_sign: - rank: 493 + rank: 494 slot_group: Antimicrobial resistance gentamicin_laboratory_typing_method: - rank: 494 - slot_group: Antimicrobial resistance - gentamicin_laboratory_typing_platform: rank: 495 slot_group: Antimicrobial resistance - gentamicin_laboratory_typing_platform_version: + gentamicin_laboratory_typing_platform: rank: 496 slot_group: Antimicrobial resistance - gentamicin_vendor_name: + gentamicin_laboratory_typing_platform_version: rank: 497 slot_group: Antimicrobial resistance - gentamicin_testing_standard: + gentamicin_vendor_name: rank: 498 slot_group: Antimicrobial resistance - gentamicin_testing_standard_version: + gentamicin_testing_standard: rank: 499 slot_group: Antimicrobial resistance - gentamicin_testing_standard_details: + gentamicin_testing_standard_version: rank: 500 slot_group: Antimicrobial resistance - gentamicin_susceptible_breakpoint: + gentamicin_testing_standard_details: rank: 501 slot_group: Antimicrobial resistance - gentamicin_intermediate_breakpoint: + gentamicin_susceptible_breakpoint: rank: 502 slot_group: Antimicrobial resistance - gentamicin_resistant_breakpoint: + gentamicin_intermediate_breakpoint: rank: 503 slot_group: Antimicrobial resistance - imipenem_resistance_phenotype: + gentamicin_resistant_breakpoint: rank: 504 slot_group: Antimicrobial resistance - imipenem_measurement: + imipenem_resistance_phenotype: rank: 505 slot_group: Antimicrobial resistance - imipenem_measurement_units: + imipenem_measurement: rank: 506 slot_group: Antimicrobial resistance - imipenem_measurement_sign: + imipenem_measurement_units: rank: 507 slot_group: Antimicrobial resistance - imipenem_laboratory_typing_method: + imipenem_measurement_sign: rank: 508 slot_group: Antimicrobial resistance - imipenem_laboratory_typing_platform: + imipenem_laboratory_typing_method: rank: 509 slot_group: Antimicrobial resistance - imipenem_laboratory_typing_platform_version: + imipenem_laboratory_typing_platform: rank: 510 slot_group: Antimicrobial resistance - imipenem_vendor_name: + imipenem_laboratory_typing_platform_version: rank: 511 slot_group: Antimicrobial resistance - imipenem_testing_standard: + imipenem_vendor_name: rank: 512 slot_group: Antimicrobial resistance - imipenem_testing_standard_version: + imipenem_testing_standard: rank: 513 slot_group: Antimicrobial resistance - imipenem_testing_standard_details: + imipenem_testing_standard_version: rank: 514 slot_group: Antimicrobial resistance - imipenem_susceptible_breakpoint: + imipenem_testing_standard_details: rank: 515 slot_group: Antimicrobial resistance - imipenem_intermediate_breakpoint: + imipenem_susceptible_breakpoint: rank: 516 slot_group: Antimicrobial resistance - imipenem_resistant_breakpoint: + imipenem_intermediate_breakpoint: rank: 517 slot_group: Antimicrobial resistance - kanamycin_resistance_phenotype: + imipenem_resistant_breakpoint: rank: 518 slot_group: Antimicrobial resistance - kanamycin_measurement: + kanamycin_resistance_phenotype: rank: 519 slot_group: Antimicrobial resistance - kanamycin_measurement_units: + kanamycin_measurement: rank: 520 slot_group: Antimicrobial resistance - kanamycin_measurement_sign: + kanamycin_measurement_units: rank: 521 slot_group: Antimicrobial resistance - kanamycin_laboratory_typing_method: + kanamycin_measurement_sign: rank: 522 slot_group: Antimicrobial resistance - kanamycin_laboratory_typing_platform: + kanamycin_laboratory_typing_method: rank: 523 slot_group: Antimicrobial resistance - kanamycin_laboratory_typing_platform_version: + kanamycin_laboratory_typing_platform: rank: 524 slot_group: Antimicrobial resistance - kanamycin_vendor_name: + kanamycin_laboratory_typing_platform_version: rank: 525 slot_group: Antimicrobial resistance - kanamycin_testing_standard: + kanamycin_vendor_name: rank: 526 slot_group: Antimicrobial resistance - kanamycin_testing_standard_version: + kanamycin_testing_standard: rank: 527 slot_group: Antimicrobial resistance - kanamycin_testing_standard_details: + kanamycin_testing_standard_version: rank: 528 slot_group: Antimicrobial resistance - kanamycin_susceptible_breakpoint: + kanamycin_testing_standard_details: rank: 529 slot_group: Antimicrobial resistance - kanamycin_intermediate_breakpoint: + kanamycin_susceptible_breakpoint: rank: 530 slot_group: Antimicrobial resistance - kanamycin_resistant_breakpoint: + kanamycin_intermediate_breakpoint: rank: 531 slot_group: Antimicrobial resistance - levofloxacin_resistance_phenotype: + kanamycin_resistant_breakpoint: rank: 532 slot_group: Antimicrobial resistance - levofloxacin_measurement: + levofloxacin_resistance_phenotype: rank: 533 slot_group: Antimicrobial resistance - levofloxacin_measurement_units: + levofloxacin_measurement: rank: 534 slot_group: Antimicrobial resistance - levofloxacin_measurement_sign: + levofloxacin_measurement_units: rank: 535 slot_group: Antimicrobial resistance - levofloxacin_laboratory_typing_method: + levofloxacin_measurement_sign: rank: 536 slot_group: Antimicrobial resistance - levofloxacin_laboratory_typing_platform: + levofloxacin_laboratory_typing_method: rank: 537 slot_group: Antimicrobial resistance - levofloxacin_laboratory_typing_platform_version: + levofloxacin_laboratory_typing_platform: rank: 538 slot_group: Antimicrobial resistance - levofloxacin_vendor_name: + levofloxacin_laboratory_typing_platform_version: rank: 539 slot_group: Antimicrobial resistance - levofloxacin_testing_standard: + levofloxacin_vendor_name: rank: 540 slot_group: Antimicrobial resistance - levofloxacin_testing_standard_version: + levofloxacin_testing_standard: rank: 541 slot_group: Antimicrobial resistance - levofloxacin_testing_standard_details: + levofloxacin_testing_standard_version: rank: 542 slot_group: Antimicrobial resistance - levofloxacin_susceptible_breakpoint: + levofloxacin_testing_standard_details: rank: 543 slot_group: Antimicrobial resistance - levofloxacin_intermediate_breakpoint: + levofloxacin_susceptible_breakpoint: rank: 544 slot_group: Antimicrobial resistance - levofloxacin_resistant_breakpoint: + levofloxacin_intermediate_breakpoint: rank: 545 slot_group: Antimicrobial resistance - linezolid_resistance_phenotype: + levofloxacin_resistant_breakpoint: rank: 546 slot_group: Antimicrobial resistance - linezolid_measurement: + linezolid_resistance_phenotype: rank: 547 slot_group: Antimicrobial resistance - linezolid_measurement_units: + linezolid_measurement: rank: 548 slot_group: Antimicrobial resistance - linezolid_measurement_sign: + linezolid_measurement_units: rank: 549 slot_group: Antimicrobial resistance - linezolid_laboratory_typing_method: + linezolid_measurement_sign: rank: 550 slot_group: Antimicrobial resistance - linezolid_laboratory_typing_platform: + linezolid_laboratory_typing_method: rank: 551 slot_group: Antimicrobial resistance - linezolid_laboratory_typing_platform_version: + linezolid_laboratory_typing_platform: rank: 552 slot_group: Antimicrobial resistance - linezolid_vendor_name: + linezolid_laboratory_typing_platform_version: rank: 553 slot_group: Antimicrobial resistance - linezolid_testing_standard: + linezolid_vendor_name: rank: 554 slot_group: Antimicrobial resistance - linezolid_testing_standard_version: + linezolid_testing_standard: rank: 555 slot_group: Antimicrobial resistance - linezolid_testing_standard_details: + linezolid_testing_standard_version: rank: 556 slot_group: Antimicrobial resistance - linezolid_susceptible_breakpoint: + linezolid_testing_standard_details: rank: 557 slot_group: Antimicrobial resistance - linezolid_intermediate_breakpoint: + linezolid_susceptible_breakpoint: rank: 558 slot_group: Antimicrobial resistance - linezolid_resistant_breakpoint: + linezolid_intermediate_breakpoint: rank: 559 slot_group: Antimicrobial resistance - meropenem_resistance_phenotype: + linezolid_resistant_breakpoint: rank: 560 slot_group: Antimicrobial resistance - meropenem_measurement: + meropenem_resistance_phenotype: rank: 561 slot_group: Antimicrobial resistance - meropenem_measurement_units: + meropenem_measurement: rank: 562 slot_group: Antimicrobial resistance - meropenem_measurement_sign: + meropenem_measurement_units: rank: 563 slot_group: Antimicrobial resistance - meropenem_laboratory_typing_method: + meropenem_measurement_sign: rank: 564 slot_group: Antimicrobial resistance - meropenem_laboratory_typing_platform: + meropenem_laboratory_typing_method: rank: 565 slot_group: Antimicrobial resistance - meropenem_laboratory_typing_platform_version: + meropenem_laboratory_typing_platform: rank: 566 slot_group: Antimicrobial resistance - meropenem_vendor_name: + meropenem_laboratory_typing_platform_version: rank: 567 slot_group: Antimicrobial resistance - meropenem_testing_standard: + meropenem_vendor_name: rank: 568 slot_group: Antimicrobial resistance - meropenem_testing_standard_version: + meropenem_testing_standard: rank: 569 slot_group: Antimicrobial resistance - meropenem_testing_standard_details: + meropenem_testing_standard_version: rank: 570 slot_group: Antimicrobial resistance - meropenem_susceptible_breakpoint: + meropenem_testing_standard_details: rank: 571 slot_group: Antimicrobial resistance - meropenem_intermediate_breakpoint: + meropenem_susceptible_breakpoint: rank: 572 slot_group: Antimicrobial resistance - meropenem_resistant_breakpoint: + meropenem_intermediate_breakpoint: rank: 573 slot_group: Antimicrobial resistance - nalidixic_acid_resistance_phenotype: + meropenem_resistant_breakpoint: rank: 574 slot_group: Antimicrobial resistance - nalidixic_acid_measurement: + nalidixic_acid_resistance_phenotype: rank: 575 slot_group: Antimicrobial resistance - nalidixic_acid_measurement_units: + nalidixic_acid_measurement: rank: 576 slot_group: Antimicrobial resistance - nalidixic_acid_measurement_sign: + nalidixic_acid_measurement_units: rank: 577 slot_group: Antimicrobial resistance - nalidixic_acid_laboratory_typing_method: + nalidixic_acid_measurement_sign: rank: 578 slot_group: Antimicrobial resistance - nalidixic_acid_laboratory_typing_platform: + nalidixic_acid_laboratory_typing_method: rank: 579 slot_group: Antimicrobial resistance - nalidixic_acid_laboratory_typing_platform_version: + nalidixic_acid_laboratory_typing_platform: rank: 580 slot_group: Antimicrobial resistance - nalidixic_acid_vendor_name: + nalidixic_acid_laboratory_typing_platform_version: rank: 581 slot_group: Antimicrobial resistance - nalidixic_acid_testing_standard: + nalidixic_acid_vendor_name: rank: 582 slot_group: Antimicrobial resistance - nalidixic_acid_testing_standard_version: + nalidixic_acid_testing_standard: rank: 583 slot_group: Antimicrobial resistance - nalidixic_acid_testing_standard_details: + nalidixic_acid_testing_standard_version: rank: 584 slot_group: Antimicrobial resistance - nalidixic_acid_susceptible_breakpoint: + nalidixic_acid_testing_standard_details: rank: 585 slot_group: Antimicrobial resistance - nalidixic_acid_intermediate_breakpoint: + nalidixic_acid_susceptible_breakpoint: rank: 586 slot_group: Antimicrobial resistance - nalidixic_acid_resistant_breakpoint: + nalidixic_acid_intermediate_breakpoint: rank: 587 slot_group: Antimicrobial resistance - nitrofurantoin_resistance_phenotype: + nalidixic_acid_resistant_breakpoint: rank: 588 slot_group: Antimicrobial resistance - nitrofurantoin_measurement: + neomycin_resistance_phenotype: rank: 589 slot_group: Antimicrobial resistance - nitrofurantoin_measurement_units: + neomycin_measurement: rank: 590 slot_group: Antimicrobial resistance - nitrofurantoin_measurement_sign: + neomycin_measurement_units: rank: 591 slot_group: Antimicrobial resistance - nitrofurantoin_laboratory_typing_method: + neomycin_measurement_sign: rank: 592 slot_group: Antimicrobial resistance - nitrofurantoin_laboratory_typing_platform: + neomycin_laboratory_typing_method: rank: 593 slot_group: Antimicrobial resistance - nitrofurantoin_laboratory_typing_platform_version: + neomycin_laboratory_typing_platform: rank: 594 slot_group: Antimicrobial resistance - nitrofurantoin_vendor_name: + neomycin_laboratory_typing_platform_version: rank: 595 slot_group: Antimicrobial resistance - nitrofurantoin_testing_standard: + neomycin_vendor_name: rank: 596 slot_group: Antimicrobial resistance - nitrofurantoin_testing_standard_version: + neomycin_testing_standard: rank: 597 slot_group: Antimicrobial resistance - nitrofurantoin_testing_standard_details: + neomycin_testing_standard_version: rank: 598 slot_group: Antimicrobial resistance - nitrofurantoin_susceptible_breakpoint: + neomycin_testing_standard_details: rank: 599 slot_group: Antimicrobial resistance - nitrofurantoin_intermediate_breakpoint: + neomycin_susceptible_breakpoint: rank: 600 slot_group: Antimicrobial resistance - nitrofurantoin_resistant_breakpoint: + neomycin_intermediate_breakpoint: rank: 601 slot_group: Antimicrobial resistance - norfloxacin_resistance_phenotype: + neomycin_resistant_breakpoint: rank: 602 slot_group: Antimicrobial resistance - norfloxacin_measurement: + nitrofurantoin_resistance_phenotype: rank: 603 slot_group: Antimicrobial resistance - norfloxacin_measurement_units: + nitrofurantoin_measurement: rank: 604 slot_group: Antimicrobial resistance - norfloxacin_measurement_sign: + nitrofurantoin_measurement_units: rank: 605 slot_group: Antimicrobial resistance - norfloxacin_laboratory_typing_method: + nitrofurantoin_measurement_sign: rank: 606 slot_group: Antimicrobial resistance - norfloxacin_laboratory_typing_platform: + nitrofurantoin_laboratory_typing_method: rank: 607 slot_group: Antimicrobial resistance - norfloxacin_laboratory_typing_platform_version: + nitrofurantoin_laboratory_typing_platform: rank: 608 slot_group: Antimicrobial resistance - norfloxacin_vendor_name: + nitrofurantoin_laboratory_typing_platform_version: rank: 609 slot_group: Antimicrobial resistance - norfloxacin_testing_standard: + nitrofurantoin_vendor_name: rank: 610 slot_group: Antimicrobial resistance - norfloxacin_testing_standard_version: + nitrofurantoin_testing_standard: rank: 611 slot_group: Antimicrobial resistance - norfloxacin_testing_standard_details: + nitrofurantoin_testing_standard_version: rank: 612 slot_group: Antimicrobial resistance - norfloxacin_susceptible_breakpoint: + nitrofurantoin_testing_standard_details: rank: 613 slot_group: Antimicrobial resistance - norfloxacin_intermediate_breakpoint: + nitrofurantoin_susceptible_breakpoint: rank: 614 slot_group: Antimicrobial resistance - norfloxacin_resistant_breakpoint: + nitrofurantoin_intermediate_breakpoint: rank: 615 slot_group: Antimicrobial resistance - oxolinicacid_resistance_phenotype: + nitrofurantoin_resistant_breakpoint: rank: 616 slot_group: Antimicrobial resistance - oxolinicacid_measurement: + norfloxacin_resistance_phenotype: rank: 617 slot_group: Antimicrobial resistance - oxolinicacid_measurement_units: + norfloxacin_measurement: rank: 618 slot_group: Antimicrobial resistance - oxolinicacid_measurement_sign: + norfloxacin_measurement_units: rank: 619 slot_group: Antimicrobial resistance - oxolinicacid_laboratory_typing_method: + norfloxacin_measurement_sign: rank: 620 slot_group: Antimicrobial resistance - oxolinicacid_laboratory_typing_platform: + norfloxacin_laboratory_typing_method: rank: 621 slot_group: Antimicrobial resistance - oxolinicacid_laboratory_typing_platform_version: + norfloxacin_laboratory_typing_platform: rank: 622 slot_group: Antimicrobial resistance - oxolinicacid_vendor_name: + norfloxacin_laboratory_typing_platform_version: rank: 623 slot_group: Antimicrobial resistance - oxolinicacid_testing_standard: + norfloxacin_vendor_name: rank: 624 slot_group: Antimicrobial resistance - oxolinicacid_testing_standard_version: + norfloxacin_testing_standard: rank: 625 slot_group: Antimicrobial resistance - oxolinicacid_testing_standard_details: + norfloxacin_testing_standard_version: rank: 626 slot_group: Antimicrobial resistance - oxolinicacid_susceptible_breakpoint: + norfloxacin_testing_standard_details: rank: 627 slot_group: Antimicrobial resistance - oxolinicacid_intermediate_breakpoint: + norfloxacin_susceptible_breakpoint: rank: 628 slot_group: Antimicrobial resistance - oxolinicacid_resistant_breakpoint: + norfloxacin_intermediate_breakpoint: rank: 629 slot_group: Antimicrobial resistance - oxytetracycline_resistance_phenotype: + norfloxacin_resistant_breakpoint: rank: 630 slot_group: Antimicrobial resistance - oxytetracycline_measurement: + oxolinicacid_resistance_phenotype: rank: 631 slot_group: Antimicrobial resistance - oxytetracycline_measurement_units: + oxolinicacid_measurement: rank: 632 slot_group: Antimicrobial resistance - oxytetracycline_measurement_sign: + oxolinicacid_measurement_units: rank: 633 slot_group: Antimicrobial resistance - oxytetracycline_laboratory_typing_method: + oxolinicacid_measurement_sign: rank: 634 slot_group: Antimicrobial resistance - oxytetracycline_laboratory_typing_platform: + oxolinicacid_laboratory_typing_method: rank: 635 slot_group: Antimicrobial resistance - oxytetracycline_laboratory_typing_platform_version: + oxolinicacid_laboratory_typing_platform: rank: 636 slot_group: Antimicrobial resistance - oxytetracycline_vendor_name: + oxolinicacid_laboratory_typing_platform_version: rank: 637 slot_group: Antimicrobial resistance - oxytetracycline_testing_standard: + oxolinicacid_vendor_name: rank: 638 slot_group: Antimicrobial resistance - oxytetracycline_testing_standard_version: + oxolinicacid_testing_standard: rank: 639 slot_group: Antimicrobial resistance - oxytetracycline_testing_standard_details: + oxolinicacid_testing_standard_version: rank: 640 slot_group: Antimicrobial resistance - oxytetracycline_susceptible_breakpoint: + oxolinicacid_testing_standard_details: rank: 641 slot_group: Antimicrobial resistance - oxytetracycline_intermediate_breakpoint: + oxolinicacid_susceptible_breakpoint: rank: 642 slot_group: Antimicrobial resistance - oxytetracycline_resistant_breakpoint: + oxolinicacid_intermediate_breakpoint: rank: 643 slot_group: Antimicrobial resistance - piperacillin_resistance_phenotype: + oxolinicacid_resistant_breakpoint: rank: 644 slot_group: Antimicrobial resistance - piperacillin_measurement: + oxytetracycline_resistance_phenotype: rank: 645 slot_group: Antimicrobial resistance - piperacillin_measurement_units: + oxytetracycline_measurement: rank: 646 slot_group: Antimicrobial resistance - piperacillin_measurement_sign: + oxytetracycline_measurement_units: rank: 647 slot_group: Antimicrobial resistance - piperacillin_laboratory_typing_method: + oxytetracycline_measurement_sign: rank: 648 slot_group: Antimicrobial resistance - piperacillin_laboratory_typing_platform: + oxytetracycline_laboratory_typing_method: rank: 649 slot_group: Antimicrobial resistance - piperacillin_laboratory_typing_platform_version: + oxytetracycline_laboratory_typing_platform: rank: 650 slot_group: Antimicrobial resistance - piperacillin_vendor_name: + oxytetracycline_laboratory_typing_platform_version: rank: 651 slot_group: Antimicrobial resistance - piperacillin_testing_standard: + oxytetracycline_vendor_name: rank: 652 slot_group: Antimicrobial resistance - piperacillin_testing_standard_version: + oxytetracycline_testing_standard: rank: 653 slot_group: Antimicrobial resistance - piperacillin_testing_standard_details: + oxytetracycline_testing_standard_version: rank: 654 slot_group: Antimicrobial resistance - piperacillin_susceptible_breakpoint: + oxytetracycline_testing_standard_details: rank: 655 slot_group: Antimicrobial resistance - piperacillin_intermediate_breakpoint: + oxytetracycline_susceptible_breakpoint: rank: 656 slot_group: Antimicrobial resistance - piperacillin_resistant_breakpoint: + oxytetracycline_intermediate_breakpoint: rank: 657 slot_group: Antimicrobial resistance - piperacillintazobactam_resistance_phenotype: + oxytetracycline_resistant_breakpoint: rank: 658 slot_group: Antimicrobial resistance - piperacillintazobactam_measurement: + penicillin_resistance_phenotype: rank: 659 slot_group: Antimicrobial resistance - piperacillintazobactam_measurement_units: + penicillin_measurement: rank: 660 slot_group: Antimicrobial resistance - piperacillintazobactam_measurement_sign: + penicillin_measurement_units: rank: 661 slot_group: Antimicrobial resistance - piperacillintazobactam_laboratory_typing_method: + penicillin_measurement_sign: rank: 662 slot_group: Antimicrobial resistance - piperacillintazobactam_laboratory_typing_platform: + penicillin_laboratory_typing_method: rank: 663 slot_group: Antimicrobial resistance - piperacillintazobactam_laboratory_typing_platform_version: + penicillin_laboratory_typing_platform: rank: 664 slot_group: Antimicrobial resistance - piperacillintazobactam_vendor_name: + penicillin_laboratory_typing_platform_version: rank: 665 slot_group: Antimicrobial resistance - piperacillintazobactam_testing_standard: + penicillin_vendor_name: rank: 666 slot_group: Antimicrobial resistance - piperacillintazobactam_testing_standard_version: + penicillin_testing_standard: rank: 667 slot_group: Antimicrobial resistance - piperacillintazobactam_testing_standard_details: + penicillin_testing_standard_version: rank: 668 slot_group: Antimicrobial resistance - piperacillintazobactam_susceptible_breakpoint: + penicillin_testing_standard_details: rank: 669 slot_group: Antimicrobial resistance - piperacillintazobactam_intermediate_breakpoint: + penicillin_susceptible_breakpoint: rank: 670 slot_group: Antimicrobial resistance - piperacillintazobactam_resistant_breakpoint: + penicillin_intermediate_breakpoint: rank: 671 slot_group: Antimicrobial resistance - polymyxinb_resistance_phenotype: + penicillin_resistant_breakpoint: rank: 672 slot_group: Antimicrobial resistance - polymyxinb_measurement: + piperacillin_resistance_phenotype: rank: 673 slot_group: Antimicrobial resistance - polymyxinb_measurement_units: + piperacillin_measurement: rank: 674 slot_group: Antimicrobial resistance - polymyxinb_measurement_sign: + piperacillin_measurement_units: rank: 675 slot_group: Antimicrobial resistance - polymyxinb_laboratory_typing_method: + piperacillin_measurement_sign: rank: 676 slot_group: Antimicrobial resistance - polymyxinb_laboratory_typing_platform: + piperacillin_laboratory_typing_method: rank: 677 slot_group: Antimicrobial resistance - polymyxinb_laboratory_typing_platform_version: + piperacillin_laboratory_typing_platform: rank: 678 slot_group: Antimicrobial resistance - polymyxinb_vendor_name: + piperacillin_laboratory_typing_platform_version: rank: 679 slot_group: Antimicrobial resistance - polymyxinb_testing_standard: + piperacillin_vendor_name: rank: 680 slot_group: Antimicrobial resistance - polymyxinb_testing_standard_version: + piperacillin_testing_standard: rank: 681 slot_group: Antimicrobial resistance - polymyxinb_testing_standard_details: + piperacillin_testing_standard_version: rank: 682 slot_group: Antimicrobial resistance - polymyxinb_susceptible_breakpoint: + piperacillin_testing_standard_details: rank: 683 slot_group: Antimicrobial resistance - polymyxinb_intermediate_breakpoint: + piperacillin_susceptible_breakpoint: rank: 684 slot_group: Antimicrobial resistance - polymyxinb_resistant_breakpoint: + piperacillin_intermediate_breakpoint: rank: 685 slot_group: Antimicrobial resistance - quinupristindalfopristin_resistance_phenotype: + piperacillin_resistant_breakpoint: rank: 686 slot_group: Antimicrobial resistance - quinupristindalfopristin_measurement: + piperacillintazobactam_resistance_phenotype: rank: 687 slot_group: Antimicrobial resistance - quinupristindalfopristin_measurement_units: + piperacillintazobactam_measurement: rank: 688 slot_group: Antimicrobial resistance - quinupristindalfopristin_measurement_sign: + piperacillintazobactam_measurement_units: rank: 689 slot_group: Antimicrobial resistance - quinupristindalfopristin_laboratory_typing_method: + piperacillintazobactam_measurement_sign: rank: 690 slot_group: Antimicrobial resistance - quinupristindalfopristin_laboratory_typing_platform: + piperacillintazobactam_laboratory_typing_method: rank: 691 slot_group: Antimicrobial resistance - quinupristindalfopristin_laboratory_typing_platform_version: + piperacillintazobactam_laboratory_typing_platform: rank: 692 slot_group: Antimicrobial resistance - quinupristindalfopristin_vendor_name: + piperacillintazobactam_laboratory_typing_platform_version: rank: 693 slot_group: Antimicrobial resistance - quinupristindalfopristin_testing_standard: + piperacillintazobactam_vendor_name: rank: 694 slot_group: Antimicrobial resistance - quinupristindalfopristin_testing_standard_version: + piperacillintazobactam_testing_standard: rank: 695 slot_group: Antimicrobial resistance - quinupristindalfopristin_testing_standard_details: + piperacillintazobactam_testing_standard_version: rank: 696 slot_group: Antimicrobial resistance - quinupristindalfopristin_susceptible_breakpoint: + piperacillintazobactam_testing_standard_details: rank: 697 slot_group: Antimicrobial resistance - quinupristindalfopristin_intermediate_breakpoint: + piperacillintazobactam_susceptible_breakpoint: rank: 698 slot_group: Antimicrobial resistance - quinupristindalfopristin_resistant_breakpoint: + piperacillintazobactam_intermediate_breakpoint: rank: 699 slot_group: Antimicrobial resistance - streptomycin_resistance_phenotype: + piperacillintazobactam_resistant_breakpoint: rank: 700 slot_group: Antimicrobial resistance - streptomycin_measurement: + polymyxinb_resistance_phenotype: rank: 701 slot_group: Antimicrobial resistance - streptomycin_measurement_units: + polymyxinb_measurement: rank: 702 slot_group: Antimicrobial resistance - streptomycin_measurement_sign: + polymyxinb_measurement_units: rank: 703 slot_group: Antimicrobial resistance - streptomycin_laboratory_typing_method: + polymyxinb_measurement_sign: rank: 704 slot_group: Antimicrobial resistance - streptomycin_laboratory_typing_platform: + polymyxinb_laboratory_typing_method: rank: 705 slot_group: Antimicrobial resistance - streptomycin_laboratory_typing_platform_version: + polymyxinb_laboratory_typing_platform: rank: 706 slot_group: Antimicrobial resistance - streptomycin_vendor_name: + polymyxinb_laboratory_typing_platform_version: rank: 707 slot_group: Antimicrobial resistance - streptomycin_testing_standard: + polymyxinb_vendor_name: rank: 708 slot_group: Antimicrobial resistance - streptomycin_testing_standard_version: + polymyxinb_testing_standard: rank: 709 slot_group: Antimicrobial resistance - streptomycin_testing_standard_details: + polymyxinb_testing_standard_version: rank: 710 slot_group: Antimicrobial resistance - streptomycin_susceptible_breakpoint: + polymyxinb_testing_standard_details: rank: 711 slot_group: Antimicrobial resistance - streptomycin_intermediate_breakpoint: + polymyxinb_susceptible_breakpoint: rank: 712 slot_group: Antimicrobial resistance - streptomycin_resistant_breakpoint: + polymyxinb_intermediate_breakpoint: rank: 713 slot_group: Antimicrobial resistance - sulfisoxazole_resistance_phenotype: + polymyxinb_resistant_breakpoint: rank: 714 slot_group: Antimicrobial resistance - sulfisoxazole_measurement: + quinupristindalfopristin_resistance_phenotype: rank: 715 slot_group: Antimicrobial resistance - sulfisoxazole_measurement_units: + quinupristindalfopristin_measurement: rank: 716 slot_group: Antimicrobial resistance - sulfisoxazole_measurement_sign: + quinupristindalfopristin_measurement_units: rank: 717 slot_group: Antimicrobial resistance - sulfisoxazole_laboratory_typing_method: + quinupristindalfopristin_measurement_sign: rank: 718 slot_group: Antimicrobial resistance - sulfisoxazole_laboratory_typing_platform: + quinupristindalfopristin_laboratory_typing_method: rank: 719 slot_group: Antimicrobial resistance - sulfisoxazole_laboratory_typing_platform_version: + quinupristindalfopristin_laboratory_typing_platform: rank: 720 slot_group: Antimicrobial resistance - sulfisoxazole_vendor_name: + quinupristindalfopristin_laboratory_typing_platform_version: rank: 721 slot_group: Antimicrobial resistance - sulfisoxazole_testing_standard: + quinupristindalfopristin_vendor_name: rank: 722 slot_group: Antimicrobial resistance - sulfisoxazole_testing_standard_version: + quinupristindalfopristin_testing_standard: rank: 723 slot_group: Antimicrobial resistance - sulfisoxazole_testing_standard_details: + quinupristindalfopristin_testing_standard_version: rank: 724 slot_group: Antimicrobial resistance - sulfisoxazole_susceptible_breakpoint: + quinupristindalfopristin_testing_standard_details: rank: 725 slot_group: Antimicrobial resistance - sulfisoxazole_intermediate_breakpoint: + quinupristindalfopristin_susceptible_breakpoint: rank: 726 slot_group: Antimicrobial resistance - sulfisoxazole_resistant_breakpoint: + quinupristindalfopristin_intermediate_breakpoint: rank: 727 slot_group: Antimicrobial resistance - telithromycin_resistance_phenotype: + quinupristindalfopristin_resistant_breakpoint: rank: 728 slot_group: Antimicrobial resistance - telithromycin_measurement: + streptomycin_resistance_phenotype: rank: 729 slot_group: Antimicrobial resistance - telithromycin_measurement_units: + streptomycin_measurement: rank: 730 slot_group: Antimicrobial resistance - telithromycin_measurement_sign: + streptomycin_measurement_units: rank: 731 slot_group: Antimicrobial resistance - telithromycin_laboratory_typing_method: + streptomycin_measurement_sign: rank: 732 slot_group: Antimicrobial resistance - telithromycin_laboratory_typing_platform: + streptomycin_laboratory_typing_method: rank: 733 slot_group: Antimicrobial resistance - telithromycin_laboratory_typing_platform_version: + streptomycin_laboratory_typing_platform: rank: 734 slot_group: Antimicrobial resistance - telithromycin_vendor_name: + streptomycin_laboratory_typing_platform_version: rank: 735 slot_group: Antimicrobial resistance - telithromycin_testing_standard: + streptomycin_vendor_name: rank: 736 slot_group: Antimicrobial resistance - telithromycin_testing_standard_version: + streptomycin_testing_standard: rank: 737 slot_group: Antimicrobial resistance - telithromycin_testing_standard_details: + streptomycin_testing_standard_version: rank: 738 slot_group: Antimicrobial resistance - telithromycin_susceptible_breakpoint: + streptomycin_testing_standard_details: rank: 739 slot_group: Antimicrobial resistance - telithromycin_intermediate_breakpoint: + streptomycin_susceptible_breakpoint: rank: 740 slot_group: Antimicrobial resistance - telithromycin_resistant_breakpoint: + streptomycin_intermediate_breakpoint: rank: 741 slot_group: Antimicrobial resistance - tetracycline_resistance_phenotype: + streptomycin_resistant_breakpoint: rank: 742 slot_group: Antimicrobial resistance - tetracycline_measurement: + sulfisoxazole_resistance_phenotype: rank: 743 slot_group: Antimicrobial resistance - tetracycline_measurement_units: + sulfisoxazole_measurement: rank: 744 slot_group: Antimicrobial resistance - tetracycline_measurement_sign: + sulfisoxazole_measurement_units: rank: 745 slot_group: Antimicrobial resistance - tetracycline_laboratory_typing_method: + sulfisoxazole_measurement_sign: rank: 746 slot_group: Antimicrobial resistance - tetracycline_laboratory_typing_platform: + sulfisoxazole_laboratory_typing_method: rank: 747 slot_group: Antimicrobial resistance - tetracycline_laboratory_typing_platform_version: + sulfisoxazole_laboratory_typing_platform: rank: 748 slot_group: Antimicrobial resistance - tetracycline_vendor_name: + sulfisoxazole_laboratory_typing_platform_version: rank: 749 slot_group: Antimicrobial resistance - tetracycline_testing_standard: + sulfisoxazole_vendor_name: rank: 750 slot_group: Antimicrobial resistance - tetracycline_testing_standard_version: + sulfisoxazole_testing_standard: rank: 751 slot_group: Antimicrobial resistance - tetracycline_testing_standard_details: + sulfisoxazole_testing_standard_version: rank: 752 slot_group: Antimicrobial resistance - tetracycline_susceptible_breakpoint: + sulfisoxazole_testing_standard_details: rank: 753 slot_group: Antimicrobial resistance - tetracycline_intermediate_breakpoint: + sulfisoxazole_susceptible_breakpoint: rank: 754 slot_group: Antimicrobial resistance - tetracycline_resistant_breakpoint: + sulfisoxazole_intermediate_breakpoint: rank: 755 slot_group: Antimicrobial resistance - tigecycline_resistance_phenotype: + sulfisoxazole_resistant_breakpoint: rank: 756 slot_group: Antimicrobial resistance - tigecycline_measurement: + telithromycin_resistance_phenotype: rank: 757 slot_group: Antimicrobial resistance - tigecycline_measurement_units: + telithromycin_measurement: rank: 758 slot_group: Antimicrobial resistance - tigecycline_measurement_sign: + telithromycin_measurement_units: rank: 759 slot_group: Antimicrobial resistance - tigecycline_laboratory_typing_method: + telithromycin_measurement_sign: rank: 760 slot_group: Antimicrobial resistance - tigecycline_laboratory_typing_platform: + telithromycin_laboratory_typing_method: rank: 761 slot_group: Antimicrobial resistance - tigecycline_laboratory_typing_platform_version: + telithromycin_laboratory_typing_platform: rank: 762 slot_group: Antimicrobial resistance - tigecycline_vendor_name: + telithromycin_laboratory_typing_platform_version: rank: 763 slot_group: Antimicrobial resistance - tigecycline_testing_standard: + telithromycin_vendor_name: rank: 764 slot_group: Antimicrobial resistance - tigecycline_testing_standard_version: + telithromycin_testing_standard: rank: 765 slot_group: Antimicrobial resistance - tigecycline_testing_standard_details: + telithromycin_testing_standard_version: rank: 766 slot_group: Antimicrobial resistance - tigecycline_susceptible_breakpoint: + telithromycin_testing_standard_details: rank: 767 slot_group: Antimicrobial resistance + telithromycin_susceptible_breakpoint: + rank: 768 + slot_group: Antimicrobial resistance + telithromycin_intermediate_breakpoint: + rank: 769 + slot_group: Antimicrobial resistance + telithromycin_resistant_breakpoint: + rank: 770 + slot_group: Antimicrobial resistance + tetracycline_resistance_phenotype: + rank: 771 + slot_group: Antimicrobial resistance + tetracycline_measurement: + rank: 772 + slot_group: Antimicrobial resistance + tetracycline_measurement_units: + rank: 773 + slot_group: Antimicrobial resistance + tetracycline_measurement_sign: + rank: 774 + slot_group: Antimicrobial resistance + tetracycline_laboratory_typing_method: + rank: 775 + slot_group: Antimicrobial resistance + tetracycline_laboratory_typing_platform: + rank: 776 + slot_group: Antimicrobial resistance + tetracycline_laboratory_typing_platform_version: + rank: 777 + slot_group: Antimicrobial resistance + tetracycline_vendor_name: + rank: 778 + slot_group: Antimicrobial resistance + tetracycline_testing_standard: + rank: 779 + slot_group: Antimicrobial resistance + tetracycline_testing_standard_version: + rank: 780 + slot_group: Antimicrobial resistance + tetracycline_testing_standard_details: + rank: 781 + slot_group: Antimicrobial resistance + tetracycline_susceptible_breakpoint: + rank: 782 + slot_group: Antimicrobial resistance + tetracycline_intermediate_breakpoint: + rank: 783 + slot_group: Antimicrobial resistance + tetracycline_resistant_breakpoint: + rank: 784 + slot_group: Antimicrobial resistance + tigecycline_resistance_phenotype: + rank: 785 + slot_group: Antimicrobial resistance + tigecycline_measurement: + rank: 786 + slot_group: Antimicrobial resistance + tigecycline_measurement_units: + rank: 787 + slot_group: Antimicrobial resistance + tigecycline_measurement_sign: + rank: 788 + slot_group: Antimicrobial resistance + tigecycline_laboratory_typing_method: + rank: 789 + slot_group: Antimicrobial resistance + tigecycline_laboratory_typing_platform: + rank: 790 + slot_group: Antimicrobial resistance + tigecycline_laboratory_typing_platform_version: + rank: 791 + slot_group: Antimicrobial resistance + tigecycline_vendor_name: + rank: 792 + slot_group: Antimicrobial resistance + tigecycline_testing_standard: + rank: 793 + slot_group: Antimicrobial resistance + tigecycline_testing_standard_version: + rank: 794 + slot_group: Antimicrobial resistance + tigecycline_testing_standard_details: + rank: 795 + slot_group: Antimicrobial resistance + tigecycline_susceptible_breakpoint: + rank: 796 + slot_group: Antimicrobial resistance tigecycline_intermediate_breakpoint: - rank: 768 + rank: 797 slot_group: Antimicrobial resistance tigecycline_resistant_breakpoint: - rank: 769 + rank: 798 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_resistance_phenotype: - rank: 770 + rank: 799 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_measurement: - rank: 771 + rank: 800 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_measurement_units: - rank: 772 + rank: 801 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_measurement_sign: - rank: 773 + rank: 802 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_laboratory_typing_method: - rank: 774 + rank: 803 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_laboratory_typing_platform: - rank: 775 + rank: 804 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_laboratory_typing_platform_version: - rank: 776 + rank: 805 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_vendor_name: - rank: 777 + rank: 806 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_testing_standard: - rank: 778 + rank: 807 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_testing_standard_version: - rank: 779 + rank: 808 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_testing_standard_details: - rank: 780 + rank: 809 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_susceptible_breakpoint: - rank: 781 + rank: 810 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_intermediate_breakpoint: - rank: 782 + rank: 811 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_resistant_breakpoint: - rank: 783 + rank: 812 slot_group: Antimicrobial resistance authors: - rank: 784 + rank: 813 slot_group: Contributor acknowledgement dataharmonizer_provenance: - rank: 785 + rank: 814 slot_group: Contributor acknowledgement slots: sample_collector_sample_id: @@ -4714,6 +4830,21 @@ slots: - value: Research [GENEPIO:0100003] exact_mappings: - BIOSAMPLE:purpose_of_sequencing + sequencing_date: + name: sequencing_date + title: sequencing_date + description: The date the sample was sequenced. + comments: ISO 8601 standard "YYYY-MM-DD". + slot_uri: GENEPIO:0001447 + any_of: + - range: date + - range: NullValueMenu + todos: + - '>={sample_collection_date}' + - <={today} + required: true + examples: + - value: '2020-06-22' sequencing_project_name: name: sequencing_project_name title: sequencing_project_name @@ -10376,6 +10507,157 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' + neomycin_resistance_phenotype: + name: neomycin_resistance_phenotype + title: neomycin_resistance_phenotype + description: The antimicrobial resistance phenotype, as determined by the antibiotic + susceptibility measurement and testing standard for this antibiotic + comments: Select a phenotype from the pick list provided. + any_of: + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu + recommended: true + examples: + - value: Susceptible antimicrobial phenotype [ARO:3004302] + neomycin_measurement: + name: neomycin_measurement + title: neomycin_measurement + description: The measured value of neomycin resistance. + comments: This field should only contain a number (either an integer or a number + with decimals). + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + required: true + examples: + - value: '4' + neomycin_measurement_units: + name: neomycin_measurement_units + title: neomycin_measurement_units + description: The units of the antimicrobial resistance measurement. + comments: Select the units from the pick list provided. Use the Term Request System + to request the addition of other units if necessary. + any_of: + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu + required: true + examples: + - value: ug/mL [UO:0000274] + neomycin_measurement_sign: + name: neomycin_measurement_sign + title: neomycin_measurement_sign + description: The qualifier associated with the antimicrobial resistance measurement + comments: Select the comparator sign from the pick list provided. Use the Term + Request System to request the addition of other signs if necessary. + any_of: + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu + required: true + examples: + - value: greater than (>) [GENEPIO:0001006] + neomycin_laboratory_typing_method: + name: neomycin_laboratory_typing_method + title: neomycin_laboratory_typing_method + description: The general method used for antimicrobial susceptibility testing. + comments: Select a typing method from the pick list provided. Use the Term Request + System to request the addition of other methods if necessary. + any_of: + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu + examples: + - value: Broth dilution [ARO:3004397] + neomycin_laboratory_typing_platform: + name: neomycin_laboratory_typing_platform + title: neomycin_laboratory_typing_platform + description: The brand/platform used for antimicrobial susceptibility testing. + comments: Select a typing platform from the pick list provided. Use the Term Request + System to request the addition of other platforms if necessary. + any_of: + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu + examples: + - value: Sensitire [ARO:3004402] + neomycin_laboratory_typing_platform_version: + name: neomycin_laboratory_typing_platform_version + title: neomycin_laboratory_typing_platform_version + description: The specific name and version of the plate, panel, or other platform + used for antimicrobial susceptibility testing. + comments: Include any additional information about the antimicrobial susceptibility + test such as the drug panel details. + range: WhitespaceMinimizedString + examples: + - value: CMV3AGNF + neomycin_vendor_name: + name: neomycin_vendor_name + title: neomycin_vendor_name + description: The name of the vendor of the testing platform used. + comments: Provide the full name of the company (avoid abbreviations). + any_of: + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu + examples: + - value: Sensititre + neomycin_testing_standard: + name: neomycin_testing_standard + title: neomycin_testing_standard + description: The testing standard used for determination of resistance phenotype + comments: Select a testing standard from the pick list provided. + any_of: + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu + recommended: true + examples: + - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + neomycin_testing_standard_version: + name: neomycin_testing_standard_version + title: neomycin_testing_standard_version + description: The version number associated with the testing standard used for + determination of antimicrobial resistance phenotype. If applicable, include + a version number for the testing standard used. + comments: If applicable, include a version number for the testing standard used. + range: WhitespaceMinimizedString + examples: + - value: M100 + neomycin_testing_standard_details: + name: neomycin_testing_standard_details + title: neomycin_testing_standard_details + description: Additional details associated with the testing standard used for + determination of antimicrobial resistance phenotype + comments: This information may include the year or location where the testing + standard was published. If not applicable, leave blank. + range: WhitespaceMinimizedString + examples: + - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' + - value: '2017.' + neomycin_susceptible_breakpoint: + name: neomycin_susceptible_breakpoint + title: neomycin_susceptible_breakpoint + description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ + \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." + comments: "This field should only contain a number (either an integer or a number\ + \ with decimals), since the \u201C<=\u201D qualifier is implied." + range: WhitespaceMinimizedString + examples: + - value: '8' + neomycin_intermediate_breakpoint: + name: neomycin_intermediate_breakpoint + title: neomycin_intermediate_breakpoint + description: "The intermediate measurement(s), in the units specified in the \u201C\ + AMR_measurement_units\u201D field, where a sample would be considered to have\ + \ an \u201Cintermediate\u201D phenotype for this antimicrobial." + range: WhitespaceMinimizedString + examples: + - value: '16' + neomycin_resistant_breakpoint: + name: neomycin_resistant_breakpoint + title: neomycin_resistant_breakpoint + description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ + \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." + comments: "This field should only contain a number (either an integer or a number\ + \ with decimals), since the \u201C>=\u201D qualifier is implied." + range: WhitespaceMinimizedString + examples: + - value: '32' nitrofurantoin_resistance_phenotype: name: nitrofurantoin_resistance_phenotype title: nitrofurantoin_resistance_phenotype @@ -11044,6 +11326,157 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' + penicillin_resistance_phenotype: + name: penicillin_resistance_phenotype + title: penicillin_resistance_phenotype + description: The antimicrobial resistance phenotype, as determined by the antibiotic + susceptibility measurement and testing standard for this antibiotic + comments: Select a phenotype from the pick list provided. + any_of: + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu + recommended: true + examples: + - value: Susceptible antimicrobial phenotype [ARO:3004302] + penicillin_measurement: + name: penicillin_measurement + title: penicillin_measurement + description: The measured value of penicillin resistance. + comments: This field should only contain a number (either an integer or a number + with decimals). + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + required: true + examples: + - value: '4' + penicillin_measurement_units: + name: penicillin_measurement_units + title: penicillin_measurement_units + description: The units of the antimicrobial resistance measurement. + comments: Select the units from the pick list provided. Use the Term Request System + to request the addition of other units if necessary. + any_of: + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu + required: true + examples: + - value: ug/mL [UO:0000274] + penicillin_measurement_sign: + name: penicillin_measurement_sign + title: penicillin_measurement_sign + description: The qualifier associated with the antimicrobial resistance measurement + comments: Select the comparator sign from the pick list provided. Use the Term + Request System to request the addition of other signs if necessary. + any_of: + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu + required: true + examples: + - value: greater than (>) [GENEPIO:0001006] + penicillin_laboratory_typing_method: + name: penicillin_laboratory_typing_method + title: penicillin_laboratory_typing_method + description: The general method used for antimicrobial susceptibility testing. + comments: Select a typing method from the pick list provided. Use the Term Request + System to request the addition of other methods if necessary. + any_of: + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu + examples: + - value: Broth dilution [ARO:3004397] + penicillin_laboratory_typing_platform: + name: penicillin_laboratory_typing_platform + title: penicillin_laboratory_typing_platform + description: The brand/platform used for antimicrobial susceptibility testing. + comments: Select a typing platform from the pick list provided. Use the Term Request + System to request the addition of other platforms if necessary. + any_of: + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu + examples: + - value: Sensitire [ARO:3004402] + penicillin_laboratory_typing_platform_version: + name: penicillin_laboratory_typing_platform_version + title: penicillin_laboratory_typing_platform_version + description: The specific name and version of the plate, panel, or other platform + used for antimicrobial susceptibility testing. + comments: Include any additional information about the antimicrobial susceptibility + test such as the drug panel details. + range: WhitespaceMinimizedString + examples: + - value: CMV3AGNF + penicillin_vendor_name: + name: penicillin_vendor_name + title: penicillin_vendor_name + description: The name of the vendor of the testing platform used. + comments: Provide the full name of the company (avoid abbreviations). + any_of: + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu + examples: + - value: Sensititre + penicillin_testing_standard: + name: penicillin_testing_standard + title: penicillin_testing_standard + description: The testing standard used for determination of resistance phenotype + comments: Select a testing standard from the pick list provided. + any_of: + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu + recommended: true + examples: + - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + penicillin_testing_standard_version: + name: penicillin_testing_standard_version + title: penicillin_testing_standard_version + description: The version number associated with the testing standard used for + determination of antimicrobial resistance phenotype. If applicable, include + a version number for the testing standard used. + comments: If applicable, include a version number for the testing standard used. + range: WhitespaceMinimizedString + examples: + - value: M100 + penicillin_testing_standard_details: + name: penicillin_testing_standard_details + title: penicillin_testing_standard_details + description: Additional details associated with the testing standard used for + determination of antimicrobial resistance phenotype + comments: This information may include the year or location where the testing + standard was published. If not applicable, leave blank. + range: WhitespaceMinimizedString + examples: + - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' + - value: '2017.' + penicillin_susceptible_breakpoint: + name: penicillin_susceptible_breakpoint + title: penicillin_susceptible_breakpoint + description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ + \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." + comments: "This field should only contain a number (either an integer or a number\ + \ with decimals), since the \u201C<=\u201D qualifier is implied." + range: WhitespaceMinimizedString + examples: + - value: '8' + penicillin_intermediate_breakpoint: + name: penicillin_intermediate_breakpoint + title: penicillin_intermediate_breakpoint + description: "The intermediate measurement(s), in the units specified in the \u201C\ + AMR_measurement_units\u201D field, where a sample would be considered to have\ + \ an \u201Cintermediate\u201D phenotype for this antimicrobial." + range: WhitespaceMinimizedString + examples: + - value: '16' + penicillin_resistant_breakpoint: + name: penicillin_resistant_breakpoint + title: penicillin_resistant_breakpoint + description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ + \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." + comments: "This field should only contain a number (either an integer or a number\ + \ with decimals), since the \u201C>=\u201D qualifier is implied." + range: WhitespaceMinimizedString + examples: + - value: '32' piperacillin_resistance_phenotype: name: piperacillin_resistance_phenotype title: piperacillin_resistance_phenotype @@ -12766,18 +13199,26 @@ enums: name: SampleCollectedByMenu title: sample_collected_by menu permissible_values: - Public Health Agency of Canada (PHAC) [GENEPIO:0100551]: - text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]: - text: Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553]: text: Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554]: - text: Health Canada (HC) [GENEPIO:0100554] + BCCDC Public Health Laboratory [GENEPIO:0102053]: + text: BCCDC Public Health Laboratory [GENEPIO:0102053] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]: + text: Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]: text: Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]: text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + Health Canada (HC) [GENEPIO:0100554]: + text: Health Canada (HC) [GENEPIO:0100554] + "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ) [GENEPIO:0102056]": + text: "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ) [GENEPIO:0102056]" + Manitoba Cadham Provincial Laboratory [GENEPIO:0102054]: + text: Manitoba Cadham Provincial Laboratory [GENEPIO:0102054] + "New Brunswick - Vitalit\xE9 Health Network [GENEPIO:0102055]": + text: "New Brunswick - Vitalit\xE9 Health Network [GENEPIO:0102055]" + Public Health Agency of Canada (PHAC) [GENEPIO:0100551]: + text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] University of Manitoba (UM) [GENEPIO:0004434]: text: University of Manitoba (UM) [GENEPIO:0004434] PurposeOfSamplingMenu: @@ -16872,6 +17313,10 @@ enums: text: nalidixic_acid exact_mappings: - NCBI_ANTIBIOGRAM:nalidixic%20acid + neomycin: + text: neomycin + exact_mappings: + - NCBI_ANTIBIOGRAM:neomycin nitrofurantoin: text: nitrofurantoin exact_mappings: @@ -16888,6 +17333,10 @@ enums: text: oxytetracycline exact_mappings: - NCBI_ANTIBIOGRAM:oxytetracycline + penicillin: + text: penicillin + exact_mappings: + - NCBI_ANTIBIOGRAM:penicillin piperacillin: text: piperacillin exact_mappings: diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index 64797dcb..03792717 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -6,15 +6,18 @@ null value menu NullValueMenu Not Applicable [GENEPIO:0001619] Not applic Not Provided [GENEPIO:0001668] Not provided Restricted Access [GENEPIO:0001810] Restricted access -sample_collected_by menu SampleCollectedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] +sample_collected_by menu SampleCollectedByMenu Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + BCCDC Public Health Laboratory [GENEPIO:0102053] Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + Health Canada (HC) [GENEPIO:0100554] + Laboratoire de santé publique du Québec (LSPQ) [GENEPIO:0102056] + Manitoba Cadham Provincial Laboratory [GENEPIO:0102054] + New Brunswick - Vitalité Health Network [GENEPIO:0102055] + Public Health Agency of Canada (PHAC) [GENEPIO:0100551] University of Manitoba (UM) [GENEPIO:0004434] - purpose_of_sampling menu PurposeOfSamplingMenu Cluster/Outbreak investigation [GENEPIO:0100001] Diagnostic testing [GENEPIO:0100002] Environmental testing [GENEPIO:0100548] @@ -333,23 +336,23 @@ geo_loc_name (country) menu GeoLocNameCountryMenu Afghanistan [GAZ:00006882] geo_loc_name (state/province/region) menu GeoLocNameStateProvinceRegionMenu Atlantic region (Canada) [wikidata:Q246972] - New Brunswick [GAZ:00002570] - Newfoundland & Labrador [GAZ:00002567] - Nova Scotia [GAZ:00002565] - Prince Edward Island [GAZ:00002572] + New Brunswick [GAZ:00002570] + Newfoundland & Labrador [GAZ:00002567] + Nova Scotia [GAZ:00002565] + Prince Edward Island [GAZ:00002572] Central region (Canada) [wikidata:Q1048064] - Ontario [GAZ:00002563] - Quebec [GAZ:00002569] + Ontario [GAZ:00002563] + Quebec [GAZ:00002569] Northern region (Canada) [wikidata:Q764146] - Northwest Territories [GAZ:00002575] - Nunuvut [GAZ:00002574] - Yukon [GAZ:00002576] + Northwest Territories [GAZ:00002575] + Nunuvut [GAZ:00002574] + Yukon [GAZ:00002576] Pacific region (Canada) [wikidata:Q122953299] - British Columbia [GAZ:00002562] + British Columbia [GAZ:00002562] Prairie region (Canada) [wikidata:Q1364746] - Alberta [GAZ:00002566] - Manitoba [GAZ:00002571] - Saskatchewan [GAZ:00002564] + Alberta [GAZ:00002566] + Manitoba [GAZ:00002571] + Saskatchewan [GAZ:00002564] sample_collection_date_precision menu SampleCollectionDatePrecisionMenu year [UO:0000036] @@ -1568,10 +1571,12 @@ Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu ami linezolid linezolid meropenem meropenem nalidixic_acid nalidixic acid + neomycin neomycin nitrofurantoin nitrofurantoin norfloxacin norfloxacin oxolinic-acid oxolinic-acid oxytetracycline oxytetracycline + penicillin penicillin piperacillin piperacillin piperacillin-tazobactam piperacillin-tazobactam polymyxin-b polymyxin-b diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index 6413607a..28c2d66e 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -1,6 +1,6 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM -GRDI GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name/biosample_accession +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM +GRDI GENEPIO:0001150 Sample collection and processing + Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name/biosample_accession Sample collection and processing GENEPIO:0100427 alternative_sample_ID alternative_sample_id WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. """Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA @@ -8,96 +8,96 @@ Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC -Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.""" ABCD1234[PHAC]; 12345rev[CFIA] - Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by - Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name - Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken - Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 - Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling - Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] - Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. - Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol - Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] - Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] - Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. - Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 - Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) geo_loc_name - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region GeoLocNameStateProvinceRegionMenu NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) geo_loc_name - Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) - Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin - Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] - Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon - Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon - Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date TRUE {today} The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date collection_date - Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] - Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date NullValueMenu TRUE {sample_collection_date} {today} The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 - Sample collection and processing GENEPIO:0100763 sample_processing_date sample_processing_date date NullValueMenu {sample_collection_date} {today} The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 - Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST - Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST - Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning - Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 1900-01-03 - Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour - Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date date {sample_collection_date} {today} The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli - Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env - Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source - Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic - Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] - Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source - Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source - Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source - Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] - Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type - Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source - Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims - Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source - Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod - Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap - Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date {today} A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date - Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date {today} A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 - Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source - Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source - Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 - Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] - Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] - Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport - Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol - Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] - Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit NucleicAcidStorageDurationUnitMenu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] - Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] - Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria - Environmental conditions and measurements - Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 - Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 - Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 - Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 - Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] - Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Rain [ENVO:01001564] - Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 - Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch - Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection - GENEPIO:0001268 Host information host_information - Host information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host - Host information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host - Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety - Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed - Host information GENEPIO:0100452 host (food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host - Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age - Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease - GENEPIO:0100453 Strain and isolation information strain_and_isolation_information - Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 - Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain - Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain sample_name/biosample_accession +Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.""" ABCD1234[PHAC]; 12345rev[CFIA] + Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by + Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name + Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken + Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 + Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling + Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] + Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. + Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol + Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] + Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] + Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. + Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 + Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) geo_loc_name + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region GeoLocNameStateProvinceRegionMenu NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) geo_loc_name + Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) + Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin + Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] + Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon + Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon + Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date TRUE {today} The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date collection_date + Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] + Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date NullValueMenu TRUE {sample_collection_date} {today} The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 + Sample collection and processing GENEPIO:0100763 sample_processing_date sample_processing_date date NullValueMenu {sample_collection_date} {today} The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 + Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST + Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST + Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning + Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 1900-01-03 + Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour + Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date date {sample_collection_date} {today} The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli + Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env + Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source + Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic + Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] + Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source + Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source + Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source + Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] + Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type + Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source + Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims + Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source + Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod + Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap + Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date {today} A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date + Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date {today} A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 + Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source + Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source + Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 + Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] + Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] + Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport + Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol + Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] + Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit NucleicAcidStorageDurationUnitMenu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] + Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] + Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria + Environmental conditions and measurements + Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 + Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 + Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 + Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 + Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] + Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Rain [ENVO:01001564] + Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 + Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch + Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection + GENEPIO:0001268 Host information host_information + Host information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host + Host information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host + Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety + Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed + Host information GENEPIO:0100452 host (food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host + Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease + GENEPIO:0100453 Strain and isolation information strain_and_isolation_information + Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 + Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain + Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain sample_name/biosample_accession Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA @@ -106,707 +106,736 @@ Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] -Multiple alternative isolate IDs can be provided, separated by semi-colons." GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias - Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 - Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 - Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 - Strain and isolation information GENEPIO:0100461 isolated_by isolated_by IsolatedByMenu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Strain and isolation information GENEPIO:0100465 isolation_date isolation_date date {today} The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date - Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString {today} The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Strain and isolation information GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism organism - Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] - Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument - Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar - Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 - Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 - GENEPIO:0001441 Sequence information sequence_information - Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 - Sequence information GENEPIO:0100416 sequenced_by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by - Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing - Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) - Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] - Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] - Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] - Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT - Sequence information GENEPIO:0100843 DNA_fragment_length dna_fragment_length integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 - Sequence information GENEPIO:0100966 genomic_target_enrichment_method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] - Sequence information GENEPIO:0100967 genomic_target_enrichment_method_details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel - Sequence information GENEPIO:0001456 amplicon_pcr_primer_scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 - Sequence information GENEPIO:0001449 amplicon_size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 - Sequence information GENEPIO:0101102 sequencing_flow_cell_version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 - Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no - Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz - Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz - Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 - Sequence information GENEPIO:0101715 genome_sequence_filename genome_sequence_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics GENEPIO:0100557 quality_control_method_name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools - Bioinformatics and QC metrics GENEPIO:0100558 quality_control_method_version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 - Bioinformatics and QC metrics GENEPIO:0100559 quality_control_determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control - Bioinformatics and QC metrics GENEPIO:0100560 quality_control_issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage - Bioinformatics and QC metrics GENEPIO:0100561 quality_control_details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. - Bioinformatics and QC metrics GENEPIO:0001458 raw_sequence_data_processing_method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 - Bioinformatics and QC metrics GENEPIO:0001459 dehosting_method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper - Bioinformatics and QC metrics GENEPIO:0100825 sequence_assembly_software_name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet - Bioinformatics and QC metrics GENEPIO:0100826 sequence_assembly_software_version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 - Bioinformatics and QC metrics GENEPIO:0001463 consensus_sequence_software_name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar - Bioinformatics and QC metrics GENEPIO:0001469 consensus_sequence_software_version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 - Bioinformatics and QC metrics GENEPIO:0001472 breadth_of_coverage_value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 - Bioinformatics and QC metrics GENEPIO:0001474 depth_of_coverage_value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 - Bioinformatics and QC metrics GENEPIO:0001475 depth_of_coverage_threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 - Bioinformatics and QC metrics GENEPIO:0100844 genome_completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 - Bioinformatics and QC metrics GENEPIO:0001482 number_of_base_pairs_sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics GENEPIO:0100827 number_of_total_reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 - Bioinformatics and QC metrics GENEPIO:0100828 number_of_unique_reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 - Bioinformatics and QC metrics GENEPIO:0100829 minimum_post-trimming_read_length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 - Bioinformatics and QC metrics GENEPIO:0100937 number_of_contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 - Bioinformatics and QC metrics GENEPIO:0100830 percent_Ns_across_total_genome_length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0001484 Ns_per_100_kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 - Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 - Bioinformatics and QC metrics GENEPIO:0100845 percent_read_contamination_ percent_read_contamination_ integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0100846 sequence_assembly_length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 - Bioinformatics and QC metrics GENEPIO:0001483 consensus_genome_length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 - Bioinformatics and QC metrics GENEPIO:0001485 reference_genome_accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 - Bioinformatics and QC metrics GENEPIO:0100831 deduplication_method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics_protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf - GENEPIO:0101082 Taxonomic identification information - Taxonomic identification information GENEPIO:0100832 read_mapping_software_name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat - Taxonomic identification information GENEPIO:0100833 read_mapping_software_version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 - Taxonomic identification information GENEPIO:0100834 taxonomic_reference_database_name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon - Taxonomic identification information GENEPIO:0100835 taxonomic_reference_database_version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 - Taxonomic identification information GENEPIO:0101074 taxonomic_analysis_report_filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc - Taxonomic identification information GENEPIO:0101075 taxonomic_analysis_date taxonomic_analysis_date date {today} The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 - Taxonomic identification information GENEPIO:0100836 read_mapping_criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 - GENEPIO:0100477 Public repository information public_repository_information - Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca - Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 - Public repository information GENEPIO:0100476 attribute_package attribute_package AttributePackageMenu NullValueMenu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] - Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession - Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID - Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 - Public repository information GENEPIO:0001145 GenBank_accession genbank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 - GENEPIO:0100478 Risk assessment information risk_assessment_information - Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples - Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. - Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production WhitespaceMinimizedString NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] - Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention - Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed - GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance - Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AmrTestingByMenu NullValueMenu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date date {today} The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 - Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name AntimicrobialVendorName NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint trimethoprimsulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint trimethoprimsulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file +Multiple alternative isolate IDs can be provided, separated by semi-colons." GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias + Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 + Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 + Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 + Strain and isolation information GENEPIO:0100461 isolated_by isolated_by IsolatedByMenu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Strain and isolation information GENEPIO:0100465 isolation_date isolation_date date {today} The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date + Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString {today} The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Strain and isolation information GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism organism + Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] + Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument + Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar + Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 + Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 + GENEPIO:0001441 Sequence information sequence_information + Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 + Sequence information GENEPIO:0100416 sequenced_by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by + Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing + Sequence information GENEPIO:0001447 sequencing_date sequencing_date date NullValueMenu TRUE {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 + Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) + Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] + Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] + Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] + Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT + Sequence information GENEPIO:0100843 DNA_fragment_length dna_fragment_length integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 + Sequence information GENEPIO:0100966 genomic_target_enrichment_method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] + Sequence information GENEPIO:0100967 genomic_target_enrichment_method_details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel + Sequence information GENEPIO:0001456 amplicon_pcr_primer_scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 + Sequence information GENEPIO:0001449 amplicon_size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 + Sequence information GENEPIO:0101102 sequencing_flow_cell_version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 + Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no + Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz + Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz + Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 + Sequence information GENEPIO:0101715 genome_sequence_filename genome_sequence_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta + GENEPIO:0001457 Bioinformatics and QC metrics + Bioinformatics and QC metrics GENEPIO:0100557 quality_control_method_name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools + Bioinformatics and QC metrics GENEPIO:0100558 quality_control_method_version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 + Bioinformatics and QC metrics GENEPIO:0100559 quality_control_determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control + Bioinformatics and QC metrics GENEPIO:0100560 quality_control_issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage + Bioinformatics and QC metrics GENEPIO:0100561 quality_control_details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. + Bioinformatics and QC metrics GENEPIO:0001458 raw_sequence_data_processing_method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 + Bioinformatics and QC metrics GENEPIO:0001459 dehosting_method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper + Bioinformatics and QC metrics GENEPIO:0100825 sequence_assembly_software_name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet + Bioinformatics and QC metrics GENEPIO:0100826 sequence_assembly_software_version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 + Bioinformatics and QC metrics GENEPIO:0001463 consensus_sequence_software_name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar + Bioinformatics and QC metrics GENEPIO:0001469 consensus_sequence_software_version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 + Bioinformatics and QC metrics GENEPIO:0001472 breadth_of_coverage_value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 + Bioinformatics and QC metrics GENEPIO:0001474 depth_of_coverage_value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 + Bioinformatics and QC metrics GENEPIO:0001475 depth_of_coverage_threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 + Bioinformatics and QC metrics GENEPIO:0100844 genome_completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 + Bioinformatics and QC metrics GENEPIO:0001482 number_of_base_pairs_sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 + Bioinformatics and QC metrics GENEPIO:0100827 number_of_total_reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 + Bioinformatics and QC metrics GENEPIO:0100828 number_of_unique_reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 + Bioinformatics and QC metrics GENEPIO:0100829 minimum_post-trimming_read_length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 + Bioinformatics and QC metrics GENEPIO:0100937 number_of_contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 + Bioinformatics and QC metrics GENEPIO:0100830 percent_Ns_across_total_genome_length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0001484 Ns_per_100_kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 + Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 + Bioinformatics and QC metrics GENEPIO:0100845 percent_read_contamination_ percent_read_contamination_ integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0100846 sequence_assembly_length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 + Bioinformatics and QC metrics GENEPIO:0001483 consensus_genome_length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 + Bioinformatics and QC metrics GENEPIO:0001485 reference_genome_accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 + Bioinformatics and QC metrics GENEPIO:0100831 deduplication_method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics_protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf + GENEPIO:0101082 Taxonomic identification information + Taxonomic identification information GENEPIO:0100832 read_mapping_software_name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat + Taxonomic identification information GENEPIO:0100833 read_mapping_software_version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 + Taxonomic identification information GENEPIO:0100834 taxonomic_reference_database_name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon + Taxonomic identification information GENEPIO:0100835 taxonomic_reference_database_version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 + Taxonomic identification information GENEPIO:0101074 taxonomic_analysis_report_filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc + Taxonomic identification information GENEPIO:0101075 taxonomic_analysis_date taxonomic_analysis_date date {today} The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 + Taxonomic identification information GENEPIO:0100836 read_mapping_criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 + GENEPIO:0100477 Public repository information public_repository_information + Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca + Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 + Public repository information GENEPIO:0100476 attribute_package attribute_package AttributePackageMenu NullValueMenu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] + Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession + Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID + Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 + Public repository information GENEPIO:0001145 GenBank_accession genbank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 + GENEPIO:0100478 Risk assessment information risk_assessment_information + Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples + Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. + Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production WhitespaceMinimizedString NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] + Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention + Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed + GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance + Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AmrTestingByMenu NullValueMenu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date date {today} The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 + Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name AntimicrobialVendorName NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance neomycin_resistance_phenotype neomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] + Antimicrobial resistance neomycin_measurement neomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of neomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 + Antimicrobial resistance neomycin_measurement_units neomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] + Antimicrobial resistance neomycin_measurement_sign neomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] + Antimicrobial resistance neomycin_laboratory_typing_method neomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] + Antimicrobial resistance neomycin_laboratory_typing_platform neomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] + Antimicrobial resistance neomycin_laboratory_typing_platform_version neomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance neomycin_vendor_name neomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre + Antimicrobial resistance neomycin_testing_standard neomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + Antimicrobial resistance neomycin_testing_standard_version neomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance neomycin_testing_standard_details neomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance neomycin_susceptible_breakpoint neomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance neomycin_intermediate_breakpoint neomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance neomycin_resistant_breakpoint neomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance penicillin_resistance_phenotype penicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] + Antimicrobial resistance penicillin_measurement penicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of penicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 + Antimicrobial resistance penicillin_measurement_units penicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] + Antimicrobial resistance penicillin_measurement_sign penicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] + Antimicrobial resistance penicillin_laboratory_typing_method penicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] + Antimicrobial resistance penicillin_laboratory_typing_platform penicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] + Antimicrobial resistance penicillin_laboratory_typing_platform_version penicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance penicillin_vendor_name penicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre + Antimicrobial resistance penicillin_testing_standard penicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + Antimicrobial resistance penicillin_testing_standard_version penicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance penicillin_testing_standard_details penicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance penicillin_susceptible_breakpoint penicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance penicillin_intermediate_breakpoint penicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance penicillin_resistant_breakpoint penicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint trimethoprimsulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint trimethoprimsulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + GENEPIO:0001516 Contributor acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file