diff --git a/web/templates/grdi/schema_1m.json b/web/templates/grdi/schema_1m.json deleted file mode 100644 index 2e87e06b..00000000 --- a/web/templates/grdi/schema_1m.json +++ /dev/null @@ -1,10243 +0,0 @@ -{ - "name": "GRDI", - "description": "", - "id": "https://example.com/GRDI", - "version": "8.9.8", - "prefixes": { - "linkml": { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - "GENEPIO": { - "prefix_prefix": "GENEPIO", - "prefix_reference": "http://purl.obolibrary.org/obo/GENEPIO_" - }, - "xsd": { - "prefix_prefix": "xsd", - "prefix_reference": "http://www.w3.org/2001/XMLSchema#" - }, - "shex": { - "prefix_prefix": "shex", - "prefix_reference": "http://www.w3.org/ns/shex#" - }, - "schema": { - "prefix_prefix": "schema", - "prefix_reference": "http://schema.org/" - } - }, - "default_prefix": "https://example.com/GRDI/", - "types": { - "WhitespaceMinimizedString": { - "name": "WhitespaceMinimizedString", - "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", - "from_schema": "https://example.com/GRDI", - "typeof": "string", - "base": "str", - "uri": "xsd:token" - }, - "Provenance": { - "name": "Provenance", - "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", - "from_schema": "https://example.com/GRDI", - "typeof": "string", - "base": "str", - "uri": "xsd:token" - }, - "string": { - "name": "string", - "description": "A character string", - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "xsd:string" - }, - "integer": { - "name": "integer", - "description": "An integer", - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "xsd:integer" - }, - "boolean": { - "name": "boolean", - "description": "A binary (true or false) value", - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "xsd:boolean", - "repr": "bool" - }, - "float": { - "name": "float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "xsd:float" - }, - "double": { - "name": "double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://example.com/GRDI", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "xsd:double" - }, - "decimal": { - "name": "decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://example.com/GRDI", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "xsd:decimal" - }, - "time": { - "name": "time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "xsd:dateTime", - "repr": "str" - }, - "date": { - "name": "date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "xsd:date", - "repr": "str" - }, - "datetime": { - "name": "datetime", - "description": "The combination of a date and time", - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "xsd:dateTime", - "repr": "str" - }, - "date_or_datetime": { - "name": "date_or_datetime", - "description": "Either a date or a datetime", - "from_schema": "https://example.com/GRDI", - "base": "str", - "uri": "linkml:DateOrDatetime", - "repr": "str" - }, - "uriorcurie": { - "name": "uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://example.com/GRDI", - "base": "URIorCURIE", - "uri": "xsd:anyURI", - "repr": "str" - }, - "curie": { - "name": "curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://example.com/GRDI", - "base": "Curie", - "uri": "xsd:string", - "repr": "str" - }, - "uri": { - "name": "uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://example.com/GRDI", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "xsd:anyURI", - "repr": "str" - }, - "ncname": { - "name": "ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://example.com/GRDI", - "base": "NCName", - "uri": "xsd:string", - "repr": "str" - }, - "objectidentifier": { - "name": "objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritence and type checking" - ], - "from_schema": "https://example.com/GRDI", - "base": "ElementIdentifier", - "uri": "shex:iri", - "repr": "str" - }, - "nodeidentifier": { - "name": "nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://example.com/GRDI", - "base": "NodeIdentifier", - "uri": "shex:nonLiteral", - "repr": "str" - } - }, - "enums": { - "null value menu": { - "name": "null value menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Not Applicable [GENEPIO:0001619]": { - "text": "Not Applicable [GENEPIO:0001619]" - }, - "Missing [GENEPIO:0001618]": { - "text": "Missing [GENEPIO:0001618]" - }, - "Not Collected [GENEPIO:0001620]": { - "text": "Not Collected [GENEPIO:0001620]" - }, - "Not Provided [GENEPIO:0001668]": { - "text": "Not Provided [GENEPIO:0001668]" - }, - "Restricted Access [GENEPIO:0001810]": { - "text": "Restricted Access [GENEPIO:0001810]" - } - } - }, - "sample_collected_by menu": { - "name": "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]" - }, - "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]" - }, - "University of Manitoba (UM) [GENEPIO:0004434]": { - "text": "University of Manitoba (UM) [GENEPIO:0004434]" - } - } - }, - "purpose_of_sampling menu": { - "name": "purpose_of_sampling menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Cluster/Outbreak investigation [GENEPIO:0100001]": { - "text": "Cluster/Outbreak investigation [GENEPIO:0100001]" - }, - "Diagnostic testing [GENEPIO:0100002]": { - "text": "Diagnostic testing [GENEPIO:0100002]" - }, - "Environmental testing [GENEPIO:0100548]": { - "text": "Environmental testing [GENEPIO:0100548]" - }, - "Research [GENEPIO:0100003]": { - "text": "Research [GENEPIO:0100003]" - }, - "Clinical trial [GENEPIO:0100549]": { - "text": "Clinical trial [GENEPIO:0100549]", - "is_a": "Research [GENEPIO:0100003]" - }, - "Field experiment [GENEPIO:0100550]": { - "text": "Field experiment [GENEPIO:0100550]", - "is_a": "Research [GENEPIO:0100003]" - }, - "Survey study [GENEPIO:0100582]": { - "text": "Survey study [GENEPIO:0100582]", - "is_a": "Research [GENEPIO:0100003]" - }, - "Surveillance [GENEPIO:0100004]": { - "text": "Surveillance [GENEPIO:0100004]" - } - } - }, - "presampling_activity menu": { - "name": "presampling_activity menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Addition of substances to food/water [GENEPIO:0100536]": { - "text": "Addition of substances to food/water [GENEPIO:0100536]" - }, - "Antimicrobial pre-treatment [GENEPIO:0100537]": { - "text": "Antimicrobial pre-treatment [GENEPIO:0100537]" - }, - "Certified animal husbandry practices [GENEPIO:0100538]": { - "text": "Certified animal husbandry practices [GENEPIO:0100538]" - }, - "Certified humane animal husbandry practices [GENEPIO:0100894]": { - "text": "Certified humane animal husbandry practices [GENEPIO:0100894]", - "is_a": "Certified animal husbandry practices [GENEPIO:0100538]" - }, - "Certified organic farming practices [GENEPIO:0100539]": { - "text": "Certified organic farming practices [GENEPIO:0100539]" - }, - "Conventional farming practices [GENEPIO:0100895]": { - "text": "Conventional farming practices [GENEPIO:0100895]" - }, - "Change in storage conditions [GENEPIO:0100540]": { - "text": "Change in storage conditions [GENEPIO:0100540]" - }, - "Cleaning/disinfection [GENEPIO:0100541]": { - "text": "Cleaning/disinfection [GENEPIO:0100541]" - }, - "Extended downtime between activities [GENEPIO:0100542]": { - "text": "Extended downtime between activities [GENEPIO:0100542]" - }, - "Fertilizer pre-treatment [GENEPIO:0100543]": { - "text": "Fertilizer pre-treatment [GENEPIO:0100543]" - }, - "Genetic mutation [GENEPIO:0100544[": { - "text": "Genetic mutation [GENEPIO:0100544[" - }, - "Logistic slaughter [GENEPIO:0100545]": { - "text": "Logistic slaughter [GENEPIO:0100545]" - }, - "Microbial pre-treatment [GENEPIO:0100546]": { - "text": "Microbial pre-treatment [GENEPIO:0100546]" - }, - "Probiotic pre-treatment [GENEPIO:0100547]": { - "text": "Probiotic pre-treatment [GENEPIO:0100547]" - }, - "Vaccination [NCIT:C15346]": { - "text": "Vaccination [NCIT:C15346]" - } - } - }, - "specimen_processing menu": { - "name": "specimen_processing menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Biological replicate [OBI:0000198]": { - "text": "Biological replicate [OBI:0000198]" - }, - "Samples pooled [OBI:0600016]": { - "text": "Samples pooled [OBI:0600016]" - }, - "Technical replicate [OBI:0000249]": { - "text": "Technical replicate [OBI:0000249]" - }, - "Isolated from single source [GENEPIO:0100926]": { - "text": "Isolated from single source [GENEPIO:0100926]" - } - } - }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Afghanistan [GAZ:00006882]": { - "text": "Afghanistan [GAZ:00006882]" - }, - "Albania [GAZ:00002953]": { - "text": "Albania [GAZ:00002953]" - }, - "Algeria [GAZ:00000563]": { - "text": "Algeria [GAZ:00000563]" - }, - "American Samoa [GAZ:00003957]": { - "text": "American Samoa [GAZ:00003957]" - }, - "Andorra [GAZ:00002948]": { - "text": "Andorra [GAZ:00002948]" - }, - "Angola [GAZ:00001095]": { - "text": "Angola [GAZ:00001095]" - }, - "Anguilla [GAZ:00009159]": { - "text": "Anguilla [GAZ:00009159]" - }, - "Antarctica [GAZ:00000462]": { - "text": "Antarctica [GAZ:00000462]" - }, - "Antigua and Barbuda [GAZ:00006883]": { - "text": "Antigua and Barbuda [GAZ:00006883]" - }, - "Argentina [GAZ:00002928]": { - "text": "Argentina [GAZ:00002928]" - }, - "Armenia [GAZ:00004094]": { - "text": "Armenia [GAZ:00004094]" - }, - "Aruba [GAZ:00004025]": { - "text": "Aruba [GAZ:00004025]" - }, - "Ashmore and Cartier Islands [GAZ:00005901]": { - "text": "Ashmore and Cartier Islands [GAZ:00005901]" - }, - "Australia [GAZ:00000463]": { - "text": "Australia [GAZ:00000463]" - }, - "Austria [GAZ:00002942]": { - "text": "Austria [GAZ:00002942]" - }, - "Azerbaijan [GAZ:00004941]": { - "text": "Azerbaijan [GAZ:00004941]" - }, - "Bahamas [GAZ:00002733]": { - "text": "Bahamas [GAZ:00002733]" - }, - "Bahrain [GAZ:00005281]": { - "text": "Bahrain [GAZ:00005281]" - }, - "Baker Island [GAZ:00007117]": { - "text": "Baker Island [GAZ:00007117]" - }, - "Bangladesh [GAZ:00003750]": { - "text": "Bangladesh [GAZ:00003750]" - }, - "Barbados [GAZ:00001251]": { - "text": "Barbados [GAZ:00001251]" - }, - "Bassas da India [GAZ:00005810]": { - "text": "Bassas da India [GAZ:00005810]" - }, - "Belarus [GAZ:00006886]": { - "text": "Belarus [GAZ:00006886]" - }, - "Belgium [GAZ:00002938]": { - "text": "Belgium [GAZ:00002938]" - }, - "Belize [GAZ:00002934]": { - "text": "Belize [GAZ:00002934]" - }, - "Benin [GAZ:00000904]": { - "text": "Benin [GAZ:00000904]" - }, - "Bermuda [GAZ:00001264]": { - "text": "Bermuda [GAZ:00001264]" - }, - "Bhutan [GAZ:00003920]": { - "text": "Bhutan [GAZ:00003920]" - }, - "Bolivia [GAZ:00002511]": { - "text": "Bolivia [GAZ:00002511]" - }, - "Borneo [GAZ:00025355]": { - "text": "Borneo [GAZ:00025355]" - }, - "Bosnia and Herzegovina [GAZ:00006887]": { - "text": "Bosnia and Herzegovina [GAZ:00006887]" - }, - "Botswana [GAZ:00001097]": { - "text": "Botswana [GAZ:00001097]" - }, - "Bouvet Island [GAZ:00001453]": { - "text": "Bouvet Island [GAZ:00001453]" - }, - "Brazil [GAZ:00002828]": { - "text": "Brazil [GAZ:00002828]" - }, - "British Virgin Islands [GAZ:00003961]": { - "text": "British Virgin Islands [GAZ:00003961]" - }, - "Brunei [GAZ:00003901]": { - "text": "Brunei [GAZ:00003901]" - }, - "Bulgaria [GAZ:00002950]": { - "text": "Bulgaria [GAZ:00002950]" - }, - "Burkina Faso [GAZ:00000905]": { - "text": "Burkina Faso [GAZ:00000905]" - }, - "Burundi [GAZ:00001090]": { - "text": "Burundi [GAZ:00001090]" - }, - "Cambodia [GAZ:00006888]": { - "text": "Cambodia [GAZ:00006888]" - }, - "Cameroon [GAZ:00001093]": { - "text": "Cameroon [GAZ:00001093]" - }, - "Canada [GAZ:00002560]": { - "text": "Canada [GAZ:00002560]" - }, - "Cape Verde [GAZ:00001227]": { - "text": "Cape Verde [GAZ:00001227]" - }, - "Cayman Islands [GAZ:00003986]": { - "text": "Cayman Islands [GAZ:00003986]" - }, - "Central African Republic [GAZ:00001089]": { - "text": "Central African Republic [GAZ:00001089]" - }, - "Chad [GAZ:00000586]": { - "text": "Chad [GAZ:00000586]" - }, - "Chile [GAZ:00002825]": { - "text": "Chile [GAZ:00002825]" - }, - "China [GAZ:00002845]": { - "text": "China [GAZ:00002845]" - }, - "Christmas Island [GAZ:00005915]": { - "text": "Christmas Island [GAZ:00005915]" - }, - "Clipperton Island [GAZ:00005838]": { - "text": "Clipperton Island [GAZ:00005838]" - }, - "Cocos Islands [GAZ:00009721]": { - "text": "Cocos Islands [GAZ:00009721]" - }, - "Colombia [GAZ:00002929]": { - "text": "Colombia [GAZ:00002929]" - }, - "Comoros [GAZ:00005820]": { - "text": "Comoros [GAZ:00005820]" - }, - "Cook Islands [GAZ:00053798]": { - "text": "Cook Islands [GAZ:00053798]" - }, - "Coral Sea Islands [GAZ:00005917]": { - "text": "Coral Sea Islands [GAZ:00005917]" - }, - "Costa Rica [GAZ:00002901]": { - "text": "Costa Rica [GAZ:00002901]" - }, - "Cote d'Ivoire [GAZ:00000906]": { - "text": "Cote d'Ivoire [GAZ:00000906]" - }, - "Croatia [GAZ:00002719]": { - "text": "Croatia [GAZ:00002719]" - }, - "Cuba [GAZ:00003762]": { - "text": "Cuba [GAZ:00003762]" - }, - "Curacao [GAZ:00012582]": { - "text": "Curacao [GAZ:00012582]" - }, - "Cyprus [GAZ:00004006]": { - "text": "Cyprus [GAZ:00004006]" - }, - "Czech Republic [GAZ:00002954]": { - "text": "Czech Republic [GAZ:00002954]" - }, - "Democratic Republic of the Congo [GAZ:00001086]": { - "text": "Democratic Republic of the Congo [GAZ:00001086]" - }, - "Denmark [GAZ:00005852]": { - "text": "Denmark [GAZ:00005852]" - }, - "Djibouti [GAZ:00000582]": { - "text": "Djibouti [GAZ:00000582]" - }, - "Dominica [GAZ:00006890]": { - "text": "Dominica [GAZ:00006890]" - }, - "Dominican Republic [GAZ:00003952]": { - "text": "Dominican Republic [GAZ:00003952]" - }, - "Ecuador [GAZ:00002912]": { - "text": "Ecuador [GAZ:00002912]" - }, - "Egypt [GAZ:00003934]": { - "text": "Egypt [GAZ:00003934]" - }, - "El Salvador [GAZ:00002935]": { - "text": "El Salvador [GAZ:00002935]" - }, - "Equatorial Guinea [GAZ:00001091]": { - "text": "Equatorial Guinea [GAZ:00001091]" - }, - "Eritrea [GAZ:00000581]": { - "text": "Eritrea [GAZ:00000581]" - }, - "Estonia [GAZ:00002959]": { - "text": "Estonia [GAZ:00002959]" - }, - "Eswatini [GAZ:00001099]": { - "text": "Eswatini [GAZ:00001099]" - }, - "Ethiopia [GAZ:00000567]": { - "text": "Ethiopia [GAZ:00000567]" - }, - "Europa Island [GAZ:00005811]": { - "text": "Europa Island [GAZ:00005811]" - }, - "Falkland Islands (Islas Malvinas) [GAZ:00001412]": { - "text": "Falkland Islands (Islas Malvinas) [GAZ:00001412]" - }, - "Faroe Islands [GAZ:00059206]": { - "text": "Faroe Islands [GAZ:00059206]" - }, - "Fiji [GAZ:00006891]": { - "text": "Fiji [GAZ:00006891]" - }, - "Finland [GAZ:00002937]": { - "text": "Finland [GAZ:00002937]" - }, - "France [GAZ:00003940]": { - "text": "France [GAZ:00003940]" - }, - "French Guiana [GAZ:00002516]": { - "text": "French Guiana [GAZ:00002516]" - }, - "French Polynesia [GAZ:00002918]": { - "text": "French Polynesia [GAZ:00002918]" - }, - "French Southern and Antarctic Lands [GAZ:00003753]": { - "text": "French Southern and Antarctic Lands [GAZ:00003753]" - }, - "Gabon [GAZ:00001092]": { - "text": "Gabon [GAZ:00001092]" - }, - "Gambia [GAZ:00000907]": { - "text": "Gambia [GAZ:00000907]" - }, - "Gaza Strip [GAZ:00009571]": { - "text": "Gaza Strip [GAZ:00009571]" - }, - "Georgia [GAZ:00004942]": { - "text": "Georgia [GAZ:00004942]" - }, - "Germany [GAZ:00002646]": { - "text": "Germany [GAZ:00002646]" - }, - "Ghana [GAZ:00000908]": { - "text": "Ghana [GAZ:00000908]" - }, - "Gibraltar [GAZ:00003987]": { - "text": "Gibraltar [GAZ:00003987]" - }, - "Glorioso Islands [GAZ:00005808]": { - "text": "Glorioso Islands [GAZ:00005808]" - }, - "Greece [GAZ:00002945]": { - "text": "Greece [GAZ:00002945]" - }, - "Greenland [GAZ:00001507]": { - "text": "Greenland [GAZ:00001507]" - }, - "Grenada [GAZ:02000573]": { - "text": "Grenada [GAZ:02000573]" - }, - "Guadeloupe [GAZ:00067142]": { - "text": "Guadeloupe [GAZ:00067142]" - }, - "Guam [GAZ:00003706]": { - "text": "Guam [GAZ:00003706]" - }, - "Guatemala [GAZ:00002936]": { - "text": "Guatemala [GAZ:00002936]" - }, - "Guernsey [GAZ:00001550]": { - "text": "Guernsey [GAZ:00001550]" - }, - "Guinea [GAZ:00000909]": { - "text": "Guinea [GAZ:00000909]" - }, - "Guinea-Bissau [GAZ:00000910]": { - "text": "Guinea-Bissau [GAZ:00000910]" - }, - "Guyana [GAZ:00002522]": { - "text": "Guyana [GAZ:00002522]" - }, - "Haiti [GAZ:00003953]": { - "text": "Haiti [GAZ:00003953]" - }, - "Heard Island and McDonald Islands [GAZ:00009718]": { - "text": "Heard Island and McDonald Islands [GAZ:00009718]" - }, - "Honduras [GAZ:00002894]": { - "text": "Honduras [GAZ:00002894]" - }, - "Hong Kong [GAZ:00003203]": { - "text": "Hong Kong [GAZ:00003203]" - }, - "Howland Island [GAZ:00007120]": { - "text": "Howland Island [GAZ:00007120]" - }, - "Hungary [GAZ:00002952]": { - "text": "Hungary [GAZ:00002952]" - }, - "Iceland [GAZ:00000843]": { - "text": "Iceland [GAZ:00000843]" - }, - "India [GAZ:00002839]": { - "text": "India [GAZ:00002839]" - }, - "Indonesia [GAZ:00003727]": { - "text": "Indonesia [GAZ:00003727]" - }, - "Iran [GAZ:00004474]": { - "text": "Iran [GAZ:00004474]" - }, - "Iraq [GAZ:00004483]": { - "text": "Iraq [GAZ:00004483]" - }, - "Ireland [GAZ:00002943]": { - "text": "Ireland [GAZ:00002943]" - }, - "Isle of Man [GAZ:00052477]": { - "text": "Isle of Man [GAZ:00052477]" - }, - "Israel [GAZ:00002476]": { - "text": "Israel [GAZ:00002476]" - }, - "Italy [GAZ:00002650]": { - "text": "Italy [GAZ:00002650]" - }, - "Jamaica [GAZ:00003781]": { - "text": "Jamaica [GAZ:00003781]" - }, - "Jan Mayen [GAZ:00005853]": { - "text": "Jan Mayen [GAZ:00005853]" - }, - "Japan [GAZ:00002747]": { - "text": "Japan [GAZ:00002747]" - }, - "Jarvis Island [GAZ:00007118]": { - "text": "Jarvis Island [GAZ:00007118]" - }, - "Jersey [GAZ:00001551]": { - "text": "Jersey [GAZ:00001551]" - }, - "Johnston Atoll [GAZ:00007114]": { - "text": "Johnston Atoll [GAZ:00007114]" - }, - "Jordan [GAZ:00002473]": { - "text": "Jordan [GAZ:00002473]" - }, - "Juan de Nova Island [GAZ:00005809]": { - "text": "Juan de Nova Island [GAZ:00005809]" - }, - "Kazakhstan [GAZ:00004999]": { - "text": "Kazakhstan [GAZ:00004999]" - }, - "Kenya [GAZ:00001101]": { - "text": "Kenya [GAZ:00001101]" - }, - "Kerguelen Archipelago [GAZ:00005682]": { - "text": "Kerguelen Archipelago [GAZ:00005682]" - }, - "Kingman Reef [GAZ:00007116]": { - "text": "Kingman Reef [GAZ:00007116]" - }, - "Kiribati [GAZ:00006894]": { - "text": "Kiribati [GAZ:00006894]" - }, - "Kosovo [GAZ:00011337]": { - "text": "Kosovo [GAZ:00011337]" - }, - "Kuwait [GAZ:00005285]": { - "text": "Kuwait [GAZ:00005285]" - }, - "Kyrgyzstan [GAZ:00006893]": { - "text": "Kyrgyzstan [GAZ:00006893]" - }, - "Laos [GAZ:00006889]": { - "text": "Laos [GAZ:00006889]" - }, - "Latvia [GAZ:00002958]": { - "text": "Latvia [GAZ:00002958]" - }, - "Lebanon [GAZ:00002478]": { - "text": "Lebanon [GAZ:00002478]" - }, - "Lesotho [GAZ:00001098]": { - "text": "Lesotho [GAZ:00001098]" - }, - "Liberia [GAZ:00000911]": { - "text": "Liberia [GAZ:00000911]" - }, - "Libya [GAZ:00000566]": { - "text": "Libya [GAZ:00000566]" - }, - "Liechtenstein [GAZ:00003858]": { - "text": "Liechtenstein [GAZ:00003858]" - }, - "Line Islands [GAZ:00007144]": { - "text": "Line Islands [GAZ:00007144]" - }, - "Lithuania [GAZ:00002960]": { - "text": "Lithuania [GAZ:00002960]" - }, - "Luxembourg [GAZ:00002947]": { - "text": "Luxembourg [GAZ:00002947]" - }, - "Macau [GAZ:00003202]": { - "text": "Macau [GAZ:00003202]" - }, - "Madagascar [GAZ:00001108]": { - "text": "Madagascar [GAZ:00001108]" - }, - "Malawi [GAZ:00001105]": { - "text": "Malawi [GAZ:00001105]" - }, - "Malaysia [GAZ:00003902]": { - "text": "Malaysia [GAZ:00003902]" - }, - "Maldives [GAZ:00006924]": { - "text": "Maldives [GAZ:00006924]" - }, - "Mali [GAZ:00000584]": { - "text": "Mali [GAZ:00000584]" - }, - "Malta [GAZ:00004017]": { - "text": "Malta [GAZ:00004017]" - }, - "Marshall Islands [GAZ:00007161]": { - "text": "Marshall Islands [GAZ:00007161]" - }, - "Martinique [GAZ:00067143]": { - "text": "Martinique [GAZ:00067143]" - }, - "Mauritania [GAZ:00000583]": { - "text": "Mauritania [GAZ:00000583]" - }, - "Mauritius [GAZ:00003745]": { - "text": "Mauritius [GAZ:00003745]" - }, - "Mayotte [GAZ:00003943]": { - "text": "Mayotte [GAZ:00003943]" - }, - "Mexico [GAZ:00002852]": { - "text": "Mexico [GAZ:00002852]" - }, - "Micronesia [GAZ:00005862]": { - "text": "Micronesia [GAZ:00005862]" - }, - "Midway Islands [GAZ:00007112]": { - "text": "Midway Islands [GAZ:00007112]" - }, - "Moldova [GAZ:00003897]": { - "text": "Moldova [GAZ:00003897]" - }, - "Monaco [GAZ:00003857]": { - "text": "Monaco [GAZ:00003857]" - }, - "Mongolia [GAZ:00008744]": { - "text": "Mongolia [GAZ:00008744]" - }, - "Montenegro [GAZ:00006898]": { - "text": "Montenegro [GAZ:00006898]" - }, - "Montserrat [GAZ:00003988]": { - "text": "Montserrat [GAZ:00003988]" - }, - "Morocco [GAZ:00000565]": { - "text": "Morocco [GAZ:00000565]" - }, - "Mozambique [GAZ:00001100]": { - "text": "Mozambique [GAZ:00001100]" - }, - "Myanmar [GAZ:00006899]": { - "text": "Myanmar [GAZ:00006899]" - }, - "Namibia [GAZ:00001096]": { - "text": "Namibia [GAZ:00001096]" - }, - "Nauru [GAZ:00006900]": { - "text": "Nauru [GAZ:00006900]" - }, - "Navassa Island [GAZ:00007119]": { - "text": "Navassa Island [GAZ:00007119]" - }, - "Nepal [GAZ:00004399]": { - "text": "Nepal [GAZ:00004399]" - }, - "Netherlands [GAZ:00002946]": { - "text": "Netherlands [GAZ:00002946]" - }, - "New Caledonia [GAZ:00005206]": { - "text": "New Caledonia [GAZ:00005206]" - }, - "New Zealand [GAZ:00000469]": { - "text": "New Zealand [GAZ:00000469]" - }, - "Nicaragua [GAZ:00002978]": { - "text": "Nicaragua [GAZ:00002978]" - }, - "Niger [GAZ:00000585]": { - "text": "Niger [GAZ:00000585]" - }, - "Nigeria [GAZ:00000912]": { - "text": "Nigeria [GAZ:00000912]" - }, - "Niue [GAZ:00006902]": { - "text": "Niue [GAZ:00006902]" - }, - "Norfolk Island [GAZ:00005908]": { - "text": "Norfolk Island [GAZ:00005908]" - }, - "North Korea [GAZ:00002801]": { - "text": "North Korea [GAZ:00002801]" - }, - "North Macedonia [GAZ:00006895]": { - "text": "North Macedonia [GAZ:00006895]" - }, - "North Sea [GAZ:00002284]": { - "text": "North Sea [GAZ:00002284]" - }, - "Northern Mariana Islands [GAZ:00003958]": { - "text": "Northern Mariana Islands [GAZ:00003958]" - }, - "Norway [GAZ:00002699]": { - "text": "Norway [GAZ:00002699]" - }, - "Oman [GAZ:00005283]": { - "text": "Oman [GAZ:00005283]" - }, - "Pakistan [GAZ:00005246]": { - "text": "Pakistan [GAZ:00005246]" - }, - "Palau [GAZ:00006905]": { - "text": "Palau [GAZ:00006905]" - }, - "Panama [GAZ:00002892]": { - "text": "Panama [GAZ:00002892]" - }, - "Papua New Guinea [GAZ:00003922]": { - "text": "Papua New Guinea [GAZ:00003922]" - }, - "Paracel Islands [GAZ:00010832]": { - "text": "Paracel Islands [GAZ:00010832]" - }, - "Paraguay [GAZ:00002933]": { - "text": "Paraguay [GAZ:00002933]" - }, - "Peru [GAZ:00002932]": { - "text": "Peru [GAZ:00002932]" - }, - "Philippines [GAZ:00004525]": { - "text": "Philippines [GAZ:00004525]" - }, - "Pitcairn Islands [GAZ:00005867]": { - "text": "Pitcairn Islands [GAZ:00005867]" - }, - "Poland [GAZ:00002939]": { - "text": "Poland [GAZ:00002939]" - }, - "Portugal [GAZ:00004126]": { - "text": "Portugal [GAZ:00004126]" - }, - "Puerto Rico [GAZ:00006935]": { - "text": "Puerto Rico [GAZ:00006935]" - }, - "Qatar [GAZ:00005286]": { - "text": "Qatar [GAZ:00005286]" - }, - "Republic of the Congo [GAZ:00001088]": { - "text": "Republic of the Congo [GAZ:00001088]" - }, - "Reunion [GAZ:00003945]": { - "text": "Reunion [GAZ:00003945]" - }, - "Romania [GAZ:00002951]": { - "text": "Romania [GAZ:00002951]" - }, - "Ross Sea [GAZ:00023304]": { - "text": "Ross Sea [GAZ:00023304]" - }, - "Russia [GAZ:00002721]": { - "text": "Russia [GAZ:00002721]" - }, - "Rwanda [GAZ:00001087]": { - "text": "Rwanda [GAZ:00001087]" - }, - "Saint Helena [GAZ:00000849]": { - "text": "Saint Helena [GAZ:00000849]" - }, - "Saint Kitts and Nevis [GAZ:00006906]": { - "text": "Saint Kitts and Nevis [GAZ:00006906]" - }, - "Saint Lucia [GAZ:00006909]": { - "text": "Saint Lucia [GAZ:00006909]" - }, - "Saint Pierre and Miquelon [GAZ:00003942]": { - "text": "Saint Pierre and Miquelon [GAZ:00003942]" - }, - "Saint Martin [GAZ:00005841]": { - "text": "Saint Martin [GAZ:00005841]" - }, - "Saint Vincent and the Grenadines [GAZ:02000565]": { - "text": "Saint Vincent and the Grenadines [GAZ:02000565]" - }, - "Samoa [GAZ:00006910]": { - "text": "Samoa [GAZ:00006910]" - }, - "San Marino [GAZ:00003102]": { - "text": "San Marino [GAZ:00003102]" - }, - "Sao Tome and Principe [GAZ:00006927]": { - "text": "Sao Tome and Principe [GAZ:00006927]" - }, - "Saudi Arabia [GAZ:00005279]": { - "text": "Saudi Arabia [GAZ:00005279]" - }, - "Senegal [GAZ:00000913]": { - "text": "Senegal [GAZ:00000913]" - }, - "Serbia [GAZ:00002957]": { - "text": "Serbia [GAZ:00002957]" - }, - "Seychelles [GAZ:00006922]": { - "text": "Seychelles [GAZ:00006922]" - }, - "Sierra Leone [GAZ:00000914]": { - "text": "Sierra Leone [GAZ:00000914]" - }, - "Singapore [GAZ:00003923]": { - "text": "Singapore [GAZ:00003923]" - }, - "Sint Maarten [GAZ:00012579]": { - "text": "Sint Maarten [GAZ:00012579]" - }, - "Slovakia [GAZ:00002956]": { - "text": "Slovakia [GAZ:00002956]" - }, - "Slovenia [GAZ:00002955]": { - "text": "Slovenia [GAZ:00002955]" - }, - "Solomon Islands [GAZ:00005275]": { - "text": "Solomon Islands [GAZ:00005275]" - }, - "Somalia [GAZ:00001104]": { - "text": "Somalia [GAZ:00001104]" - }, - "South Africa [GAZ:00001094]": { - "text": "South Africa [GAZ:00001094]" - }, - "South Georgia and the South Sandwich Islands [GAZ:00003990]": { - "text": "South Georgia and the South Sandwich Islands [GAZ:00003990]" - }, - "South Korea [GAZ:00002802]": { - "text": "South Korea [GAZ:00002802]" - }, - "South Sudan [GAZ:00233439]": { - "text": "South Sudan [GAZ:00233439]" - }, - "Spain [GAZ:00003936]": { - "text": "Spain [GAZ:00003936]" - }, - "Spratly Islands [GAZ:00010831]": { - "text": "Spratly Islands [GAZ:00010831]" - }, - "Sri Lanka [GAZ:00003924]": { - "text": "Sri Lanka [GAZ:00003924]" - }, - "State of Palestine [GAZ:00002475]": { - "text": "State of Palestine [GAZ:00002475]" - }, - "Sudan [GAZ:00000560]": { - "text": "Sudan [GAZ:00000560]" - }, - "Suriname [GAZ:00002525]": { - "text": "Suriname [GAZ:00002525]" - }, - "Svalbard [GAZ:00005396]": { - "text": "Svalbard [GAZ:00005396]" - }, - "Swaziland [GAZ:00001099]": { - "text": "Swaziland [GAZ:00001099]" - }, - "Sweden [GAZ:00002729]": { - "text": "Sweden [GAZ:00002729]" - }, - "Switzerland [GAZ:00002941]": { - "text": "Switzerland [GAZ:00002941]" - }, - "Syria [GAZ:00002474]": { - "text": "Syria [GAZ:00002474]" - }, - "Taiwan [GAZ:00005341]": { - "text": "Taiwan [GAZ:00005341]" - }, - "Tajikistan [GAZ:00006912]": { - "text": "Tajikistan [GAZ:00006912]" - }, - "Tanzania [GAZ:00001103]": { - "text": "Tanzania [GAZ:00001103]" - }, - "Thailand [GAZ:00003744]": { - "text": "Thailand [GAZ:00003744]" - }, - "Timor-Leste [GAZ:00006913]": { - "text": "Timor-Leste [GAZ:00006913]" - }, - "Togo [GAZ:00000915]": { - "text": "Togo [GAZ:00000915]" - }, - "Tokelau [GAZ:00260188]": { - "text": "Tokelau [GAZ:00260188]" - }, - "Tonga [GAZ:00006916]": { - "text": "Tonga [GAZ:00006916]" - }, - "Trinidad and Tobago [GAZ:00003767]": { - "text": "Trinidad and Tobago [GAZ:00003767]" - }, - "Tromelin Island [GAZ:00005812]": { - "text": "Tromelin Island [GAZ:00005812]" - }, - "Tunisia [GAZ:00000562]": { - "text": "Tunisia [GAZ:00000562]" - }, - "Turkey [GAZ:00000558]": { - "text": "Turkey [GAZ:00000558]" - }, - "Turkmenistan [GAZ:00005018]": { - "text": "Turkmenistan [GAZ:00005018]" - }, - "Turks and Caicos Islands [GAZ:00003955]": { - "text": "Turks and Caicos Islands [GAZ:00003955]" - }, - "Tuvalu [GAZ:00009715]": { - "text": "Tuvalu [GAZ:00009715]" - }, - "United States of America [GAZ:00002459]": { - "text": "United States of America [GAZ:00002459]" - }, - "Uganda [GAZ:00001102]": { - "text": "Uganda [GAZ:00001102]" - }, - "Ukraine [GAZ:00002724]": { - "text": "Ukraine [GAZ:00002724]" - }, - "United Arab Emirates [GAZ:00005282]": { - "text": "United Arab Emirates [GAZ:00005282]" - }, - "United Kingdom [GAZ:00002637]": { - "text": "United Kingdom [GAZ:00002637]" - }, - "Uruguay [GAZ:00002930]": { - "text": "Uruguay [GAZ:00002930]" - }, - "Uzbekistan [GAZ:00004979]": { - "text": "Uzbekistan [GAZ:00004979]" - }, - "Vanuatu [GAZ:00006918]": { - "text": "Vanuatu [GAZ:00006918]" - }, - "Venezuela [GAZ:00002931]": { - "text": "Venezuela [GAZ:00002931]" - }, - "Viet Nam [GAZ:00003756]": { - "text": "Viet Nam [GAZ:00003756]" - }, - "Virgin Islands [GAZ:00003959]": { - "text": "Virgin Islands [GAZ:00003959]" - }, - "Wake Island [GAZ:00007111]": { - "text": "Wake Island [GAZ:00007111]" - }, - "Wallis and Futuna [GAZ:00007191]": { - "text": "Wallis and Futuna [GAZ:00007191]" - }, - "West Bank [GAZ:00009572]": { - "text": "West Bank [GAZ:00009572]" - }, - "Western Sahara [GAZ:00000564]": { - "text": "Western Sahara [GAZ:00000564]" - }, - "Yemen [GAZ:00005284]": { - "text": "Yemen [GAZ:00005284]" - }, - "Zambia [GAZ:00001107]": { - "text": "Zambia [GAZ:00001107]" - }, - "Zimbabwe [GAZ:00001106]": { - "text": "Zimbabwe [GAZ:00001106]" - } - } - }, - "geo_loc_name (state/province/region) menu": { - "name": "geo_loc_name (state/province/region) menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Atlantic region (Canada) [wikidata:Q246972]": { - "text": "Atlantic region (Canada) [wikidata:Q246972]" - }, - "New Brunswick [GAZ:00002570]": { - "text": "New Brunswick [GAZ:00002570]", - "is_a": "Atlantic region (Canada) [wikidata:Q246972]" - }, - "Newfoundland & Labrador [GAZ:00002567]": { - "text": "Newfoundland & Labrador [GAZ:00002567]", - "is_a": "Atlantic region (Canada) [wikidata:Q246972]" - }, - "Nova Scotia [GAZ:00002565]": { - "text": "Nova Scotia [GAZ:00002565]", - "is_a": "Atlantic region (Canada) [wikidata:Q246972]" - }, - "Prince Edward Island [GAZ:00002572]": { - "text": "Prince Edward Island [GAZ:00002572]", - "is_a": "Atlantic region (Canada) [wikidata:Q246972]" - }, - "Central region (Canada) [wikidata:Q1048064]": { - "text": "Central region (Canada) [wikidata:Q1048064]" - }, - "Ontario [GAZ:00002563]": { - "text": "Ontario [GAZ:00002563]", - "is_a": "Central region (Canada) [wikidata:Q1048064]" - }, - "Quebec [GAZ:00002569]": { - "text": "Quebec [GAZ:00002569]", - "is_a": "Central region (Canada) [wikidata:Q1048064]" - }, - "Northern region (Canada) [wikidata:Q764146]": { - "text": "Northern region (Canada) [wikidata:Q764146]" - }, - "Northwest Territories [GAZ:00002575]": { - "text": "Northwest Territories [GAZ:00002575]", - "is_a": "Northern region (Canada) [wikidata:Q764146]" - }, - "Nunuvut [GAZ:00002574]": { - "text": "Nunuvut [GAZ:00002574]", - "is_a": "Northern region (Canada) [wikidata:Q764146]" - }, - "Yukon [GAZ:00002576]": { - "text": "Yukon [GAZ:00002576]", - "is_a": "Northern region (Canada) [wikidata:Q764146]" - }, - "Pacific region (Canada) [wikidata:Q122953299]": { - "text": "Pacific region (Canada) [wikidata:Q122953299]" - }, - "British Columbia [GAZ:00002562]": { - "text": "British Columbia [GAZ:00002562]", - "is_a": "Pacific region (Canada) [wikidata:Q122953299]" - }, - "Prairie region (Canada) [wikidata:Q1364746]": { - "text": "Prairie region (Canada) [wikidata:Q1364746]" - }, - "Alberta [GAZ:00002566]": { - "text": "Alberta [GAZ:00002566]", - "is_a": "Prairie region (Canada) [wikidata:Q1364746]" - }, - "Manitoba [GAZ:00002571]": { - "text": "Manitoba [GAZ:00002571]", - "is_a": "Prairie region (Canada) [wikidata:Q1364746]" - }, - "Saskatchewan [GAZ:00002564]": { - "text": "Saskatchewan [GAZ:00002564]", - "is_a": "Prairie region (Canada) [wikidata:Q1364746]" - } - } - }, - "sample_collection_date_precision menu": { - "name": "sample_collection_date_precision menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "year [UO:0000036]": { - "text": "year [UO:0000036]" - }, - "month [UO:0000035]": { - "text": "month [UO:0000035]" - }, - "day [UO:0000033]": { - "text": "day [UO:0000033]" - } - } - }, - "environmental_site menu": { - "name": "environmental_site menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Abattoir [ENVO:01000925]": { - "text": "Abattoir [ENVO:01000925]" - }, - "Agricultural Field [ENVO:00000114]": { - "text": "Agricultural Field [ENVO:00000114]" - }, - "Alluvial fan [ENVO:00000314]": { - "text": "Alluvial fan [ENVO:00000314]" - }, - "Animal cage [ENVO:01000922]": { - "text": "Animal cage [ENVO:01000922]" - }, - "Aquarium [ENVO:00002196]": { - "text": "Aquarium [ENVO:00002196]" - }, - "Artificial wetland [ENVO:03501406]": { - "text": "Artificial wetland [ENVO:03501406]" - }, - "Breeding ground [ENVO:03501441]": { - "text": "Breeding ground [ENVO:03501441]" - }, - "Building [ENVO:00000073]": { - "text": "Building [ENVO:00000073]" - }, - "Barn [EOL:0001898]": { - "text": "Barn [EOL:0001898]", - "is_a": "Building [ENVO:00000073]" - }, - "Breeder barn [ENVO:03501383]": { - "text": "Breeder barn [ENVO:03501383]", - "is_a": "Barn [EOL:0001898]" - }, - "Broiler barn [ENVO:03501386]": { - "text": "Broiler barn [ENVO:03501386]", - "is_a": "Barn [EOL:0001898]" - }, - "Sheep barn [ENVO:03501385]": { - "text": "Sheep barn [ENVO:03501385]", - "is_a": "Barn [EOL:0001898]" - }, - "Biodome [ENVO:03501397]": { - "text": "Biodome [ENVO:03501397]", - "is_a": "Building [ENVO:00000073]" - }, - "Cottage [ENVO:03501393]": { - "text": "Cottage [ENVO:03501393]", - "is_a": "Building [ENVO:00000073]" - }, - "Dairy [ENVO:00003862]": { - "text": "Dairy [ENVO:00003862]", - "is_a": "Building [ENVO:00000073]" - }, - "Hospital [ENVO:00002173]": { - "text": "Hospital [ENVO:00002173]", - "is_a": "Building [ENVO:00000073]" - }, - "Laboratory facility [ENVO:01001406]": { - "text": "Laboratory facility [ENVO:01001406]", - "is_a": "Building [ENVO:00000073]" - }, - "Pigsty [ENVO:03501413]": { - "text": "Pigsty [ENVO:03501413]", - "is_a": "Building [ENVO:00000073]" - }, - "Building part (organizational term)": { - "text": "Building part (organizational term)" - }, - "Air intake [ENVO:03501380]": { - "text": "Air intake [ENVO:03501380]", - "is_a": "Building part (organizational term)" - }, - "Animal pen [ENVO:03501387]": { - "text": "Animal pen [ENVO:03501387]", - "is_a": "Building part (organizational term)" - }, - "Building floor [ENVO:01000486]": { - "text": "Building floor [ENVO:01000486]", - "is_a": "Building part (organizational term)" - }, - "Building wall [ENVO:01000465]": { - "text": "Building wall [ENVO:01000465]", - "is_a": "Building part (organizational term)" - }, - "Countertop [ENVO:03501404]": { - "text": "Countertop [ENVO:03501404]", - "is_a": "Building part (organizational term)" - }, - "Shelf [ENVO:03501403]": { - "text": "Shelf [ENVO:03501403]", - "is_a": "Building part (organizational term)" - }, - "Stall [EOL:0001903]": { - "text": "Stall [EOL:0001903]", - "is_a": "Building part (organizational term)" - }, - "Window sill [ENVO:03501381]": { - "text": "Window sill [ENVO:03501381]", - "is_a": "Building part (organizational term)" - }, - "Creek [ENVO:03501405]": { - "text": "Creek [ENVO:03501405]" - }, - "Farm [ENVO:00000078]": { - "text": "Farm [ENVO:00000078]" - }, - "Beef farm [ENVO:03501443]": { - "text": "Beef farm [ENVO:03501443]", - "is_a": "Farm [ENVO:00000078]" - }, - "Breeder farm [ENVO:03501384]": { - "text": "Breeder farm [ENVO:03501384]", - "is_a": "Farm [ENVO:00000078]" - }, - "Dairy farm [ENVO:03501416]": { - "text": "Dairy farm [ENVO:03501416]", - "is_a": "Farm [ENVO:00000078]" - }, - "Feedlot [ENVO:01000627]": { - "text": "Feedlot [ENVO:01000627]", - "is_a": "Farm [ENVO:00000078]" - }, - "Beef cattle feedlot [ENVO:03501444]": { - "text": "Beef cattle feedlot [ENVO:03501444]", - "is_a": "Feedlot [ENVO:01000627]" - }, - "Fish farm [ENVO:00000294]": { - "text": "Fish farm [ENVO:00000294]", - "is_a": "Farm [ENVO:00000078]" - }, - "Research farm [ENVO:03501417]": { - "text": "Research farm [ENVO:03501417]", - "is_a": "Farm [ENVO:00000078]" - }, - "Central Experimental Farm [GAZ:00004603]": { - "text": "Central Experimental Farm [GAZ:00004603]", - "is_a": "Farm [ENVO:00000078]" - }, - "Freshwater environment [ENVO:01000306]": { - "text": "Freshwater environment [ENVO:01000306]" - }, - "Hatchery [ENVO:01001873]": { - "text": "Hatchery [ENVO:01001873]" - }, - "Poultry hatchery [ENVO:01001874]": { - "text": "Poultry hatchery [ENVO:01001874]", - "is_a": "Hatchery [ENVO:01001873]" - }, - "Lake [ENVO:00000020]": { - "text": "Lake [ENVO:00000020]" - }, - "Manure digester facility [ENVO:03501422]": { - "text": "Manure digester facility [ENVO:03501422]" - }, - "Manure lagoon (Anaerobic lagoon) [ENVO:03501423]": { - "text": "Manure lagoon (Anaerobic lagoon) [ENVO:03501423]" - }, - "Manure pit [ENVO:01001872]": { - "text": "Manure pit [ENVO:01001872]" - }, - "Marine environment [ENVO:01000320]": { - "text": "Marine environment [ENVO:01000320]" - }, - "Benthic zone [ENVO:03501440]": { - "text": "Benthic zone [ENVO:03501440]", - "is_a": "Marine environment [ENVO:01000320]" - }, - "Pelagic zone [ENVO:00000208]": { - "text": "Pelagic zone [ENVO:00000208]", - "is_a": "Marine environment [ENVO:01000320]" - }, - "Park [ENVO:00000562]": { - "text": "Park [ENVO:00000562]" - }, - "Pond [ENVO:00000033]": { - "text": "Pond [ENVO:00000033]" - }, - "Reservoir [ENVO:00000025]": { - "text": "Reservoir [ENVO:00000025]" - }, - "Irrigation reservoir [ENVO:00000450]": { - "text": "Irrigation reservoir [ENVO:00000450]", - "is_a": "Reservoir [ENVO:00000025]" - }, - "Retail environment [ENVO:01001448]": { - "text": "Retail environment [ENVO:01001448]" - }, - "Shop [ENVO:00002221]": { - "text": "Shop [ENVO:00002221]", - "is_a": "Retail environment [ENVO:01001448]" - }, - "Butcher shop [ENVO:03501396]": { - "text": "Butcher shop [ENVO:03501396]", - "is_a": "Shop [ENVO:00002221]" - }, - "Pet store [ENVO:03501395]": { - "text": "Pet store [ENVO:03501395]", - "is_a": "Shop [ENVO:00002221]" - }, - "Supermarket [ENVO:01000984]": { - "text": "Supermarket [ENVO:01000984]", - "is_a": "Shop [ENVO:00002221]" - }, - "River [ENVO:00000022]": { - "text": "River [ENVO:00000022]" - }, - "Roost (bird) [ENVO:03501439]": { - "text": "Roost (bird) [ENVO:03501439]" - }, - "Rural area [ENVO:01000772]": { - "text": "Rural area [ENVO:01000772]" - }, - "Slough [ENVO:03501438]": { - "text": "Slough [ENVO:03501438]" - }, - "Stream [ENVO:00000023]": { - "text": "Stream [ENVO:00000023]" - }, - "Trailer [ENVO:03501394]": { - "text": "Trailer [ENVO:03501394]" - }, - "Tributary [ENVO:00000495]": { - "text": "Tributary [ENVO:00000495]" - }, - "Truck [ENVO:01000602]": { - "text": "Truck [ENVO:01000602]" - }, - "Urban area [ENVO:03501437]": { - "text": "Urban area [ENVO:03501437]" - }, - "Water surface [ENVO:01001191]": { - "text": "Water surface [ENVO:01001191]" - }, - "Woodland area [ENVO:00000109]": { - "text": "Woodland area [ENVO:00000109]" - }, - "Zoo [ENVO:00010625]": { - "text": "Zoo [ENVO:00010625]" - } - } - }, - "antimicrobial_resistance_test_drug menu": { - "name": "antimicrobial_resistance_test_drug menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "amikacin": { - "text": "amikacin" - }, - "amoxicillin-clavulanic_acid": { - "text": "amoxicillin-clavulanic_acid" - }, - "ampicillin": { - "text": "ampicillin" - }, - "azithromycin": { - "text": "azithromycin" - }, - "cefazolin": { - "text": "cefazolin" - }, - "cefepime": { - "text": "cefepime" - }, - "cefotaxime": { - "text": "cefotaxime" - }, - "cefotaxime-clavulanic_acid": { - "text": "cefotaxime-clavulanic_acid" - }, - "cefoxitin": { - "text": "cefoxitin" - }, - "cefpodoxime": { - "text": "cefpodoxime" - }, - "ceftazidime": { - "text": "ceftazidime" - }, - "ceftazidime-clavulanic_acid": { - "text": "ceftazidime-clavulanic_acid" - }, - "ceftiofur": { - "text": "ceftiofur" - }, - "ceftriaxone": { - "text": "ceftriaxone" - }, - "cephalothin": { - "text": "cephalothin" - }, - "chloramphenicol": { - "text": "chloramphenicol" - }, - "ciprofloxacin": { - "text": "ciprofloxacin" - }, - "clindamycin": { - "text": "clindamycin" - }, - "doxycycline": { - "text": "doxycycline" - }, - "enrofloxacin": { - "text": "enrofloxacin" - }, - "erythromycin": { - "text": "erythromycin" - }, - "florfenicol": { - "text": "florfenicol" - }, - "gentamicin": { - "text": "gentamicin" - }, - "imipenem": { - "text": "imipenem" - }, - "kanamycin": { - "text": "kanamycin" - }, - "levofloxacin": { - "text": "levofloxacin" - }, - "linezolid": { - "text": "linezolid" - }, - "meropenem": { - "text": "meropenem" - }, - "nalidixic_acid": { - "text": "nalidixic_acid" - }, - "nitrofurantoin": { - "text": "nitrofurantoin" - }, - "norfloxacin": { - "text": "norfloxacin" - }, - "oxolinic-acid": { - "text": "oxolinic-acid" - }, - "oxytetracycline": { - "text": "oxytetracycline" - }, - "piperacillin": { - "text": "piperacillin" - }, - "piperacillin-tazobactam": { - "text": "piperacillin-tazobactam" - }, - "polymyxin-b": { - "text": "polymyxin-b" - }, - "quinupristin-dalfopristin": { - "text": "quinupristin-dalfopristin" - }, - "streptomycin": { - "text": "streptomycin" - }, - "sulfisoxazole": { - "text": "sulfisoxazole" - }, - "telithromycin": { - "text": "telithromycin" - }, - "tetracycline": { - "text": "tetracycline" - }, - "tigecycline": { - "text": "tigecycline" - }, - "trimethoprim-sulfamethoxazole": { - "text": "trimethoprim-sulfamethoxazole" - } - } - }, - "available_data_types menu": { - "name": "available_data_types menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Documentation [GENEPIO:0100702]": { - "text": "Documentation [GENEPIO:0100702]" - }, - "Experimental parameters documentation [GENEPIO:0100703]": { - "text": "Experimental parameters documentation [GENEPIO:0100703]", - "is_a": "Documentation [GENEPIO:0100702]" - }, - "Feed history [GENEPIO:0100704]": { - "text": "Feed history [GENEPIO:0100704]", - "is_a": "Documentation [GENEPIO:0100702]" - }, - "Land use information [GENEPIO:0100705]": { - "text": "Land use information [GENEPIO:0100705]", - "is_a": "Documentation [GENEPIO:0100702]" - }, - "Therapeutic administration history [GENEPIO:0100706]": { - "text": "Therapeutic administration history [GENEPIO:0100706]", - "is_a": "Documentation [GENEPIO:0100702]" - }, - "Chemical characterization [GENEPIO:0100707]": { - "text": "Chemical characterization [GENEPIO:0100707]" - }, - "pH measurement [GENEPIO:0100708]": { - "text": "pH measurement [GENEPIO:0100708]", - "is_a": "Chemical characterization [GENEPIO:0100707]" - }, - "Dissolved oxygen measurement [GENEPIO:0100709]": { - "text": "Dissolved oxygen measurement [GENEPIO:0100709]", - "is_a": "Chemical characterization [GENEPIO:0100707]" - }, - "Nitrate measurement [GENEPIO:0100710]": { - "text": "Nitrate measurement [GENEPIO:0100710]", - "is_a": "Chemical characterization [GENEPIO:0100707]" - }, - "Nitrite measurement [GENEPIO:0100711]": { - "text": "Nitrite measurement [GENEPIO:0100711]", - "is_a": "Chemical characterization [GENEPIO:0100707]" - }, - "Phosphorous measurement [GENEPIO:0100712]": { - "text": "Phosphorous measurement [GENEPIO:0100712]", - "is_a": "Chemical characterization [GENEPIO:0100707]" - }, - "Salinity measurement [GENEPIO:0100713]": { - "text": "Salinity measurement [GENEPIO:0100713]", - "is_a": "Chemical characterization [GENEPIO:0100707]" - }, - "Microbiological characterization [GENEPIO:0100714]": { - "text": "Microbiological characterization [GENEPIO:0100714]" - }, - "Microbiological identification [GENEPIO:0100715]": { - "text": "Microbiological identification [GENEPIO:0100715]", - "is_a": "Microbiological characterization [GENEPIO:0100714]" - }, - "Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]": { - "text": "Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Microbiological identification (bioMérieux API) [GENEPIO:0100717]": { - "text": "Microbiological identification (bioMérieux API) [GENEPIO:0100717]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Microbiological identification (Biolog) [GENEPIO:0100718]": { - "text": "Microbiological identification (Biolog) [GENEPIO:0100718]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Microbiological identification (FAME) [GENEPIO:0100719]": { - "text": "Microbiological identification (FAME) [GENEPIO:0100719]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Microbiological identification (Sensititre) [GENEPIO:0100720]": { - "text": "Microbiological identification (Sensititre) [GENEPIO:0100720]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Microbiological identification (ViTek) [GENEPIO:0100721]": { - "text": "Microbiological identification (ViTek) [GENEPIO:0100721]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Phage type [GENEPIO:0100722]": { - "text": "Phage type [GENEPIO:0100722]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Serotype [GENEPIO:0100723]": { - "text": "Serotype [GENEPIO:0100723]", - "is_a": "Microbiological identification [GENEPIO:0100715]" - }, - "Phenotypic microbiological characterization [GENEPIO:0100724]": { - "text": "Phenotypic microbiological characterization [GENEPIO:0100724]", - "is_a": "Microbiological characterization [GENEPIO:0100714]" - }, - "AMR phenotypic testing [GENEPIO:0100725]": { - "text": "AMR phenotypic testing [GENEPIO:0100725]", - "is_a": "Phenotypic microbiological characterization [GENEPIO:0100724]" - }, - "Biolog phenotype microarray [GENEPIO:0100726]": { - "text": "Biolog phenotype microarray [GENEPIO:0100726]", - "is_a": "Phenotypic microbiological characterization [GENEPIO:0100724]" - }, - "Microbiological quantification [GENEPIO:0100727]": { - "text": "Microbiological quantification [GENEPIO:0100727]" - }, - "Colony count [GENEPIO:0100728]": { - "text": "Colony count [GENEPIO:0100728]", - "is_a": "Microbiological quantification [GENEPIO:0100727]" - }, - "Total coliform count [GENEPIO:0100729]": { - "text": "Total coliform count [GENEPIO:0100729]", - "is_a": "Colony count [GENEPIO:0100728]" - }, - "Total fecal coliform count [GENEPIO:0100730]": { - "text": "Total fecal coliform count [GENEPIO:0100730]", - "is_a": "Colony count [GENEPIO:0100728]" - }, - "Infectivity assay [GENEPIO:0100731]": { - "text": "Infectivity assay [GENEPIO:0100731]", - "is_a": "Microbiological quantification [GENEPIO:0100727]" - }, - "ELISA toxin binding [GENEPIO:0100732]": { - "text": "ELISA toxin binding [GENEPIO:0100732]", - "is_a": "Microbiological quantification [GENEPIO:0100727]" - }, - "Molecular characterization [GENEPIO:0100733]": { - "text": "Molecular characterization [GENEPIO:0100733]" - }, - "16S rRNA Sanger sequencing [GENEPIO:0100734]": { - "text": "16S rRNA Sanger sequencing [GENEPIO:0100734]", - "is_a": "Molecular characterization [GENEPIO:0100733]" - }, - "PCR marker detection [GENEPIO:0100735]": { - "text": "PCR marker detection [GENEPIO:0100735]", - "is_a": "Molecular characterization [GENEPIO:0100733]" - }, - "BOX PCR fingerprint [GENEPIO:0100736]": { - "text": "BOX PCR fingerprint [GENEPIO:0100736]", - "is_a": "PCR marker detection [GENEPIO:0100735]" - }, - "ERIC PCR fingerprint [GENEPIO:0100737]": { - "text": "ERIC PCR fingerprint [GENEPIO:0100737]", - "is_a": "PCR marker detection [GENEPIO:0100735]" - }, - "Plasmid type [GENEPIO:0100738]": { - "text": "Plasmid type [GENEPIO:0100738]", - "is_a": "Molecular characterization [GENEPIO:0100733]" - }, - "Ribotype [GENEPIO:0100739]": { - "text": "Ribotype [GENEPIO:0100739]", - "is_a": "Molecular characterization [GENEPIO:0100733]" - }, - "Molecular quantification [GENEPIO:0100740]": { - "text": "Molecular quantification [GENEPIO:0100740]" - }, - "qPCR marker organism quantification [GENEPIO:0100741]": { - "text": "qPCR marker organism quantification [GENEPIO:0100741]", - "is_a": "Molecular quantification [GENEPIO:0100740]" - }, - "Physical characterization [GENEPIO:0100742]": { - "text": "Physical characterization [GENEPIO:0100742]" - }, - "Conductivity measurement [GENEPIO:0100743]": { - "text": "Conductivity measurement [GENEPIO:0100743]", - "is_a": "Physical characterization [GENEPIO:0100742]" - }, - "Mollusc shell measurement [GENEPIO:0100744]": { - "text": "Mollusc shell measurement [GENEPIO:0100744]", - "is_a": "Physical characterization [GENEPIO:0100742]" - }, - "Mollusc shell length [GENEPIO:0100745]": { - "text": "Mollusc shell length [GENEPIO:0100745]", - "is_a": "Mollusc shell measurement [GENEPIO:0100744]" - }, - "Matter compostion [GENEPIO:0100746]": { - "text": "Matter compostion [GENEPIO:0100746]", - "is_a": "Physical characterization [GENEPIO:0100742]" - }, - "Dry matter composition [GENEPIO:0100747]": { - "text": "Dry matter composition [GENEPIO:0100747]", - "is_a": "Matter compostion [GENEPIO:0100746]" - }, - "Organic matter composition [GENEPIO:0100748]": { - "text": "Organic matter composition [GENEPIO:0100748]", - "is_a": "Matter compostion [GENEPIO:0100746]" - }, - "Turbidity measurement [GENEPIO:0100749]": { - "text": "Turbidity measurement [GENEPIO:0100749]", - "is_a": "Physical characterization [GENEPIO:0100742]" - } - } - }, - "weather_type menu": { - "name": "weather_type menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Cloudy/Overcast [ENVO:03501418]": { - "text": "Cloudy/Overcast [ENVO:03501418]" - }, - "Partially cloudy [ENVO:03501419]": { - "text": "Partially cloudy [ENVO:03501419]", - "is_a": "Cloudy/Overcast [ENVO:03501418]" - }, - "Drizzle [ENVO:03501420]": { - "text": "Drizzle [ENVO:03501420]" - }, - "Fog [ENVO:01000844]": { - "text": "Fog [ENVO:01000844]" - }, - "Rain [ENVO:01001564]": { - "text": "Rain [ENVO:01001564]" - }, - "Snow [ENVO:01000406]": { - "text": "Snow [ENVO:01000406]" - }, - "Storm [ENVO:01000876]": { - "text": "Storm [ENVO:01000876]" - }, - "Sunny/Clear [ENVO:03501421]": { - "text": "Sunny/Clear [ENVO:03501421]" - } - } - }, - "animal_or_plant_population menu": { - "name": "animal_or_plant_population menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Algae [FOODON:03411301]": { - "text": "Algae [FOODON:03411301]" - }, - "Algal bloom [ENVO:2000004]": { - "text": "Algal bloom [ENVO:2000004]", - "is_a": "Algae [FOODON:03411301]" - }, - "Cattle [FOODON:03411161]": { - "text": "Cattle [FOODON:03411161]" - }, - "Beef cattle [HSO:0000022]": { - "text": "Beef cattle [HSO:0000022]", - "is_a": "Cattle [FOODON:03411161]" - }, - "Dairy cattle [FOODON:00002505]": { - "text": "Dairy cattle [FOODON:00002505]", - "is_a": "Cattle [FOODON:03411161]" - }, - "Chicken [NCBITaxon:9031]": { - "text": "Chicken [NCBITaxon:9031]" - }, - "Crop [AGRO:00000325]": { - "text": "Crop [AGRO:00000325]" - }, - "Fish [FOODON:03411222]": { - "text": "Fish [FOODON:03411222]" - }, - "Pig [NCBITaxon:9823]": { - "text": "Pig [NCBITaxon:9823]" - }, - "Poultry [FOODON:00004298]": { - "text": "Poultry [FOODON:00004298]" - }, - "Sheep [NCBITaxon:9940]": { - "text": "Sheep [NCBITaxon:9940]" - }, - "Shellfish [FOODON:03411433]": { - "text": "Shellfish [FOODON:03411433]" - }, - "Crustacean [FOODON:03411374]": { - "text": "Crustacean [FOODON:03411374]", - "is_a": "Shellfish [FOODON:03411433]" - }, - "Mollusc [FOODON:03412112]": { - "text": "Mollusc [FOODON:03412112]", - "is_a": "Shellfish [FOODON:03411433]" - }, - "Tropical fish [FOODON:00004283]": { - "text": "Tropical fish [FOODON:00004283]" - }, - "Turkey [NCBITaxon:9103]": { - "text": "Turkey [NCBITaxon:9103]" - }, - "Wildlife [FOODON:00004503]": { - "text": "Wildlife [FOODON:00004503]" - }, - "Wild bird [FOODON:00004505]": { - "text": "Wild bird [FOODON:00004505]", - "is_a": "Wildlife [FOODON:00004503]" - }, - "Seabird [FOODON:00004504]": { - "text": "Seabird [FOODON:00004504]", - "is_a": "Wild bird [FOODON:00004505]" - } - } - }, - "environmental_material menu": { - "name": "environmental_material menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Air [ENVO:00002005]": { - "text": "Air [ENVO:00002005]" - }, - "Alluvium [ENVO:01001202]": { - "text": "Alluvium [ENVO:01001202]" - }, - "Animal feeding equipment [AGRO:00000675]": { - "text": "Animal feeding equipment [AGRO:00000675]" - }, - "Animal feeder [AGRO:00000679]": { - "text": "Animal feeder [AGRO:00000679]", - "is_a": "Animal feeding equipment [AGRO:00000675]" - }, - "Animal drinker [AGRO:00000680]": { - "text": "Animal drinker [AGRO:00000680]", - "is_a": "Animal feeding equipment [AGRO:00000675]" - }, - "Feed pan [AGRO:00000676]": { - "text": "Feed pan [AGRO:00000676]", - "is_a": "Animal feeding equipment [AGRO:00000675]" - }, - "Watering bowl [AGRO:00000677]": { - "text": "Watering bowl [AGRO:00000677]", - "is_a": "Animal feeding equipment [AGRO:00000675]" - }, - "Animal transportation equipment [AGRO:00000671]": { - "text": "Animal transportation equipment [AGRO:00000671]" - }, - "Dead haul trailer [GENEPIO:0100896]": { - "text": "Dead haul trailer [GENEPIO:0100896]", - "is_a": "Animal transportation equipment [AGRO:00000671]" - }, - "Dead haul truck [AGRO:00000673]": { - "text": "Dead haul truck [AGRO:00000673]", - "is_a": "Animal transportation equipment [AGRO:00000671]" - }, - "Live haul trailer [GENEPIO:0100897]": { - "text": "Live haul trailer [GENEPIO:0100897]", - "is_a": "Animal transportation equipment [AGRO:00000671]" - }, - "Live haul truck [AGRO:00000674]": { - "text": "Live haul truck [AGRO:00000674]", - "is_a": "Animal transportation equipment [AGRO:00000671]" - }, - "Belt [NCIT:C49844]": { - "text": "Belt [NCIT:C49844]" - }, - "Biosolids [ENVO:00002059]": { - "text": "Biosolids [ENVO:00002059]" - }, - "Boot [GSSO:012935]": { - "text": "Boot [GSSO:012935]" - }, - "Boot cover [OBI:0002806]": { - "text": "Boot cover [OBI:0002806]", - "is_a": "Boot [GSSO:012935]" - }, - "Broom [ENVO:03501377]": { - "text": "Broom [ENVO:03501377]" - }, - "Bulk tank [ENVO:03501379]": { - "text": "Bulk tank [ENVO:03501379]" - }, - "Chick box [AGRO:00000678]": { - "text": "Chick box [AGRO:00000678]" - }, - "Chick pad [AGRO:00000672]": { - "text": "Chick pad [AGRO:00000672]" - }, - "Cleaning equipment [ENVO:03501376]": { - "text": "Cleaning equipment [ENVO:03501376]" - }, - "Compost [ENVO:00002170]": { - "text": "Compost [ENVO:00002170]" - }, - "Contaminated water [ENVO:00002186]": { - "text": "Contaminated water [ENVO:00002186]" - }, - "Fecal slurry [ENVO:03501436]": { - "text": "Fecal slurry [ENVO:03501436]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Fluid from meat rinse [GENEPIO:0004323]": { - "text": "Fluid from meat rinse [GENEPIO:0004323]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Effluent [ENVO:03501407]": { - "text": "Effluent [ENVO:03501407]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Influent [ENVO:03501442]": { - "text": "Influent [ENVO:03501442]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Surface runoff [ENVO:03501408]": { - "text": "Surface runoff [ENVO:03501408]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Poultry plucking water [AGRO_00000693]": { - "text": "Poultry plucking water [AGRO_00000693]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Wastewater [ENVO:00002001]": { - "text": "Wastewater [ENVO:00002001]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Weep fluid [AGRO_00000692]": { - "text": "Weep fluid [AGRO_00000692]", - "is_a": "Contaminated water [ENVO:00002186]" - }, - "Crate [ENVO:03501372]": { - "text": "Crate [ENVO:03501372]" - }, - "Dumpster [ENVO:03501400]": { - "text": "Dumpster [ENVO:03501400]" - }, - "Dust [ENVO:00002008]": { - "text": "Dust [ENVO:00002008]" - }, - "Egg belt [AGRO:00000670]": { - "text": "Egg belt [AGRO:00000670]" - }, - "Fan [NCIT:C49947]": { - "text": "Fan [NCIT:C49947]" - }, - "Freezer [ENVO:03501415]": { - "text": "Freezer [ENVO:03501415]" - }, - "Freezer handle [ENVO:03501414]": { - "text": "Freezer handle [ENVO:03501414]", - "is_a": "Freezer [ENVO:03501415]" - }, - "Manure [ENVO:00003031]": { - "text": "Manure [ENVO:00003031]" - }, - "Animal manure [AGRO:00000079]": { - "text": "Animal manure [AGRO:00000079]", - "is_a": "Manure [ENVO:00003031]" - }, - "Pig manure [AGRO:00000080]": { - "text": "Pig manure [AGRO:00000080]", - "is_a": "Animal manure [AGRO:00000079]" - }, - "Manure digester equipment [ENVO:03501424]": { - "text": "Manure digester equipment [ENVO:03501424]" - }, - "Nest [ENVO:03501432]": { - "text": "Nest [ENVO:03501432]" - }, - "Bird's nest [ENVO:00005805]": { - "text": "Bird's nest [ENVO:00005805]", - "is_a": "Nest [ENVO:03501432]" - }, - "Permafrost [ENVO:00000134]": { - "text": "Permafrost [ENVO:00000134]" - }, - "Plucking belt [AGRO:00000669]": { - "text": "Plucking belt [AGRO:00000669]" - }, - "Poultry fluff [UBERON:0008291]": { - "text": "Poultry fluff [UBERON:0008291]" - }, - "Poultry litter [AGRO:00000080]": { - "text": "Poultry litter [AGRO:00000080]" - }, - "Sediment [ENVO:00002007]": { - "text": "Sediment [ENVO:00002007]" - }, - "Soil [ENVO:00001998]": { - "text": "Soil [ENVO:00001998]" - }, - "Agricultural soil [ENVO:00002259]": { - "text": "Agricultural soil [ENVO:00002259]", - "is_a": "Soil [ENVO:00001998]" - }, - "Forest soil [ENVO:00002261]": { - "text": "Forest soil [ENVO:00002261]", - "is_a": "Soil [ENVO:00001998]" - }, - "Straw [ENVO:00003869]": { - "text": "Straw [ENVO:00003869]" - }, - "Canola straw": { - "text": "Canola straw", - "is_a": "Straw [ENVO:00003869]" - }, - "Oat straw [FOODON:03309878]": { - "text": "Oat straw [FOODON:03309878]", - "is_a": "Straw [ENVO:00003869]" - }, - "Water [CHEBI:15377]": { - "text": "Water [CHEBI:15377]" - }, - "Drinking water [ENVO:00003064]": { - "text": "Drinking water [ENVO:00003064]", - "is_a": "Water [CHEBI:15377]" - }, - "Groundwater [ENVO:01001004]": { - "text": "Groundwater [ENVO:01001004]", - "is_a": "Water [CHEBI:15377]" - }, - "Surface water [ENVO:00002042]": { - "text": "Surface water [ENVO:00002042]", - "is_a": "Water [CHEBI:15377]" - } - } - }, - "anatomical_material menu": { - "name": "anatomical_material menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Blood [UBERON:0000178]": { - "text": "Blood [UBERON:0000178]" - }, - "Fluid [UBERON:0006314]": { - "text": "Fluid [UBERON:0006314]" - }, - "Fluid (cerebrospinal (CSF)) [UBERON:0001359]": { - "text": "Fluid (cerebrospinal (CSF)) [UBERON:0001359]", - "is_a": "Fluid [UBERON:0006314]" - }, - "Fluid (amniotic) [UBERON:0000173]": { - "text": "Fluid (amniotic) [UBERON:0000173]", - "is_a": "Fluid [UBERON:0006314]" - }, - "Saliva [UBERON:0001836]": { - "text": "Saliva [UBERON:0001836]", - "is_a": "Fluid [UBERON:0006314]" - }, - "Tissue [UBERON:0000479]": { - "text": "Tissue [UBERON:0000479]" - } - } - }, - "body_product menu": { - "name": "body_product menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Digestive organ content [GENEPIO:0100898]": { - "text": "Digestive organ content [GENEPIO:0100898]" - }, - "Caecal content [GENEPIO:0100899]": { - "text": "Caecal content [GENEPIO:0100899]", - "is_a": "Digestive organ content [GENEPIO:0100898]" - }, - "Intestinal content [GENEPIO:0100900]": { - "text": "Intestinal content [GENEPIO:0100900]", - "is_a": "Digestive organ content [GENEPIO:0100898]" - }, - "Stomach content [GENEPIO:0100901]": { - "text": "Stomach content [GENEPIO:0100901]", - "is_a": "Digestive organ content [GENEPIO:0100898]" - }, - "Feces [UBERON:0001988]": { - "text": "Feces [UBERON:0001988]" - }, - "Fecal composite [GENEPIO:0004512]": { - "text": "Fecal composite [GENEPIO:0004512]", - "is_a": "Feces [UBERON:0001988]" - }, - "Feces (fresh) [GENEPIO:0004512]": { - "text": "Feces (fresh) [GENEPIO:0004512]", - "is_a": "Feces [UBERON:0001988]" - }, - "Feces (environmental) [GENEPIO:0004514]": { - "text": "Feces (environmental) [GENEPIO:0004514]", - "is_a": "Feces [UBERON:0001988]" - }, - "Meconium [UBERON:0007109]": { - "text": "Meconium [UBERON:0007109]", - "is_a": "Feces [UBERON:0001988]" - }, - "Milk [UBERON:0001913]": { - "text": "Milk [UBERON:0001913]" - }, - "Colostrum [UBERON:0001914]": { - "text": "Colostrum [UBERON:0001914]", - "is_a": "Milk [UBERON:0001913]" - }, - "Urine [UBERON:0001088]": { - "text": "Urine [UBERON:0001088]" - } - } - }, - "anatomical_part menu": { - "name": "anatomical_part menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Carcass [UBERON:0008979]": { - "text": "Carcass [UBERON:0008979]" - }, - "Swine carcass [FOODON:03311719]": { - "text": "Swine carcass [FOODON:03311719]", - "is_a": "Carcass [UBERON:0008979]" - }, - "Digestive system [UBERON:0001007]": { - "text": "Digestive system [UBERON:0001007]" - }, - "Caecum [UBERON:0001153]": { - "text": "Caecum [UBERON:0001153]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Colon [UBERON:0001155]": { - "text": "Colon [UBERON:0001155]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Digestive gland [UBERON:0006925]": { - "text": "Digestive gland [UBERON:0006925]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Foregut [UBERON:0006925]": { - "text": "Foregut [UBERON:0006925]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Gall bladder [UBERON:0002110]": { - "text": "Gall bladder [UBERON:0002110]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Gastrointestinal system mucosa [UBERON:0004786]": { - "text": "Gastrointestinal system mucosa [UBERON:0004786]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Gizzard [UBERON:0005052]": { - "text": "Gizzard [UBERON:0005052]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Hindgut [UBERON:0001046]": { - "text": "Hindgut [UBERON:0001046]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Intestine [UBERON:0000160]": { - "text": "Intestine [UBERON:0000160]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Small intestine [UBERON:0002108]": { - "text": "Small intestine [UBERON:0002108]", - "is_a": "Intestine [UBERON:0000160]" - }, - "Duodenum [UBERON:0002114]": { - "text": "Duodenum [UBERON:0002114]", - "is_a": "Small intestine [UBERON:0002108]" - }, - "Ileum [UBERON:0002116]": { - "text": "Ileum [UBERON:0002116]", - "is_a": "Small intestine [UBERON:0002108]" - }, - "Jejunum [UBERON:0002115]": { - "text": "Jejunum [UBERON:0002115]", - "is_a": "Small intestine [UBERON:0002108]" - }, - "Stomach [UBERON:0000945]": { - "text": "Stomach [UBERON:0000945]", - "is_a": "Digestive system [UBERON:0001007]" - }, - "Abomasum [UBERON:0007358]": { - "text": "Abomasum [UBERON:0007358]", - "is_a": "Stomach [UBERON:0000945]" - }, - "Rumen [UBERON:0007365]": { - "text": "Rumen [UBERON:0007365]", - "is_a": "Stomach [UBERON:0000945]" - }, - "Excretory system (organizational term)": { - "text": "Excretory system (organizational term)" - }, - "Anus [UBERON:0001245]": { - "text": "Anus [UBERON:0001245]", - "is_a": "Excretory system (organizational term)" - }, - "Anal gland [UBERON:0011253]": { - "text": "Anal gland [UBERON:0011253]", - "is_a": "Excretory system (organizational term)" - }, - "Cloaca [UBERON:0000162]": { - "text": "Cloaca [UBERON:0000162]", - "is_a": "Excretory system (organizational term)" - }, - "Liver [UBERON:0002107]": { - "text": "Liver [UBERON:0002107]", - "is_a": "Excretory system (organizational term)" - }, - "Kidney [UBERON:0002113]": { - "text": "Kidney [UBERON:0002113]", - "is_a": "Excretory system (organizational term)" - }, - "Rectum [UBERON:0001052]": { - "text": "Rectum [UBERON:0001052]", - "is_a": "Excretory system (organizational term)" - }, - "Spleen [UBERON:0002106]": { - "text": "Spleen [UBERON:0002106]", - "is_a": "Excretory system (organizational term)" - }, - "Urinary bladder [UBERON:0001255]": { - "text": "Urinary bladder [UBERON:0001255]", - "is_a": "Excretory system (organizational term)" - }, - "Foot [BTO:0000476]": { - "text": "Foot [BTO:0000476]" - }, - "Head [UBERON:0000033]": { - "text": "Head [UBERON:0000033]", - "is_a": "Foot [BTO:0000476]" - }, - "Brain [UBERON:0000955]": { - "text": "Brain [UBERON:0000955]", - "is_a": "Foot [BTO:0000476]" - }, - "Ear [UBERON:0001690]": { - "text": "Ear [UBERON:0001690]", - "is_a": "Foot [BTO:0000476]" - }, - "Eye [UBERON:0000970]": { - "text": "Eye [UBERON:0000970]", - "is_a": "Foot [BTO:0000476]" - }, - "Mouth [UBERON:0000165]": { - "text": "Mouth [UBERON:0000165]", - "is_a": "Foot [BTO:0000476]" - }, - "Nose [UBERON:0000004]": { - "text": "Nose [UBERON:0000004]", - "is_a": "Foot [BTO:0000476]" - }, - "Nasal turbinal [UBERON:0035612]": { - "text": "Nasal turbinal [UBERON:0035612]", - "is_a": "Nose [UBERON:0000004]" - }, - "Nasopharynx (NP) [UBERON:0001728]": { - "text": "Nasopharynx (NP) [UBERON:0001728]", - "is_a": "Nose [UBERON:0000004]" - }, - "Pair of nares [UBERON:0002109]": { - "text": "Pair of nares [UBERON:0002109]", - "is_a": "Nose [UBERON:0000004]" - }, - "Paranasal sinus [UBERON:0001825]": { - "text": "Paranasal sinus [UBERON:0001825]", - "is_a": "Nose [UBERON:0000004]" - }, - "Snout [UBERON:0006333]": { - "text": "Snout [UBERON:0006333]", - "is_a": "Nose [UBERON:0000004]" - }, - "Lymphatic system [UBERON:0006558]": { - "text": "Lymphatic system [UBERON:0006558]" - }, - "Lymph node [UBERON:0000029]": { - "text": "Lymph node [UBERON:0000029]", - "is_a": "Lymphatic system [UBERON:0006558]" - }, - "Mesenteric lymph node [UBERON:0002509]": { - "text": "Mesenteric lymph node [UBERON:0002509]", - "is_a": "Lymph node [UBERON:0000029]" - }, - "Mantle (bird) [GENEPIO:0100927]": { - "text": "Mantle (bird) [GENEPIO:0100927]" - }, - "Neck [UBERON:0000974]": { - "text": "Neck [UBERON:0000974]" - }, - "Esophagus [UBERON:0001043]": { - "text": "Esophagus [UBERON:0001043]", - "is_a": "Neck [UBERON:0000974]" - }, - "Trachea [UBERON:0003126]": { - "text": "Trachea [UBERON:0003126]", - "is_a": "Neck [UBERON:0000974]" - }, - "Nerve [UBERON:0001021]": { - "text": "Nerve [UBERON:0001021]" - }, - "Spinal cord [UBERON:0002240]": { - "text": "Spinal cord [UBERON:0002240]", - "is_a": "Nerve [UBERON:0001021]" - }, - "Organs or organ parts [GENEPIO:0001117]": { - "text": "Organs or organ parts [GENEPIO:0001117]" - }, - "Organ [UBERON:0000062]": { - "text": "Organ [UBERON:0000062]", - "is_a": "Organs or organ parts [GENEPIO:0001117]" - }, - "Muscle organ [UBERON:0001630]": { - "text": "Muscle organ [UBERON:0001630]", - "is_a": "Organ [UBERON:0000062]" - }, - "Skin of body [UBERON:0002097]": { - "text": "Skin of body [UBERON:0002097]", - "is_a": "Organ [UBERON:0000062]" - }, - "Reproductive system [UBERON:0000990]": { - "text": "Reproductive system [UBERON:0000990]" - }, - "Embryo [UBERON:0000922]": { - "text": "Embryo [UBERON:0000922]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Fetus [UBERON:0000323]": { - "text": "Fetus [UBERON:0000323]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Ovary [UBERON:0000992]": { - "text": "Ovary [UBERON:0000992]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Oviduct [UBERON:0000993]": { - "text": "Oviduct [UBERON:0000993]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Placenta [UBERON:0001987]": { - "text": "Placenta [UBERON:0001987]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Testis [UBERON:0000473]": { - "text": "Testis [UBERON:0000473]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Uterus [UBERON:0000995]": { - "text": "Uterus [UBERON:0000995]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Vagina [UBERON:0000996]": { - "text": "Vagina [UBERON:0000996]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Yolk sac [UBERON:0001040]": { - "text": "Yolk sac [UBERON:0001040]", - "is_a": "Reproductive system [UBERON:0000990]" - }, - "Respiratory system [UBERON:0001004]": { - "text": "Respiratory system [UBERON:0001004]" - }, - "Air sac [UBERON:0009060]": { - "text": "Air sac [UBERON:0009060]", - "is_a": "Respiratory system [UBERON:0001004]" - }, - "Lung [UBERON:0002048]": { - "text": "Lung [UBERON:0002048]", - "is_a": "Vascular system [UBERON:0007798]" - }, - "Pleura [UBERON:0000977]": { - "text": "Pleura [UBERON:0000977]", - "is_a": "Respiratory system [UBERON:0001004]" - }, - "Respiratory system mucosa [UBERON:0004785]": { - "text": "Respiratory system mucosa [UBERON:0004785]", - "is_a": "Respiratory system [UBERON:0001004]" - }, - "Skeletal system [UBERON:0001434]": { - "text": "Skeletal system [UBERON:0001434]" - }, - "Skeletal joint [UBERON:0000982]": { - "text": "Skeletal joint [UBERON:0000982]", - "is_a": "Skeletal system [UBERON:0001434]" - }, - "Bone element [UBERON:0001474]": { - "text": "Bone element [UBERON:0001474]", - "is_a": "Skeletal system [UBERON:0001434]" - }, - "Thoracic segment of trunk [UBERON:0000915]": { - "text": "Thoracic segment of trunk [UBERON:0000915]" - }, - "Abdomen [UBERON:0000916]": { - "text": "Abdomen [UBERON:0000916]", - "is_a": "Thoracic segment of trunk [UBERON:0000915]" - }, - "Muscle of abdomen [UBERON:0002378]": { - "text": "Muscle of abdomen [UBERON:0002378]", - "is_a": "Abdomen [UBERON:0000916]" - }, - "Peritoneum [UBERON:0002358]": { - "text": "Peritoneum [UBERON:0002358]", - "is_a": "Abdomen [UBERON:0000916]" - }, - "Vascular system [UBERON:0007798]": { - "text": "Vascular system [UBERON:0007798]" - }, - "Blood vessel [UBERON:0001981]": { - "text": "Blood vessel [UBERON:0001981]", - "is_a": "Vascular system [UBERON:0007798]" - }, - "Bursa of Fabricius [UBERON:0003903]": { - "text": "Bursa of Fabricius [UBERON:0003903]", - "is_a": "Vascular system [UBERON:0007798]" - }, - "Gill [UBERON:0002535]": { - "text": "Gill [UBERON:0002535]", - "is_a": "Vascular system [UBERON:0007798]" - }, - "Heart [UBERON:0000948]": { - "text": "Heart [UBERON:0000948]", - "is_a": "Vascular system [UBERON:0007798]" - }, - "Pericardium [UBERON:0002407]": { - "text": "Pericardium [UBERON:0002407]", - "is_a": "Vascular system [UBERON:0007798]" - }, - "Vent (anatomical) [UBERON:2000298]": { - "text": "Vent (anatomical) [UBERON:2000298]" - }, - "Bird vent [UBERON:0012464]": { - "text": "Bird vent [UBERON:0012464]", - "is_a": "Vent (anatomical) [UBERON:2000298]" - }, - "Fish vent [GENEPIO:0100902]": { - "text": "Fish vent [GENEPIO:0100902]", - "is_a": "Vent (anatomical) [UBERON:2000298]" - } - } - }, - "anatomical_region menu": { - "name": "anatomical_region menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Dorso-lateral region [BSPO:0000080]": { - "text": "Dorso-lateral region [BSPO:0000080]" - }, - "Exterior anatomical region [BSPO:0000034]": { - "text": "Exterior anatomical region [BSPO:0000034]" - }, - "Interior anatomical region [BSPO:0000033]": { - "text": "Interior anatomical region [BSPO:0000033]" - } - } - }, - "food_product menu": { - "name": "food_product menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Animal feed [ENVO:02000047]": { - "text": "Animal feed [ENVO:02000047]" - }, - "Blood meal [FOODON:00001564]": { - "text": "Blood meal [FOODON:00001564]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Bone meal [ENVO:02000054]": { - "text": "Bone meal [ENVO:02000054]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Brassica carinata meal [FOODON:00004310]": { - "text": "Brassica carinata meal [FOODON:00004310]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Canola meal [FOODON:00002694]": { - "text": "Canola meal [FOODON:00002694]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Compound feed premix [FOODON:00004323]": { - "text": "Compound feed premix [FOODON:00004323]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Compound feed premix (medicated) [FOODON:00004324]": { - "text": "Compound feed premix (medicated) [FOODON:00004324]", - "is_a": "Compound feed premix [FOODON:00004323]" - }, - "Feather meal [FOODON:00003927]": { - "text": "Feather meal [FOODON:00003927]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Fish meal [FOODON:03301620]": { - "text": "Fish meal [FOODON:03301620]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Lay ration [FOODON:00004286]": { - "text": "Lay ration [FOODON:00004286]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Meat and bone meal [FOODON:00002738]": { - "text": "Meat and bone meal [FOODON:00002738]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Meat meal [FOODON:00004282]": { - "text": "Meat meal [FOODON:00004282]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Pet food [FOODON:00002682]": { - "text": "Pet food [FOODON:00002682]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Soybean meal [FOODON:03302757]": { - "text": "Soybean meal [FOODON:03302757]", - "is_a": "Animal feed [ENVO:02000047]" - }, - "Animal feed ingredient [FOODON:00004322]": { - "text": "Animal feed ingredient [FOODON:00004322]" - }, - "Dairy food product [FOODON:00001256]": { - "text": "Dairy food product [FOODON:00001256]" - }, - "Cheese block (whole or parts) [FOODON:03000287]": { - "text": "Cheese block (whole or parts) [FOODON:03000287]", - "is_a": "Dairy food product [FOODON:00001256]" - }, - "Cow skim milk (powdered) [FOODON:03310016]": { - "text": "Cow skim milk (powdered) [FOODON:03310016]", - "is_a": "Dairy food product [FOODON:00001256]" - }, - "Milk [UBERON:0001913]": { - "text": "Milk [UBERON:0001913]", - "is_a": "Dairy food product [FOODON:00001256]" - }, - "Dietary supplement [FOODON:03401298]": { - "text": "Dietary supplement [FOODON:03401298]" - }, - "Egg or egg component [FOODON:03420194]": { - "text": "Egg or egg component [FOODON:03420194]" - }, - "Balut [FOODON:03302184]": { - "text": "Balut [FOODON:03302184]", - "is_a": "Egg or egg component [FOODON:03420194]" - }, - "Egg yolk [UBERON:0007378]": { - "text": "Egg yolk [UBERON:0007378]", - "is_a": "Egg or egg component [FOODON:03420194]" - }, - "Poultry egg [FOODON:03000414]": { - "text": "Poultry egg [FOODON:03000414]", - "is_a": "Egg or egg component [FOODON:03420194]" - }, - "Hen egg (whole) [FOODON:03316061]": { - "text": "Hen egg (whole) [FOODON:03316061]", - "is_a": "Poultry egg [FOODON:03000414]" - }, - "Poultry egg (whole, shell on) [FOODON:03000415]": { - "text": "Poultry egg (whole, shell on) [FOODON:03000415]", - "is_a": "Poultry egg [FOODON:03000414]" - }, - "Food mixture [FOODON:00004130]": { - "text": "Food mixture [FOODON:00004130]" - }, - "Food product analog (food subsitute) [FOODON:00001871]": { - "text": "Food product analog (food subsitute) [FOODON:00001871]" - }, - "Milk substitute [FOODON:03305408]": { - "text": "Milk substitute [FOODON:03305408]", - "is_a": "Food product analog (food subsitute) [FOODON:00001871]" - }, - "Meat (whole or parts) [FOODON:03317170]": { - "text": "Meat (whole or parts) [FOODON:03317170]" - }, - "Cutlet [FOODON:00003001]": { - "text": "Cutlet [FOODON:00003001]", - "is_a": "Meat (whole or parts) [FOODON:03317170]" - }, - "Filet [FOODON:03530144]": { - "text": "Filet [FOODON:03530144]", - "is_a": "Meat (whole or parts) [FOODON:03317170]" - }, - "Liver (whole, raw) [FOODON:03309772]": { - "text": "Liver (whole, raw) [FOODON:03309772]", - "is_a": "Meat (whole or parts) [FOODON:03317170]" - }, - "Meat trim [FOODON:03309475]": { - "text": "Meat trim [FOODON:03309475]", - "is_a": "Meat (whole or parts) [FOODON:03317170]" - }, - "Rib (meat cut) [FOODON:03530023]": { - "text": "Rib (meat cut) [FOODON:03530023]", - "is_a": "Meat (whole or parts) [FOODON:03317170]" - }, - "Rib chop [FOODON:00004290]": { - "text": "Rib chop [FOODON:00004290]", - "is_a": "Rib (meat cut) [FOODON:03530023]" - }, - "Shoulder (meat cut) [FOODON:03530043]": { - "text": "Shoulder (meat cut) [FOODON:03530043]", - "is_a": "Meat (whole or parts) [FOODON:03317170]" - }, - "Grains, cereals, and bakery product (organizational term)": { - "text": "Grains, cereals, and bakery product (organizational term)" - }, - "Bread loaf (whole or parts) [FOODON:03000288]": { - "text": "Bread loaf (whole or parts) [FOODON:03000288]", - "is_a": "Grains, cereals, and bakery product (organizational term)" - }, - "Breakfast cereal [FOODON:03311075]": { - "text": "Breakfast cereal [FOODON:03311075]", - "is_a": "Grains, cereals, and bakery product (organizational term)" - }, - "Bulk grain [FOODON:03309390]": { - "text": "Bulk grain [FOODON:03309390]", - "is_a": "Grains, cereals, and bakery product (organizational term)" - }, - "Oat grain [FOODON:00003429]": { - "text": "Oat grain [FOODON:00003429]", - "is_a": "Grains, cereals, and bakery product (organizational term)" - }, - "Legume food product [FOODON:00001264]": { - "text": "Legume food product [FOODON:00001264]" - }, - "Chickpea (whole) [FOODON:03306811]": { - "text": "Chickpea (whole) [FOODON:03306811]", - "is_a": "Legume food product [FOODON:00001264]" - }, - "Hummus [FOODON:00003049]": { - "text": "Hummus [FOODON:00003049]", - "is_a": "Legume food product [FOODON:00001264]" - }, - "Soybean (whole or parts) [FOODON:03000245]": { - "text": "Soybean (whole or parts) [FOODON:03000245]", - "is_a": "Legume food product [FOODON:00001264]" - }, - "Meat, poultry and fish (organizational term)": { - "text": "Meat, poultry and fish (organizational term)" - }, - "Beef (ground or minced) [FOODON:00001282]": { - "text": "Beef (ground or minced) [FOODON:00001282]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Beef (ground or minced, boneless) [FOODON:03000412]": { - "text": "Beef (ground or minced, boneless) [FOODON:03000412]", - "is_a": "Beef (ground or minced) [FOODON:00001282]" - }, - "Beef (ground or minced, extra lean) [FOODON:03000398]": { - "text": "Beef (ground or minced, extra lean) [FOODON:03000398]", - "is_a": "Beef (ground or minced) [FOODON:00001282]" - }, - "Beef (ground or minced, lean) [FOODON:03000394]": { - "text": "Beef (ground or minced, lean) [FOODON:03000394]", - "is_a": "Beef (ground or minced) [FOODON:00001282]" - }, - "Beef (ground or minced, medium) [FOODON:03000402]": { - "text": "Beef (ground or minced, medium) [FOODON:03000402]", - "is_a": "Beef (ground or minced) [FOODON:00001282]" - }, - "Beef (ground or minced, regular) [FOODON:03000406]": { - "text": "Beef (ground or minced, regular) [FOODON:03000406]", - "is_a": "Beef (ground or minced) [FOODON:00001282]" - }, - "Beef (ground or minced, Sirloin) [FOODON:03000408]": { - "text": "Beef (ground or minced, Sirloin) [FOODON:03000408]", - "is_a": "Beef (ground or minced) [FOODON:00001282]" - }, - "Beef hamburger (dish) [FOODON:00002737]": { - "text": "Beef hamburger (dish) [FOODON:00002737]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Beef shoulder [FOODON:03000377]": { - "text": "Beef shoulder [FOODON:03000377]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Beef shoulder chop [FOODON:03000387]": { - "text": "Beef shoulder chop [FOODON:03000387]", - "is_a": "Beef shoulder [FOODON:03000377]" - }, - "Beef sirloin chop [FOODON:03000389]": { - "text": "Beef sirloin chop [FOODON:03000389]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Beef stew chunk [FOODON:00004288]": { - "text": "Beef stew chunk [FOODON:00004288]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Beef tenderloin [FOODON:00003302]": { - "text": "Beef tenderloin [FOODON:00003302]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Beef (whole cut or parts) [FOODON:03000333]": { - "text": "Beef (whole cut or parts) [FOODON:03000333]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Brisket [FOODON:03530020]": { - "text": "Brisket [FOODON:03530020]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Chicken breast [FOODON:00002703]": { - "text": "Chicken breast [FOODON:00002703]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Chicken breast (back off) [FOODON:03000385]": { - "text": "Chicken breast (back off) [FOODON:03000385]", - "is_a": "Chicken breast [FOODON:00002703]" - }, - "Chicken breast (skinless) [FOODON:00003332]": { - "text": "Chicken breast (skinless) [FOODON:00003332]", - "is_a": "Chicken breast [FOODON:00002703]" - }, - "Chicken breast (with skin) [FOODON:03000374]": { - "text": "Chicken breast (with skin) [FOODON:03000374]", - "is_a": "Chicken breast [FOODON:00002703]" - }, - "Chicken breast (skinless, boneless) [FOODON:00003364]": { - "text": "Chicken breast (skinless, boneless) [FOODON:00003364]", - "is_a": "Chicken breast [FOODON:00002703]" - }, - "Chicken breast cutlet [FOODON:00004308]": { - "text": "Chicken breast cutlet [FOODON:00004308]", - "is_a": "Chicken breast [FOODON:00002703]" - }, - "Chicken drumstick [FOODON:00002716]": { - "text": "Chicken drumstick [FOODON:00002716]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Chicken drumstick (skinless) [FOODON:03000366]": { - "text": "Chicken drumstick (skinless) [FOODON:03000366]", - "is_a": "Chicken drumstick [FOODON:00002716]" - }, - "Chicken drumstick (with skin) [FOODON:03000368]": { - "text": "Chicken drumstick (with skin) [FOODON:03000368]", - "is_a": "Chicken drumstick [FOODON:00002716]" - }, - "Chicken meat [FOODON:00001040]": { - "text": "Chicken meat [FOODON:00001040]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Chicken meat (ground or minced) [FOODON:03311826]": { - "text": "Chicken meat (ground or minced) [FOODON:03311826]", - "is_a": "Chicken meat [FOODON:00001040]" - }, - "Chicken meat (ground or minced, lean) [FOODON:03000392]": { - "text": "Chicken meat (ground or minced, lean) [FOODON:03000392]", - "is_a": "Chicken meat [FOODON:00001040]" - }, - "Chicken meat (ground or minced, extra lean) [FOODON:03000396]": { - "text": "Chicken meat (ground or minced, extra lean) [FOODON:03000396]", - "is_a": "Chicken meat [FOODON:00001040]" - }, - "Chicken meat (ground or minced, medium) [FOODON:03000400]": { - "text": "Chicken meat (ground or minced, medium) [FOODON:03000400]", - "is_a": "Chicken meat [FOODON:00001040]" - }, - "Chicken meat (ground or minced, regular) [FOODON:03000404]": { - "text": "Chicken meat (ground or minced, regular) [FOODON:03000404]", - "is_a": "Chicken meat [FOODON:00001040]" - }, - "Chicken meat (ground or minced, boneless) [FOODON:03000410]": { - "text": "Chicken meat (ground or minced, boneless) [FOODON:03000410]", - "is_a": "Chicken meat [FOODON:00001040]" - }, - "Chicken nugget [FOODON:00002672]": { - "text": "Chicken nugget [FOODON:00002672]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Chicken thigh": { - "text": "Chicken thigh", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Chicken thigh (skinless) [FOODON:00003331]": { - "text": "Chicken thigh (skinless) [FOODON:00003331]", - "is_a": "Chicken thigh" - }, - "Chicken thigh (skinless, with bone)": { - "text": "Chicken thigh (skinless, with bone)", - "is_a": "Chicken thigh" - }, - "Chicken thigh (skinless, boneless) [FOODON:03000417]": { - "text": "Chicken thigh (skinless, boneless) [FOODON:03000417]", - "is_a": "Chicken thigh" - }, - "Chicken upper thigh [FOODON:03000381]": { - "text": "Chicken upper thigh [FOODON:03000381]", - "is_a": "Chicken thigh (skinless, boneless) [FOODON:03000417]" - }, - "Chicken upper thigh (with skin) [FOODON:03000383]": { - "text": "Chicken upper thigh (with skin) [FOODON:03000383]", - "is_a": "Chicken upper thigh [FOODON:03000381]" - }, - "Chicken thigh (with skin) [FOODON:00003330]": { - "text": "Chicken thigh (with skin) [FOODON:00003330]", - "is_a": "Chicken thigh" - }, - "Chicken thigh (with skin, with bone) [FOODON_00003363]": { - "text": "Chicken thigh (with skin, with bone) [FOODON_00003363]", - "is_a": "Chicken thigh" - }, - "Chicken wing [FOODON:00002674]": { - "text": "Chicken wing [FOODON:00002674]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Fish food product [FOODON:00001248]": { - "text": "Fish food product [FOODON:00001248]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Fish steak [FOODON:00002986]": { - "text": "Fish steak [FOODON:00002986]", - "is_a": "Fish food product [FOODON:00001248]" - }, - "Ham food product [FOODON:00002502]": { - "text": "Ham food product [FOODON:00002502]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Head cheese [FOODON:03315658]": { - "text": "Head cheese [FOODON:03315658]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Lamb [FOODON:03411669]": { - "text": "Lamb [FOODON:03411669]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Meat strip [FOODON:00004285]": { - "text": "Meat strip [FOODON:00004285]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Mutton [FOODON:00002912]": { - "text": "Mutton [FOODON:00002912]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Pork chop [FOODON:00001049]": { - "text": "Pork chop [FOODON:00001049]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Pork meat (ground or minced) [FOODON:03309969]": { - "text": "Pork meat (ground or minced) [FOODON:03309969]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Pork meat (ground or minced, boneless) [FOODON:03000413]": { - "text": "Pork meat (ground or minced, boneless) [FOODON:03000413]", - "is_a": "Pork meat (ground or minced) [FOODON:03309969]" - }, - "Pork meat (ground or minced, extra lean) [FOODON:03000399]": { - "text": "Pork meat (ground or minced, extra lean) [FOODON:03000399]", - "is_a": "Pork meat (ground or minced) [FOODON:03309969]" - }, - "Pork meat (ground or minced, lean) [FOODON:03000395]": { - "text": "Pork meat (ground or minced, lean) [FOODON:03000395]", - "is_a": "Pork meat (ground or minced) [FOODON:03309969]" - }, - "Pork meat (ground or minced, medium) [FOODON:03000403]": { - "text": "Pork meat (ground or minced, medium) [FOODON:03000403]", - "is_a": "Pork meat (ground or minced) [FOODON:03309969]" - }, - "Pork meat (ground or minced, regular) [FOODON:03000407]": { - "text": "Pork meat (ground or minced, regular) [FOODON:03000407]", - "is_a": "Pork meat (ground or minced) [FOODON:03309969]" - }, - "Pork meat (ground or minced, Sirloin) [FOODON:03000409]": { - "text": "Pork meat (ground or minced, Sirloin) [FOODON:03000409]", - "is_a": "Pork meat (ground or minced) [FOODON:03309969]" - }, - "Pork shoulder [FOODON:03000376]": { - "text": "Pork shoulder [FOODON:03000376]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Pork shoulder chop [FOODON:03000388]": { - "text": "Pork shoulder chop [FOODON:03000388]", - "is_a": "Pork shoulder [FOODON:03000376]" - }, - "Pork sirloin chop [FOODON:03000390]": { - "text": "Pork sirloin chop [FOODON:03000390]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Pork steak [FOODON:00003148]": { - "text": "Pork steak [FOODON:00003148]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Pork tenderloin [FOODON:03000416]": { - "text": "Pork tenderloin [FOODON:03000416]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Poultry meat [FOODON:03315883]": { - "text": "Poultry meat [FOODON:03315883]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Leg (poultry meat cut) [FOODON:03530159]": { - "text": "Leg (poultry meat cut) [FOODON:03530159]", - "is_a": "Poultry meat [FOODON:03315883]" - }, - "Poultry drumstick [FOODON:00003469]": { - "text": "Poultry drumstick [FOODON:00003469]", - "is_a": "Leg (poultry meat cut) [FOODON:03530159]" - }, - "Neck (poultry meat cut) [FOODON:03530294]": { - "text": "Neck (poultry meat cut) [FOODON:03530294]", - "is_a": "Poultry meat [FOODON:03315883]" - }, - "Thigh (poultry meat cut) [FOODON:03530160]": { - "text": "Thigh (poultry meat cut) [FOODON:03530160]", - "is_a": "Poultry meat [FOODON:03315883]" - }, - "Wing (poultry meat cut) [FOODON:03530157]": { - "text": "Wing (poultry meat cut) [FOODON:03530157]", - "is_a": "Poultry meat [FOODON:03315883]" - }, - "Sausage (whole) [FOODON:03315904]": { - "text": "Sausage (whole) [FOODON:03315904]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Pepperoni [FOODON:03311003]": { - "text": "Pepperoni [FOODON:03311003]", - "is_a": "Sausage (whole) [FOODON:03315904]" - }, - "Salami [FOODON:03312067]": { - "text": "Salami [FOODON:03312067]", - "is_a": "Sausage (whole) [FOODON:03315904]" - }, - "Shellfish [FOODON:03411433]": { - "text": "Shellfish [FOODON:03411433]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Shrimp [FOODON:03411237]": { - "text": "Shrimp [FOODON:03411237]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Turkey breast [FOODON:00002690]": { - "text": "Turkey breast [FOODON:00002690]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Turkey breast (back off) [FOODON:03000386]": { - "text": "Turkey breast (back off) [FOODON:03000386]", - "is_a": "Turkey breast [FOODON:00002690]" - }, - "Turkey breast (skinless) [FOODON:03000372]": { - "text": "Turkey breast (skinless) [FOODON:03000372]", - "is_a": "Turkey breast [FOODON:00002690]" - }, - "Turkey breast (skinless, boneless) [FOODON:03000373]": { - "text": "Turkey breast (skinless, boneless) [FOODON:03000373]", - "is_a": "Turkey breast [FOODON:00002690]" - }, - "Turkey breast (with skin) [FOODON:03000375]": { - "text": "Turkey breast (with skin) [FOODON:03000375]", - "is_a": "Turkey breast [FOODON:00002690]" - }, - "Turkey drumstick [FOODON:03000365]": { - "text": "Turkey drumstick [FOODON:03000365]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Turkey drumstick (skinless) [FOODON:03000367]": { - "text": "Turkey drumstick (skinless) [FOODON:03000367]", - "is_a": "Turkey drumstick [FOODON:03000365]" - }, - "Turkey drumstick (with skin) [FOODON:03000369]": { - "text": "Turkey drumstick (with skin) [FOODON:03000369]", - "is_a": "Turkey drumstick [FOODON:03000365]" - }, - "Turkey meat [FOODON:00001286]": { - "text": "Turkey meat [FOODON:00001286]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Turkey meat (ground or minced) [FOODON:00002714]": { - "text": "Turkey meat (ground or minced) [FOODON:00002714]", - "is_a": "Turkey meat [FOODON:00001286]" - }, - "Turkey meat (ground or minced, lean) [FOODON:03000393]": { - "text": "Turkey meat (ground or minced, lean) [FOODON:03000393]", - "is_a": "Turkey meat [FOODON:00001286]" - }, - "Turkey meat (ground or minced, extra lean) [FOODON:03000397]": { - "text": "Turkey meat (ground or minced, extra lean) [FOODON:03000397]", - "is_a": "Turkey meat [FOODON:00001286]" - }, - "Turkey meat (ground or minced, medium) [FOODON:03000401]": { - "text": "Turkey meat (ground or minced, medium) [FOODON:03000401]", - "is_a": "Turkey meat [FOODON:00001286]" - }, - "Turkey meat (ground or minced, regular) [FOODON:03000405]": { - "text": "Turkey meat (ground or minced, regular) [FOODON:03000405]", - "is_a": "Turkey meat [FOODON:00001286]" - }, - "Turkey meat (ground or minced, boneless) [FOODON:03000411]": { - "text": "Turkey meat (ground or minced, boneless) [FOODON:03000411]", - "is_a": "Turkey meat [FOODON:00001286]" - }, - "Turkey thigh [FOODON:00003325]": { - "text": "Turkey thigh [FOODON:00003325]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Turkey thigh (skinless) [FOODON:00003329]": { - "text": "Turkey thigh (skinless) [FOODON:00003329]", - "is_a": "Turkey thigh [FOODON:00003325]" - }, - "Turkey thigh (skinless, boneless) [FOODON:03000370]": { - "text": "Turkey thigh (skinless, boneless) [FOODON:03000370]", - "is_a": "Turkey thigh [FOODON:00003325]" - }, - "Turkey thigh (with skin) [FOODON:00003328]": { - "text": "Turkey thigh (with skin) [FOODON:00003328]", - "is_a": "Turkey thigh [FOODON:00003325]" - }, - "Turkey upper thigh [FOODON:03000382]": { - "text": "Turkey upper thigh [FOODON:03000382]", - "is_a": "Turkey thigh (with skin) [FOODON:00003328]" - }, - "Turkey upper thigh (with skin) [FOODON:03000384]": { - "text": "Turkey upper thigh (with skin) [FOODON:03000384]", - "is_a": "Turkey thigh (with skin) [FOODON:00003328]" - }, - "Turkey wing [FOODON:03000371]": { - "text": "Turkey wing [FOODON:03000371]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Veal [FOODON:00003083]": { - "text": "Veal [FOODON:00003083]", - "is_a": "Meat, poultry and fish (organizational term)" - }, - "Formula fed veal [FOODON:000039111]": { - "text": "Formula fed veal [FOODON:000039111]", - "is_a": "Veal [FOODON:00003083]" - }, - "Grain-fed veal [FOODON:00004280]": { - "text": "Grain-fed veal [FOODON:00004280]", - "is_a": "Veal [FOODON:00003083]" - }, - "Microbial food product [FOODON:00001145]": { - "text": "Microbial food product [FOODON:00001145]" - }, - "Yeast [FOODON:03411345]": { - "text": "Yeast [FOODON:03411345]", - "is_a": "Microbial food product [FOODON:00001145]" - }, - "Nuts and seed products": { - "text": "Nuts and seed products" - }, - "Almond (whole or parts) [FOODON:03000218]": { - "text": "Almond (whole or parts) [FOODON:03000218]", - "is_a": "Nuts and seed products" - }, - "Almond (whole) [FOODON:00003523]": { - "text": "Almond (whole) [FOODON:00003523]", - "is_a": "Almond (whole or parts) [FOODON:03000218]" - }, - "Chia seed powder [FOODON:00003925]": { - "text": "Chia seed powder [FOODON:00003925]", - "is_a": "Nuts and seed products" - }, - "Chia seed (whole or parts) [FOODON:03000241]": { - "text": "Chia seed (whole or parts) [FOODON:03000241]", - "is_a": "Nuts and seed products" - }, - "Flaxseed powder [FOODON:00004276]": { - "text": "Flaxseed powder [FOODON:00004276]", - "is_a": "Nuts and seed products" - }, - "Hazelnut [FOODON:00002933]": { - "text": "Hazelnut [FOODON:00002933]", - "is_a": "Nuts and seed products" - }, - "Nut (whole or part) [FOODON:03306632]": { - "text": "Nut (whole or part) [FOODON:03306632]", - "is_a": "Nuts and seed products" - }, - "Peanut butter [FOODON:03306867]": { - "text": "Peanut butter [FOODON:03306867]", - "is_a": "Nuts and seed products" - }, - "Sesame seed [FOODON:03310306]": { - "text": "Sesame seed [FOODON:03310306]", - "is_a": "Nuts and seed products" - }, - "Tahini [FOODON:00003855]": { - "text": "Tahini [FOODON:00003855]", - "is_a": "Nuts and seed products" - }, - "Walnut (whole or parts) [FOODON:03316466]": { - "text": "Walnut (whole or parts) [FOODON:03316466]", - "is_a": "Nuts and seed products" - }, - "Prepared food product [FOODON:00001180]": { - "text": "Prepared food product [FOODON:00001180]" - }, - "Condiment [FOODON:03315708]": { - "text": "Condiment [FOODON:03315708]", - "is_a": "Prepared food product [FOODON:00001180]" - }, - "Confectionery food product [FOODON:00001149]": { - "text": "Confectionery food product [FOODON:00001149]", - "is_a": "Prepared food product [FOODON:00001180]" - }, - "Snack food [FOODON:03315013]": { - "text": "Snack food [FOODON:03315013]", - "is_a": "Prepared food product [FOODON:00001180]" - }, - "Produce [FOODON:03305145]": { - "text": "Produce [FOODON:03305145]" - }, - "Apple (whole or parts) [FOODON:03310788]": { - "text": "Apple (whole or parts) [FOODON:03310788]", - "is_a": "Produce [FOODON:03305145]" - }, - "Apple (whole) [FOODON:00002473]": { - "text": "Apple (whole) [FOODON:00002473]", - "is_a": "Apple (whole or parts) [FOODON:03310788]" - }, - "Arugula greens (raw) [FOODON:00002426]": { - "text": "Arugula greens (raw) [FOODON:00002426]", - "is_a": "Produce [FOODON:03305145]" - }, - "Avocado [FOODON:00003600]": { - "text": "Avocado [FOODON:00003600]", - "is_a": "Produce [FOODON:03305145]" - }, - "Cantaloupe (whole or parts) [FOODON:03000243]": { - "text": "Cantaloupe (whole or parts) [FOODON:03000243]", - "is_a": "Produce [FOODON:03305145]" - }, - "Chili pepper [FOODON:03315873]": { - "text": "Chili pepper [FOODON:03315873]", - "is_a": "Produce [FOODON:03305145]" - }, - "Coconut (whole or parts) [FOODON:03309861]": { - "text": "Coconut (whole or parts) [FOODON:03309861]", - "is_a": "Produce [FOODON:03305145]" - }, - "Corn cob (whole or parts) [FOODON:03310791]": { - "text": "Corn cob (whole or parts) [FOODON:03310791]", - "is_a": "Produce [FOODON:03305145]" - }, - "Cucumber (whole or parts) [FOODON:03000229]": { - "text": "Cucumber (whole or parts) [FOODON:03000229]", - "is_a": "Produce [FOODON:03305145]" - }, - "Fruit [PO:0009001]": { - "text": "Fruit [PO:0009001]", - "is_a": "Produce [FOODON:03305145]" - }, - "Goji berry [FOODON:00004360]": { - "text": "Goji berry [FOODON:00004360]", - "is_a": "Produce [FOODON:03305145]" - }, - "Greens (raw) [FOODON:03310765]": { - "text": "Greens (raw) [FOODON:03310765]", - "is_a": "Produce [FOODON:03305145]" - }, - "Kale leaf (whole or parts) [FOODON:03000236]": { - "text": "Kale leaf (whole or parts) [FOODON:03000236]", - "is_a": "Produce [FOODON:03305145]" - }, - "Lettuce head (whole or parts) [FOODON:03000239]": { - "text": "Lettuce head (whole or parts) [FOODON:03000239]", - "is_a": "Produce [FOODON:03305145]" - }, - "Mango (whole or parts) [FOODON:03000217]": { - "text": "Mango (whole or parts) [FOODON:03000217]", - "is_a": "Produce [FOODON:03305145]" - }, - "Mushroom (fruitbody) [FOODON:00003528]": { - "text": "Mushroom (fruitbody) [FOODON:00003528]", - "is_a": "Produce [FOODON:03305145]" - }, - "Papaya (whole or parts) [FOODON:03000228]": { - "text": "Papaya (whole or parts) [FOODON:03000228]", - "is_a": "Produce [FOODON:03305145]" - }, - "Pattypan squash (whole or parts) [FOODON:03000232]": { - "text": "Pattypan squash (whole or parts) [FOODON:03000232]", - "is_a": "Produce [FOODON:03305145]" - }, - "Peach [FOODON:00002485]": { - "text": "Peach [FOODON:00002485]", - "is_a": "Produce [FOODON:03305145]" - }, - "Pepper (whole or parts) [FOODON:03000249]": { - "text": "Pepper (whole or parts) [FOODON:03000249]", - "is_a": "Produce [FOODON:03305145]" - }, - "Potato [FOODON:03315354]": { - "text": "Potato [FOODON:03315354]", - "is_a": "Produce [FOODON:03305145]" - }, - "Salad [FOODON:03316042]": { - "text": "Salad [FOODON:03316042]", - "is_a": "Produce [FOODON:03305145]" - }, - "Scallion (whole or parts) [FOODON:03000250]": { - "text": "Scallion (whole or parts) [FOODON:03000250]", - "is_a": "Produce [FOODON:03305145]" - }, - "Spinach (whole or parts) [FOODON:03000221]": { - "text": "Spinach (whole or parts) [FOODON:03000221]", - "is_a": "Produce [FOODON:03305145]" - }, - "Sprout [FOODON:03420183]": { - "text": "Sprout [FOODON:03420183]", - "is_a": "Produce [FOODON:03305145]" - }, - "Germinated or sprouted seed [FOODON:03420102]": { - "text": "Germinated or sprouted seed [FOODON:03420102]", - "is_a": "Sprout [FOODON:03420183]" - }, - "Alfalfa sprout [FOODON:00002670]": { - "text": "Alfalfa sprout [FOODON:00002670]", - "is_a": "Germinated or sprouted seed [FOODON:03420102]" - }, - "Bean sprout [FOODON:00002576]": { - "text": "Bean sprout [FOODON:00002576]", - "is_a": "Germinated or sprouted seed [FOODON:03420102]" - }, - "Chia sprout [FOODON:00004284]": { - "text": "Chia sprout [FOODON:00004284]", - "is_a": "Germinated or sprouted seed [FOODON:03420102]" - }, - "Mixed sprouts [FOODON:03000182]": { - "text": "Mixed sprouts [FOODON:03000182]", - "is_a": "Germinated or sprouted seed [FOODON:03420102]" - }, - "Mung bean sprout [FOODON:03301446]": { - "text": "Mung bean sprout [FOODON:03301446]", - "is_a": "Germinated or sprouted seed [FOODON:03420102]" - }, - "Tomato (whole or parts) [FOODON:03000227]": { - "text": "Tomato (whole or parts) [FOODON:03000227]", - "is_a": "Produce [FOODON:03305145]" - }, - "Vegetable (whole or parts) [FOODON:03315308]": { - "text": "Vegetable (whole or parts) [FOODON:03315308]", - "is_a": "Produce [FOODON:03305145]" - }, - "Spice or herb [FOODON:00001242]": { - "text": "Spice or herb [FOODON:00001242]" - }, - "Basil (whole or parts) [FOODON:03000233]": { - "text": "Basil (whole or parts) [FOODON:03000233]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Black pepper (whole or parts) [FOODON:03000242]": { - "text": "Black pepper (whole or parts) [FOODON:03000242]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Cardamom (whole or parts) [FOODON:03000246]": { - "text": "Cardamom (whole or parts) [FOODON:03000246]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Chive leaf (whole or parts) [FOODON:03000240]": { - "text": "Chive leaf (whole or parts) [FOODON:03000240]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Coriander powder [FOODON:00004274]": { - "text": "Coriander powder [FOODON:00004274]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Coriander seed (whole or parts) [FOODON:03000224]": { - "text": "Coriander seed (whole or parts) [FOODON:03000224]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Cumin powder [FOODON:00004275]": { - "text": "Cumin powder [FOODON:00004275]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Cumin seed (whole) [FOODON:00003396]": { - "text": "Cumin seed (whole) [FOODON:00003396]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Black cumin seed (whole or parts) [FOODON:03000247]": { - "text": "Black cumin seed (whole or parts) [FOODON:03000247]", - "is_a": "Cumin seed (whole) [FOODON:00003396]" - }, - "Curry leaf (whole or parts) [FOODON:03000225]": { - "text": "Curry leaf (whole or parts) [FOODON:03000225]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Curry powder [FOODON:03301842]": { - "text": "Curry powder [FOODON:03301842]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Dill spice [FOODON:03310090]": { - "text": "Dill spice [FOODON:03310090]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Fennel (whole or parts) [FOODON:03000244]": { - "text": "Fennel (whole or parts) [FOODON:03000244]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Garlic powder [FOODON:03301844]": { - "text": "Garlic powder [FOODON:03301844]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Ginger root (whole or parts) [FOODON:03000220]": { - "text": "Ginger root (whole or parts) [FOODON:03000220]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Mint leaf (whole or parts) [FOODON:03000238]": { - "text": "Mint leaf (whole or parts) [FOODON:03000238]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Oregano (whole or parts) [FOODON:03000226]": { - "text": "Oregano (whole or parts) [FOODON:03000226]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Paprika [FOODON:03301105]": { - "text": "Paprika [FOODON:03301105]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Parsley leaf (whole or parts) [FOODON:03000231]": { - "text": "Parsley leaf (whole or parts) [FOODON:03000231]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Pepper (ground) [FOODON:03301526]": { - "text": "Pepper (ground) [FOODON:03301526]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Rasam powder [FOODON:00004277]": { - "text": "Rasam powder [FOODON:00004277]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Sage [FOODON:03301560]": { - "text": "Sage [FOODON:03301560]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Turmeric (ground) [FOODON:03310841]": { - "text": "Turmeric (ground) [FOODON:03310841]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "Spice [FOODON:03303380]": { - "text": "Spice [FOODON:03303380]", - "is_a": "Spice or herb [FOODON:00001242]" - }, - "White peppercorn (whole or parts) [FOODON:03000251]": { - "text": "White peppercorn (whole or parts) [FOODON:03000251]", - "is_a": "Spice or herb [FOODON:00001242]" - } - } - }, - "food_product_properties menu": { - "name": "food_product_properties menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Food (canned) [FOODON:00002418]": { - "text": "Food (canned) [FOODON:00002418]" - }, - "Food (cooked) [FOODON:00001181]": { - "text": "Food (cooked) [FOODON:00001181]" - }, - "Food (cut) [FOODON:00004291]": { - "text": "Food (cut) [FOODON:00004291]" - }, - "Food (chopped) [FOODON:00002777]": { - "text": "Food (chopped) [FOODON:00002777]", - "is_a": "Food (cut) [FOODON:00004291]" - }, - "Food (cubed) [FOODON:00004278]": { - "text": "Food (cubed) [FOODON:00004278]", - "is_a": "Food (cut) [FOODON:00004291]" - }, - "Food (dried) [FOODON:03307539]": { - "text": "Food (dried) [FOODON:03307539]" - }, - "Food (fresh) [FOODON:00002457]": { - "text": "Food (fresh) [FOODON:00002457]" - }, - "Food (frozen) [FOODON:03302148]": { - "text": "Food (frozen) [FOODON:03302148]" - }, - "Food (raw) [FOODON:03311126]": { - "text": "Food (raw) [FOODON:03311126]" - }, - "Food (unseasoned) [FOODON:00004287]": { - "text": "Food (unseasoned) [FOODON:00004287]" - }, - "Italian-style food product [FOODON:00004321]": { - "text": "Italian-style food product [FOODON:00004321]" - }, - "Meat (boneless) [FOODON:00003467]": { - "text": "Meat (boneless) [FOODON:00003467]" - }, - "Meat (skinless) [FOODON:00003468]": { - "text": "Meat (skinless) [FOODON:00003468]" - }, - "Meat (with bone) [FOODON:02010116]": { - "text": "Meat (with bone) [FOODON:02010116]" - }, - "Meat (with skin) [FOODON:02010111]": { - "text": "Meat (with skin) [FOODON:02010111]" - }, - "Organic food claim or use [FOODON:03510128]": { - "text": "Organic food claim or use [FOODON:03510128]" - }, - "Ready-to-eat (RTE) [FOODON:03316636]": { - "text": "Ready-to-eat (RTE) [FOODON:03316636]" - }, - "Soft [PATO:0000387]": { - "text": "Soft [PATO:0000387]" - } - } - }, - "animal_source_of_food menu": { - "name": "animal_source_of_food menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Cow [NCBITaxon:9913]": { - "text": "Cow [NCBITaxon:9913]" - }, - "Fish [FOODON:03411222]": { - "text": "Fish [FOODON:03411222]" - }, - "Pig [NCBITaxon:9823]": { - "text": "Pig [NCBITaxon:9823]" - }, - "Poultry [FOODON:03411563]": { - "text": "Poultry [FOODON:03411563]" - }, - "Chicken [NCBITaxon:9031]": { - "text": "Chicken [NCBITaxon:9031]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Turkey [NCBITaxon:9103]": { - "text": "Turkey [NCBITaxon:9103]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Sheep [NCBITaxon:9940]": { - "text": "Sheep [NCBITaxon:9940]" - } - } - }, - "food_product_production_stream menu": { - "name": "food_product_production_stream menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Beef cattle production stream [FOODON:03000452]": { - "text": "Beef cattle production stream [FOODON:03000452]" - }, - "Broiler chicken production stream [FOODON:03000455]": { - "text": "Broiler chicken production stream [FOODON:03000455]" - }, - "Dairy cattle production stream [FOODON:03000453]": { - "text": "Dairy cattle production stream [FOODON:03000453]" - }, - "Egg production stream [FOODON:03000458]": { - "text": "Egg production stream [FOODON:03000458]" - }, - "Layer chicken production stream [FOODON:03000456]": { - "text": "Layer chicken production stream [FOODON:03000456]" - }, - "Meat production stream [FOODON:03000460]": { - "text": "Meat production stream [FOODON:03000460]" - }, - "Veal meat production stream [FOODON:03000461]": { - "text": "Veal meat production stream [FOODON:03000461]", - "is_a": "Meat production stream [FOODON:03000460]" - }, - "Milk production stream [FOODON:03000459]": { - "text": "Milk production stream [FOODON:03000459]" - } - } - }, - "collection_device menu": { - "name": "collection_device menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Auger (earth auger) [AGRO:00000405]": { - "text": "Auger (earth auger) [AGRO:00000405]" - }, - "Box corer [GENEPIO:0100928]": { - "text": "Box corer [GENEPIO:0100928]" - }, - "Container [OBI:0000967]": { - "text": "Container [OBI:0000967]" - }, - "Bag [GSSO:008558]": { - "text": "Bag [GSSO:008558]", - "is_a": "Container [OBI:0000967]" - }, - "Whirlpak sampling bag [GENEPIO:0002122]": { - "text": "Whirlpak sampling bag [GENEPIO:0002122]", - "is_a": "Bag [GSSO:008558]" - }, - "Bottle [FOODON:03490214]": { - "text": "Bottle [FOODON:03490214]", - "is_a": "Container [OBI:0000967]" - }, - "Vial [OBI:0000522]": { - "text": "Vial [OBI:0000522]", - "is_a": "Container [OBI:0000967]" - }, - "Culture plate [GENEPIO:0004318]": { - "text": "Culture plate [GENEPIO:0004318]" - }, - "Petri dish [NCIT:C96141]": { - "text": "Petri dish [NCIT:C96141]", - "is_a": "Culture plate [GENEPIO:0004318]" - }, - "Filter [GENEPIO:0100103]": { - "text": "Filter [GENEPIO:0100103]" - }, - "PONAR grab sampler [GENEPIO:0100929]": { - "text": "PONAR grab sampler [GENEPIO:0100929]" - }, - "Scoop [GENEPIO:0002125]": { - "text": "Scoop [GENEPIO:0002125]" - }, - "Soil sample probe [GENEPIO:0100930]": { - "text": "Soil sample probe [GENEPIO:0100930]" - }, - "Spatula [NCIT:C149941]": { - "text": "Spatula [NCIT:C149941]" - }, - "Sponge [OBI:0002819]": { - "text": "Sponge [OBI:0002819]" - }, - "Swab [GENEPIO:0100027]": { - "text": "Swab [GENEPIO:0100027]", - "is_a": "Sponge [OBI:0002819]" - }, - "Drag swab [OBI:0002822]": { - "text": "Drag swab [OBI:0002822]", - "is_a": "Swab [GENEPIO:0100027]" - }, - "Surface wipe [OBI:0002824]": { - "text": "Surface wipe [OBI:0002824]", - "is_a": "Swab [GENEPIO:0100027]" - }, - "Tube [UBERON:0000025]": { - "text": "Tube [UBERON:0000025]" - }, - "Vacuum device [GENEPIO:0002127]": { - "text": "Vacuum device [GENEPIO:0002127]" - }, - "Vacutainer [OBIB:0000032]": { - "text": "Vacutainer [OBIB:0000032]", - "is_a": "Vacuum device [GENEPIO:0002127]" - } - } - }, - "collection_method menu": { - "name": "collection_method menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Aspiration [HP:0002835]": { - "text": "Aspiration [HP:0002835]" - }, - "Biopsy [OBI:0002650]": { - "text": "Biopsy [OBI:0002650]" - }, - "Fecal grab [GENEPIO:0004326]": { - "text": "Fecal grab [GENEPIO:0004326]" - }, - "Filtration [OBI:0302885]": { - "text": "Filtration [OBI:0302885]" - }, - "Air filtration [GENEPIO:0100031]": { - "text": "Air filtration [GENEPIO:0100031]", - "is_a": "Filtration [OBI:0302885]" - }, - "Water filtration [GENEPIO:0100931]": { - "text": "Water filtration [GENEPIO:0100931]", - "is_a": "Filtration [OBI:0302885]" - }, - "Lavage [OBI:0600044]": { - "text": "Lavage [OBI:0600044]" - }, - "Bronchoalveolar lavage [GENEPIO:0100032]": { - "text": "Bronchoalveolar lavage [GENEPIO:0100032]", - "is_a": "Lavage [OBI:0600044]" - }, - "Gastric lavage [GENEPIO:0100033]": { - "text": "Gastric lavage [GENEPIO:0100033]", - "is_a": "Lavage [OBI:0600044]" - }, - "Necropsy [MMO:0000344]": { - "text": "Necropsy [MMO:0000344]" - }, - "Phlebotomy [NCIT:C28221]": { - "text": "Phlebotomy [NCIT:C28221]" - }, - "Rinsing for specimen collection [GENEPIO_0002116]": { - "text": "Rinsing for specimen collection [GENEPIO_0002116]" - }, - "Scooping [GENEPIO:0100932]": { - "text": "Scooping [GENEPIO:0100932]" - }, - "Sediment collection [GENEPIO:0100933]": { - "text": "Sediment collection [GENEPIO:0100933]" - }, - "Soil coring [GENEPIO:0100934]": { - "text": "Soil coring [GENEPIO:0100934]" - } - } - }, - "food_packaging menu": { - "name": "food_packaging menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Bag, sack or pouch [FOODON:03490197]": { - "text": "Bag, sack or pouch [FOODON:03490197]" - }, - "Paper bag, sack or pouch [FOODON:03490120]": { - "text": "Paper bag, sack or pouch [FOODON:03490120]", - "is_a": "Bag, sack or pouch [FOODON:03490197]" - }, - "Plastic bag, sack or pouch [FOODON:03490166]": { - "text": "Plastic bag, sack or pouch [FOODON:03490166]", - "is_a": "Bag, sack or pouch [FOODON:03490197]" - }, - "Plastic shrink wrap [FOODON:03490137]": { - "text": "Plastic shrink wrap [FOODON:03490137]", - "is_a": "Plastic bag, sack or pouch [FOODON:03490166]" - }, - "Plastic wrapper [FOODON:03490128]": { - "text": "Plastic wrapper [FOODON:03490128]", - "is_a": "Plastic bag, sack or pouch [FOODON:03490166]" - }, - "Bottle or jar [FOODON:03490203]": { - "text": "Bottle or jar [FOODON:03490203]" - }, - "Can (container) [FOODON:03490204]": { - "text": "Can (container) [FOODON:03490204]" - }, - "Paper container, treated [FOODON:03490330]": { - "text": "Paper container, treated [FOODON:03490330]" - }, - "Paper container, untreated [FOODON:03490334]": { - "text": "Paper container, untreated [FOODON:03490334]" - }, - "Plastic tray or pan [FOODON:03490126]": { - "text": "Plastic tray or pan [FOODON:03490126]" - } - } - }, - "host (common name) menu": { - "name": "host (common name) menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Bird [NCBITaxon:8782]": { - "text": "Bird [NCBITaxon:8782]" - }, - "Chicken [NCBITaxon:9031]": { - "text": "Chicken [NCBITaxon:9031]", - "is_a": "Bird [NCBITaxon:8782]" - }, - "Seabird [FOODON:00004504]": { - "text": "Seabird [FOODON:00004504]", - "is_a": "Bird [NCBITaxon:8782]" - }, - "Cormorant [NCBITaxon:9206]": { - "text": "Cormorant [NCBITaxon:9206]", - "is_a": "Seabird [FOODON:00004504]" - }, - "Double Crested Cormorant [NCBITaxon:56069]": { - "text": "Double Crested Cormorant [NCBITaxon:56069]", - "is_a": "Cormorant [NCBITaxon:9206]" - }, - "Crane [NCBITaxon:9109]": { - "text": "Crane [NCBITaxon:9109]", - "is_a": "Seabird [FOODON:00004504]" - }, - "Whooping Crane [NCBITaxon:9117]": { - "text": "Whooping Crane [NCBITaxon:9117]", - "is_a": "Crane [NCBITaxon:9109]" - }, - "Gull (Seagull) [NCBITaxon:8911]": { - "text": "Gull (Seagull) [NCBITaxon:8911]", - "is_a": "Seabird [FOODON:00004504]" - }, - "Glaucous-winged Gull [NCBITaxon:119606]": { - "text": "Glaucous-winged Gull [NCBITaxon:119606]", - "is_a": "Gull (Seagull) [NCBITaxon:8911]" - }, - "Great Black-backed Gull [NCBITaxon:8912]": { - "text": "Great Black-backed Gull [NCBITaxon:8912]", - "is_a": "Gull (Seagull) [NCBITaxon:8911]" - }, - "Herring Gull [NCBITaxon:35669]": { - "text": "Herring Gull [NCBITaxon:35669]", - "is_a": "Gull (Seagull) [NCBITaxon:8911]" - }, - "Ring-billed Gull [NCBITaxon:126683]": { - "text": "Ring-billed Gull [NCBITaxon:126683]", - "is_a": "Gull (Seagull) [NCBITaxon:8911]" - }, - "Eider [NCBITaxon:50366]": { - "text": "Eider [NCBITaxon:50366]", - "is_a": "Seabird [FOODON:00004504]" - }, - "Common Eider [NCBITaxon:76058]": { - "text": "Common Eider [NCBITaxon:76058]", - "is_a": "Eider [NCBITaxon:50366]" - }, - "Turkey [NCBITaxon:9103]": { - "text": "Turkey [NCBITaxon:9103]", - "is_a": "Bird [NCBITaxon:8782]" - }, - "Fish [FOODON:03411222]": { - "text": "Fish [FOODON:03411222]" - }, - "Rainbow Trout [NCBITaxon:8022]": { - "text": "Rainbow Trout [NCBITaxon:8022]", - "is_a": "Fish [FOODON:03411222]" - }, - "Salmon [FOODON:00003473]": { - "text": "Salmon [FOODON:00003473]", - "is_a": "Fish [FOODON:03411222]" - }, - "Atlantic Salmon [NCBITaxon:8030]": { - "text": "Atlantic Salmon [NCBITaxon:8030]", - "is_a": "Salmon [FOODON:00003473]" - }, - "Chinook salmon [NCBITaxon:74940]": { - "text": "Chinook salmon [NCBITaxon:74940]", - "is_a": "Salmon [FOODON:00003473]" - }, - "Mammal [FOODON:03411134]": { - "text": "Mammal [FOODON:03411134]" - }, - "Companion animal [FOODON:03000300]": { - "text": "Companion animal [FOODON:03000300]", - "is_a": "Mammal [FOODON:03411134]" - }, - "Cow [NCBITaxon:9913]": { - "text": "Cow [NCBITaxon:9913]", - "is_a": "Mammal [FOODON:03411134]" - }, - "Human [NCBITaxon:9606]": { - "text": "Human [NCBITaxon:9606]", - "is_a": "Mammal [FOODON:03411134]" - }, - "Pig [NCBITaxon:9823]": { - "text": "Pig [NCBITaxon:9823]", - "is_a": "Mammal [FOODON:03411134]" - }, - "Sheep [NCBITaxon:9940]": { - "text": "Sheep [NCBITaxon:9940]", - "is_a": "Mammal [FOODON:03411134]" - }, - "Shellfish [FOODON:03411433]": { - "text": "Shellfish [FOODON:03411433]" - }, - "Atlantic Lobster [NCBITaxon:6706]": { - "text": "Atlantic Lobster [NCBITaxon:6706]", - "is_a": "Shellfish [FOODON:03411433]" - }, - "Atlantic Oyster [NCBITaxon:6565]": { - "text": "Atlantic Oyster [NCBITaxon:6565]", - "is_a": "Shellfish [FOODON:03411433]" - }, - "Blue Mussel [NCBITaxon:6550]": { - "text": "Blue Mussel [NCBITaxon:6550]", - "is_a": "Shellfish [FOODON:03411433]" - } - } - }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Bos taurus [NCBITaxon:9913]": { - "text": "Bos taurus [NCBITaxon:9913]" - }, - "Crassostrea virginica [NCBITaxon:6565]": { - "text": "Crassostrea virginica [NCBITaxon:6565]" - }, - "Gallus gallus [NCBITaxon:9031]": { - "text": "Gallus gallus [NCBITaxon:9031]" - }, - "Grus americana [NCBITaxon:9117]": { - "text": "Grus americana [NCBITaxon:9117]" - }, - "Homarus americanus [NCBITaxon:6706]": { - "text": "Homarus americanus [NCBITaxon:6706]" - }, - "Homo sapiens [NCBITaxon:9606]": { - "text": "Homo sapiens [NCBITaxon:9606]" - }, - "Larus argentatus [NCBITaxon:35669]": { - "text": "Larus argentatus [NCBITaxon:35669]" - }, - "Larus delawarensis [NCBITaxon:126683]": { - "text": "Larus delawarensis [NCBITaxon:126683]" - }, - "Larus glaucescens [NCBITaxon:119606]": { - "text": "Larus glaucescens [NCBITaxon:119606]" - }, - "Larus marinus [NCBITaxon:8912]": { - "text": "Larus marinus [NCBITaxon:8912]" - }, - "Meleagris gallopavo [NCBITaxon:9103]": { - "text": "Meleagris gallopavo [NCBITaxon:9103]" - }, - "Mytilus edulis [NCBITaxon:6550]": { - "text": "Mytilus edulis [NCBITaxon:6550]" - }, - "Oncorhynchus mykiss [NCBITaxon:8022]": { - "text": "Oncorhynchus mykiss [NCBITaxon:8022]" - }, - "Oncorhynchus tshawytscha [NCBITaxon:74940]": { - "text": "Oncorhynchus tshawytscha [NCBITaxon:74940]" - }, - "Ovis aries [NCBITaxon:9940]": { - "text": "Ovis aries [NCBITaxon:9940]" - }, - "Phalacrocorax auritus [NCBITaxon:56069]": { - "text": "Phalacrocorax auritus [NCBITaxon:56069]" - }, - "Salmo salar [NCBITaxon:8030]": { - "text": "Salmo salar [NCBITaxon:8030]" - }, - "Somateria mollissima [NCBITaxon:76058]": { - "text": "Somateria mollissima [NCBITaxon:76058]" - }, - "Sus scrofa domesticus [NCBITaxon:9825]": { - "text": "Sus scrofa domesticus [NCBITaxon:9825]" - } - } - }, - "host (food production name) menu": { - "name": "host (food production name) menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Cow (by age/production stage) (organizational term)": { - "text": "Cow (by age/production stage) (organizational term)" - }, - "Calf [FOODON:03411349]": { - "text": "Calf [FOODON:03411349]", - "is_a": "Cow (by age/production stage) (organizational term)" - }, - "Feeder cow [FOODON:00004292]": { - "text": "Feeder cow [FOODON:00004292]", - "is_a": "Cow (by age/production stage) (organizational term)" - }, - "Finisher cow [FOODON:00004293]": { - "text": "Finisher cow [FOODON:00004293]", - "is_a": "Cow (by age/production stage) (organizational term)" - }, - "Milker cow [FOODON:03411201]": { - "text": "Milker cow [FOODON:03411201]", - "is_a": "Cow (by age/production stage) (organizational term)" - }, - "Stocker cow [FOODON:00004294]": { - "text": "Stocker cow [FOODON:00004294]", - "is_a": "Cow (by age/production stage) (organizational term)" - }, - "Weanling [FOODON:00004295]": { - "text": "Weanling [FOODON:00004295]", - "is_a": "Cow (by age/production stage) (organizational term)" - }, - "Cow (by sex/reproductive stage) (organizational term)": { - "text": "Cow (by sex/reproductive stage) (organizational term)" - }, - "Bull [FOODON:00000015]": { - "text": "Bull [FOODON:00000015]", - "is_a": "Cow (by sex/reproductive stage) (organizational term)" - }, - "Cow [NCBITaxon:9913]": { - "text": "Cow [NCBITaxon:9913]", - "is_a": "Cow (by sex/reproductive stage) (organizational term)" - }, - "Freemartin [FOODON:00004296]": { - "text": "Freemartin [FOODON:00004296]", - "is_a": "Cow (by sex/reproductive stage) (organizational term)" - }, - "Heifer [FOODON:00002518]": { - "text": "Heifer [FOODON:00002518]", - "is_a": "Cow (by sex/reproductive stage) (organizational term)" - }, - "Steer [FOODON:00002531]": { - "text": "Steer [FOODON:00002531]", - "is_a": "Cow (by sex/reproductive stage) (organizational term)" - }, - "Pig (by age/production stage) (organizational term)": { - "text": "Pig (by age/production stage) (organizational term)" - }, - "Finisher pig [FOODON:00003371]": { - "text": "Finisher pig [FOODON:00003371]", - "is_a": "Pig (by age/production stage) (organizational term)" - }, - "Grower pig [FOODON:00003370]": { - "text": "Grower pig [FOODON:00003370]", - "is_a": "Pig (by age/production stage) (organizational term)" - }, - "Nursing pig [FOODON:00004297 ]": { - "text": "Nursing pig [FOODON:00004297 ]", - "is_a": "Pig (by age/production stage) (organizational term)" - }, - "Pig [NCBITaxon:9823]": { - "text": "Pig [NCBITaxon:9823]", - "is_a": "Pig (by age/production stage) (organizational term)" - }, - "Piglet [FOODON:00003952]": { - "text": "Piglet [FOODON:00003952]", - "is_a": "Pig (by age/production stage) (organizational term)" - }, - "Weanling (weaner) pig [FOODON:00003373]": { - "text": "Weanling (weaner) pig [FOODON:00003373]", - "is_a": "Pig (by age/production stage) (organizational term)" - }, - "Pig (by sex/reproductive stage) (organizational term)": { - "text": "Pig (by sex/reproductive stage) (organizational term)" - }, - "Barrow [FOODON:03411280]": { - "text": "Barrow [FOODON:03411280]", - "is_a": "Pig (by sex/reproductive stage) (organizational term)" - }, - "Boar [FOODON:03412248]": { - "text": "Boar [FOODON:03412248]", - "is_a": "Pig (by sex/reproductive stage) (organizational term)" - }, - "Gilt [FOODON:00003369]": { - "text": "Gilt [FOODON:00003369]", - "is_a": "Pig (by sex/reproductive stage) (organizational term)" - }, - "Sow [FOODON:00003333]": { - "text": "Sow [FOODON:00003333]", - "is_a": "Pig (by sex/reproductive stage) (organizational term)" - }, - "Poultry [FOODON:03411563]": { - "text": "Poultry [FOODON:03411563]" - }, - "Broiler or fryer chicken [FOODON:03411198]": { - "text": "Broiler or fryer chicken [FOODON:03411198]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Capon [FOODON:03411711]": { - "text": "Capon [FOODON:03411711]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Chick [FOODON:00004299]": { - "text": "Chick [FOODON:00004299]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Chicken [NCBITaxon:9031]": { - "text": "Chicken [NCBITaxon:9031]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Egg [UBERON:0007379]": { - "text": "Egg [UBERON:0007379]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Hatchling [FOODON:00004300]": { - "text": "Hatchling [FOODON:00004300]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Hen [FOODON:00003282]": { - "text": "Hen [FOODON:00003282]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Layer chicken [FOODON:00004301]": { - "text": "Layer chicken [FOODON:00004301]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Layer turkey [FOODON:00004302]": { - "text": "Layer turkey [FOODON:00004302]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Poult [FOODON:00002962]": { - "text": "Poult [FOODON:00002962]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Pullet [FOODON:00004303]": { - "text": "Pullet [FOODON:00004303]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Rooster [FOODON:03411714]": { - "text": "Rooster [FOODON:03411714]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Tom (Gobbler) [FOODON:00004304 ]": { - "text": "Tom (Gobbler) [FOODON:00004304 ]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Turkey [NCBITaxon:9103]": { - "text": "Turkey [NCBITaxon:9103]", - "is_a": "Poultry [FOODON:03411563]" - }, - "Sheep [NCBITaxon:9940]": { - "text": "Sheep [NCBITaxon:9940]" - }, - "Ram [FOODON:00004305]": { - "text": "Ram [FOODON:00004305]", - "is_a": "Sheep [NCBITaxon:9940]" - }, - "Wether sheep [FOODON:00004306]": { - "text": "Wether sheep [FOODON:00004306]", - "is_a": "Sheep [NCBITaxon:9940]" - }, - "Ewe [FOODON:03412610]": { - "text": "Ewe [FOODON:03412610]", - "is_a": "Sheep [NCBITaxon:9940]" - }, - "Lamb [FOODON:03411669]": { - "text": "Lamb [FOODON:03411669]", - "is_a": "Sheep [NCBITaxon:9940]" - }, - "Fish [FOODON:03411222]": { - "text": "Fish [FOODON:03411222]" - }, - "Fish egg [FOODON_00004319]": { - "text": "Fish egg [FOODON_00004319]", - "is_a": "Fish [FOODON:03411222]" - }, - "Fry (fish) [FOODON_00004318]": { - "text": "Fry (fish) [FOODON_00004318]", - "is_a": "Fish [FOODON:03411222]" - }, - "Juvenile fish [FOODON_00004317]": { - "text": "Juvenile fish [FOODON_00004317]", - "is_a": "Fish [FOODON:03411222]" - } - } - }, - "host_age_bin menu": { - "name": "host_age_bin menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "First winter [GENEPIO:0100684]": { - "text": "First winter [GENEPIO:0100684]" - }, - "First summer [GENEPIO:0100685]": { - "text": "First summer [GENEPIO:0100685]" - }, - "Second winter [GENEPIO:0100686]": { - "text": "Second winter [GENEPIO:0100686]" - }, - "Second summer [GENEPIO:0100687]": { - "text": "Second summer [GENEPIO:0100687]" - }, - "Third winter [GENEPIO:0100688]": { - "text": "Third winter [GENEPIO:0100688]" - }, - "Third summer [GENEPIO:0100689]": { - "text": "Third summer [GENEPIO:0100689]" - } - } - }, - "isolated_by menu": { - "name": "isolated_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]" - }, - "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]" - } - } - }, - "organism menu": { - "name": "organism menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Acinetobacter [NCBITaxon:469]": { - "text": "Acinetobacter [NCBITaxon:469]" - }, - "Acinetobacter baumannii [NCBITaxon:470]": { - "text": "Acinetobacter baumannii [NCBITaxon:470]", - "is_a": "Acinetobacter [NCBITaxon:469]" - }, - "Acinetobacter bereziniae [NCBITaxon:106648]": { - "text": "Acinetobacter bereziniae [NCBITaxon:106648]", - "is_a": "Acinetobacter [NCBITaxon:469]" - }, - "Acinetobacter ursingii [NCBITaxon:108980]": { - "text": "Acinetobacter ursingii [NCBITaxon:108980]", - "is_a": "Acinetobacter [NCBITaxon:469]" - }, - "Aeromonas [NCBITaxon:642]": { - "text": "Aeromonas [NCBITaxon:642]" - }, - "Aeromonas allosaccharophila [NCBITaxon:656]": { - "text": "Aeromonas allosaccharophila [NCBITaxon:656]", - "is_a": "Aeromonas [NCBITaxon:642]" - }, - "Aeromonas hydrophila [NCBITaxon:644]": { - "text": "Aeromonas hydrophila [NCBITaxon:644]", - "is_a": "Aeromonas [NCBITaxon:642]" - }, - "Aeromonas rivipollensis [NCBITaxon:948519]": { - "text": "Aeromonas rivipollensis [NCBITaxon:948519]", - "is_a": "Aeromonas [NCBITaxon:642]" - }, - "Aeromonas salmonicida [NCBITaxon:645]": { - "text": "Aeromonas salmonicida [NCBITaxon:645]", - "is_a": "Aeromonas [NCBITaxon:642]" - }, - "Campylobacter [NCBITaxon:194]": { - "text": "Campylobacter [NCBITaxon:194]" - }, - "Campylobacter coli [NCBITaxon:195]": { - "text": "Campylobacter coli [NCBITaxon:195]", - "is_a": "Campylobacter [NCBITaxon:194]" - }, - "Campylobacter jejuni [NCBITaxon:197]": { - "text": "Campylobacter jejuni [NCBITaxon:197]", - "is_a": "Campylobacter [NCBITaxon:194]" - }, - "Campylobacter lari [NCBITaxon:201]": { - "text": "Campylobacter lari [NCBITaxon:201]", - "is_a": "Campylobacter [NCBITaxon:194]" - }, - "Citrobacter [NCBITaxon:544]": { - "text": "Citrobacter [NCBITaxon:544]" - }, - "Citrobacter braakii [NCBITaxon:57706]": { - "text": "Citrobacter braakii [NCBITaxon:57706]", - "is_a": "Citrobacter [NCBITaxon:544]" - }, - "Citrobacter freundii [NCBITaxon:546]": { - "text": "Citrobacter freundii [NCBITaxon:546]", - "is_a": "Citrobacter [NCBITaxon:544]" - }, - "Citrobacter gillenii [NCBITaxon:67828]": { - "text": "Citrobacter gillenii [NCBITaxon:67828]", - "is_a": "Citrobacter [NCBITaxon:544]" - }, - "Clostridioides [NCBITaxon:1870884]": { - "text": "Clostridioides [NCBITaxon:1870884]" - }, - "Clostridioides difficile [NCBITaxon:1496]": { - "text": "Clostridioides difficile [NCBITaxon:1496]", - "is_a": "Clostridioides [NCBITaxon:1870884]" - }, - "Clostridium [NCBITaxon:1485]": { - "text": "Clostridium [NCBITaxon:1485]" - }, - "Clostridium perfringens [NCBITaxon:1502]": { - "text": "Clostridium perfringens [NCBITaxon:1502]", - "is_a": "Clostridium [NCBITaxon:1485]" - }, - "Clostridium sporogenes [NCBITaxon:1509]": { - "text": "Clostridium sporogenes [NCBITaxon:1509]", - "is_a": "Clostridium [NCBITaxon:1485]" - }, - "Comamonas [NCBITaxon:283]": { - "text": "Comamonas [NCBITaxon:283]" - }, - "Comamonas aquatica [NCBITaxon:225991]": { - "text": "Comamonas aquatica [NCBITaxon:225991]", - "is_a": "Comamonas [NCBITaxon:283]" - }, - "Enterobacter [NCBITaxon:547]": { - "text": "Enterobacter [NCBITaxon:547]" - }, - "Enterobacter asburiae [NCBITaxon:61645]": { - "text": "Enterobacter asburiae [NCBITaxon:61645]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Enterobacter cancerogenus [NCBITaxon:69218]": { - "text": "Enterobacter cancerogenus [NCBITaxon:69218]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Enterobacter cloacae [NCBITaxon:550]": { - "text": "Enterobacter cloacae [NCBITaxon:550]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Enterobacter hormaechei [NCBITaxon:158836]": { - "text": "Enterobacter hormaechei [NCBITaxon:158836]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Enterobacter kobei [NCBITaxon:208224]": { - "text": "Enterobacter kobei [NCBITaxon:208224]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Enterobacter roggenkampii [NCBITaxon:1812935]": { - "text": "Enterobacter roggenkampii [NCBITaxon:1812935]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Lelliottia amnigena [NCBITaxon:61646]": { - "text": "Lelliottia amnigena [NCBITaxon:61646]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Pluralibacter gergoviae [NCBITaxon:61647]": { - "text": "Pluralibacter gergoviae [NCBITaxon:61647]", - "is_a": "Enterobacter [NCBITaxon:547]" - }, - "Enterococcus [NCBITaxon:1350]": { - "text": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus asini [NCBITaxon:57732]": { - "text": "Enterococcus asini [NCBITaxon:57732]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus avium [NCBITaxon:33945]": { - "text": "Enterococcus avium [NCBITaxon:33945]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus caccae [NCBITaxon:317735]": { - "text": "Enterococcus caccae [NCBITaxon:317735]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus canis [NCBITaxon:214095]": { - "text": "Enterococcus canis [NCBITaxon:214095]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus casseliflavus [NCBITaxon:37734]": { - "text": "Enterococcus casseliflavus [NCBITaxon:37734]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus cecorum [NCBITaxon:44008]": { - "text": "Enterococcus cecorum [NCBITaxon:44008]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus dispar [NCBITaxon:44009]": { - "text": "Enterococcus dispar [NCBITaxon:44009]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus durans [NCBITaxon:53345]": { - "text": "Enterococcus durans [NCBITaxon:53345]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus faecium [NCBITaxon:1352]": { - "text": "Enterococcus faecium [NCBITaxon:1352]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus faecalis [NCBITaxon:1351]": { - "text": "Enterococcus faecalis [NCBITaxon:1351]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus gallinarum [NCBITaxon:1353]": { - "text": "Enterococcus gallinarum [NCBITaxon:1353]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus hirae [NCBITaxon:1354]": { - "text": "Enterococcus hirae [NCBITaxon:1354]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus malodoratus [NCBITaxon:71451]": { - "text": "Enterococcus malodoratus [NCBITaxon:71451]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus mundtii [NCBITaxon:53346]": { - "text": "Enterococcus mundtii [NCBITaxon:53346]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus ratti [NCBITaxon:150033]": { - "text": "Enterococcus ratti [NCBITaxon:150033]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus saccharolyticus [NCBITaxon:41997]": { - "text": "Enterococcus saccharolyticus [NCBITaxon:41997]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus thailandicus [NCBITaxon:417368]": { - "text": "Enterococcus thailandicus [NCBITaxon:417368]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Enterococcus villorum [NCBITaxon:112904]": { - "text": "Enterococcus villorum [NCBITaxon:112904]", - "is_a": "Enterococcus [NCBITaxon:1350]" - }, - "Escherichia [NCBITaxon:561]": { - "text": "Escherichia [NCBITaxon:561]" - }, - "Escherichia coli [NCBITaxon:562]": { - "text": "Escherichia coli [NCBITaxon:562]", - "is_a": "Escherichia [NCBITaxon:561]" - }, - "Escherichia fergusonii [NCBITaxon:564]": { - "text": "Escherichia fergusonii [NCBITaxon:564]", - "is_a": "Escherichia [NCBITaxon:561]" - }, - "Exiguobacterium [NCBITaxon:33986]": { - "text": "Exiguobacterium [NCBITaxon:33986]" - }, - "Exiguobacterium oxidotolerans [NCBITaxon:223958]": { - "text": "Exiguobacterium oxidotolerans [NCBITaxon:223958]", - "is_a": "Exiguobacterium [NCBITaxon:33986]" - }, - "Exiguobacterium sp. [NCBITaxon:44751]": { - "text": "Exiguobacterium sp. [NCBITaxon:44751]", - "is_a": "Exiguobacterium [NCBITaxon:33986]" - }, - "Klebsiella [NCBITaxon:570]": { - "text": "Klebsiella [NCBITaxon:570]" - }, - "Klebsiella aerogenes [NCBITaxon:548]": { - "text": "Klebsiella aerogenes [NCBITaxon:548]", - "is_a": "Klebsiella [NCBITaxon:570]" - }, - "Klebsiella michiganensis [NCBITaxon:1134687]": { - "text": "Klebsiella michiganensis [NCBITaxon:1134687]", - "is_a": "Klebsiella [NCBITaxon:570]" - }, - "Klebsiella oxytoca [NCBITaxon:571]": { - "text": "Klebsiella oxytoca [NCBITaxon:571]", - "is_a": "Klebsiella [NCBITaxon:570]" - }, - "Klebsiella pneumoniae [NCBITaxon:573]": { - "text": "Klebsiella pneumoniae [NCBITaxon:573]", - "is_a": "Klebsiella [NCBITaxon:570]" - }, - "Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407]": { - "text": "Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407]", - "is_a": "Klebsiella [NCBITaxon:570]" - }, - "Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574]": { - "text": "Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574]", - "is_a": "Klebsiella [NCBITaxon:570]" - }, - "Kluyvera [NCBITaxon:579]": { - "text": "Kluyvera [NCBITaxon:579]" - }, - "Kluyvera intermedia [NCBITaxon:61648]": { - "text": "Kluyvera intermedia [NCBITaxon:61648]", - "is_a": "Kluyvera [NCBITaxon:579]" - }, - "Kosakonia [NCBITaxon:1330547]": { - "text": "Kosakonia [NCBITaxon:1330547]" - }, - "Kosakonia cowanii [NCBITaxon:208223]": { - "text": "Kosakonia cowanii [NCBITaxon:208223]", - "is_a": "Kosakonia [NCBITaxon:1330547]" - }, - "Leclercia [NCBITaxon:83654]": { - "text": "Leclercia [NCBITaxon:83654]" - }, - "Leclercia adecarboxylata [NCBITaxon:83655]": { - "text": "Leclercia adecarboxylata [NCBITaxon:83655]", - "is_a": "Leclercia [NCBITaxon:83654]" - }, - "Listeria [NCBITaxon:1637]": { - "text": "Listeria [NCBITaxon:1637]" - }, - "Listeria monocytogenes [NCBITaxon:1639]": { - "text": "Listeria monocytogenes [NCBITaxon:1639]", - "is_a": "Listeria [NCBITaxon:1637]" - }, - "Ochrobactrum [NCBITaxon:528]": { - "text": "Ochrobactrum [NCBITaxon:528]" - }, - "Pantoea [NCBITaxon:53335]": { - "text": "Pantoea [NCBITaxon:53335]" - }, - "Pantoea ananatis [NCBITaxon:553]": { - "text": "Pantoea ananatis [NCBITaxon:553]", - "is_a": "Pantoea [NCBITaxon:53335]" - }, - "Photobacterium [NCBITaxon:657]": { - "text": "Photobacterium [NCBITaxon:657]" - }, - "Photobacterium sp. [NCBITaxon:660]": { - "text": "Photobacterium sp. [NCBITaxon:660]", - "is_a": "Photobacterium [NCBITaxon:657]" - }, - "Providencia [NCBITaxon:586]": { - "text": "Providencia [NCBITaxon:586]" - }, - "Providencia rettgeri [NCBITaxon:587]": { - "text": "Providencia rettgeri [NCBITaxon:587]", - "is_a": "Providencia [NCBITaxon:586]" - }, - "Pseudoalteromonas [NCBITaxon:53246]": { - "text": "Pseudoalteromonas [NCBITaxon:53246]" - }, - "Pseudoalteromonas tetraodonis [NCBITaxon:43659]": { - "text": "Pseudoalteromonas tetraodonis [NCBITaxon:43659]", - "is_a": "Pseudoalteromonas [NCBITaxon:53246]" - }, - "Pseudomonas [NCBITaxon:286]": { - "text": "Pseudomonas [NCBITaxon:286]" - }, - "Pseudomonas aeruginosa [NCBITaxon:287]": { - "text": "Pseudomonas aeruginosa [NCBITaxon:287]", - "is_a": "Pseudomonas [NCBITaxon:286]" - }, - "Pseudomonas fluorescens [NCBITaxon:294]": { - "text": "Pseudomonas fluorescens [NCBITaxon:294]", - "is_a": "Pseudomonas [NCBITaxon:286]" - }, - "Pseudomonas soli [NCBITaxon:1306993]": { - "text": "Pseudomonas soli [NCBITaxon:1306993]", - "is_a": "Pseudomonas [NCBITaxon:286]" - }, - "Pseudomonas sp. [NCBITaxon:306]": { - "text": "Pseudomonas sp. [NCBITaxon:306]", - "is_a": "Pseudomonas [NCBITaxon:286]" - }, - "Psychrobacter [NCBITaxon:497]": { - "text": "Psychrobacter [NCBITaxon:497]" - }, - "Psychrobacter faecalis [NCBITaxon:180588]": { - "text": "Psychrobacter faecalis [NCBITaxon:180588]", - "is_a": "Psychrobacter [NCBITaxon:497]" - }, - "Psychrobacter sp. [NCBITaxon:56811]": { - "text": "Psychrobacter sp. [NCBITaxon:56811]", - "is_a": "Psychrobacter [NCBITaxon:497]" - }, - "Rahnella [NCBITaxon:34037]": { - "text": "Rahnella [NCBITaxon:34037]" - }, - "Rahnella aquatilis [NCBITaxon:34038]": { - "text": "Rahnella aquatilis [NCBITaxon:34038]", - "is_a": "Rahnella [NCBITaxon:34037]" - }, - "Raoultella [NCBITaxon:160674]": { - "text": "Raoultella [NCBITaxon:160674]" - }, - "Raoultella ornithinolytica [NCBITaxon:54291]": { - "text": "Raoultella ornithinolytica [NCBITaxon:54291]", - "is_a": "Raoultella [NCBITaxon:160674]" - }, - "Raoultella planticola [NCBITaxon:575]": { - "text": "Raoultella planticola [NCBITaxon:575]", - "is_a": "Raoultella [NCBITaxon:160674]" - }, - "Salmonella enterica [NCBITaxon:28901]": { - "text": "Salmonella enterica [NCBITaxon:28901]" - }, - "Salmonella enterica subsp. enterica [NCBITaxon:59201]": { - "text": "Salmonella enterica subsp. enterica [NCBITaxon:59201]", - "is_a": "Salmonella enterica [NCBITaxon:28901]" - }, - "Salmonella enterica subsp. arizonae [NCBITaxon:59203]": { - "text": "Salmonella enterica subsp. arizonae [NCBITaxon:59203]", - "is_a": "Salmonella enterica [NCBITaxon:28901]" - }, - "Serratia [NCBITaxon:613]": { - "text": "Serratia [NCBITaxon:613]" - }, - "Shewanella [NCBITaxon:22]": { - "text": "Shewanella [NCBITaxon:22]" - }, - "Shewanella pealeana [NCBITaxon:70864]": { - "text": "Shewanella pealeana [NCBITaxon:70864]", - "is_a": "Shewanella [NCBITaxon:22]" - }, - "Shewanella putrefaciens [NCBITaxon:24]": { - "text": "Shewanella putrefaciens [NCBITaxon:24]", - "is_a": "Shewanella [NCBITaxon:22]" - }, - "Shewanella sp. [NCBITaxon:50422]": { - "text": "Shewanella sp. [NCBITaxon:50422]", - "is_a": "Shewanella [NCBITaxon:22]" - }, - "Staphylococcus [NCBITaxon:1279]": { - "text": "Staphylococcus [NCBITaxon:1279]" - }, - "Staphylococcus aureus [NCBITaxon:1280]": { - "text": "Staphylococcus aureus [NCBITaxon:1280]", - "is_a": "Staphylococcus [NCBITaxon:1279]" - }, - "Streptococcus [NCBITaxon:1301]": { - "text": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus alactolyticus [NCBITaxon:29389]": { - "text": "Streptococcus alactolyticus [NCBITaxon:29389]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus bovis [NCBITaxon:1335]": { - "text": "Streptococcus bovis [NCBITaxon:1335]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus equinus [NCBITaxon:1335]": { - "text": "Streptococcus equinus [NCBITaxon:1335]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus gallolyticus [NCBITaxon:315405]": { - "text": "Streptococcus gallolyticus [NCBITaxon:315405]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus infantarius [NCBITaxon:102684]": { - "text": "Streptococcus infantarius [NCBITaxon:102684]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus lutetiensis [NCBITaxon:150055]": { - "text": "Streptococcus lutetiensis [NCBITaxon:150055]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus macedonicus [NCBITaxon:59310]": { - "text": "Streptococcus macedonicus [NCBITaxon:59310]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus pasteurianus [NCBITaxon:197614]": { - "text": "Streptococcus pasteurianus [NCBITaxon:197614]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Streptococcus suis [NCBITaxon:1307]": { - "text": "Streptococcus suis [NCBITaxon:1307]", - "is_a": "Streptococcus [NCBITaxon:1301]" - }, - "Vibrio [NCBITaxon:662]": { - "text": "Vibrio [NCBITaxon:662]" - }, - "Vibrio cholerae [NCBITaxon:666]": { - "text": "Vibrio cholerae [NCBITaxon:666]", - "is_a": "Vibrio [NCBITaxon:662]" - } - } - }, - "taxonomic_identification_process menu": { - "name": "taxonomic_identification_process menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Whole genome sequencing assay [OBI:0002117]": { - "text": "Whole genome sequencing assay [OBI:0002117]" - }, - "16S ribosomal gene sequencing assay [OBI:0002763]": { - "text": "16S ribosomal gene sequencing assay [OBI:0002763]" - }, - "PCR assay [OBI:0002740]": { - "text": "PCR assay [OBI:0002740]" - }, - "Comparative phenotypic assessment [OBI:0001546]": { - "text": "Comparative phenotypic assessment [OBI:0001546]" - } - } - }, - "sequenced_by menu": { - "name": "sequenced_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]" - }, - "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]" - } - } - }, - "purpose_of_sequencing menu": { - "name": "purpose_of_sequencing menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Cluster/Outbreak investigation [GENEPIO:0100001]": { - "text": "Cluster/Outbreak investigation [GENEPIO:0100001]" - }, - "Diagnostic testing [GENEPIO:0100001]": { - "text": "Diagnostic testing [GENEPIO:0100001]" - }, - "Environmental testing [GENEPIO:0100548]": { - "text": "Environmental testing [GENEPIO:0100548]" - }, - "Research [GENEPIO:0100003]": { - "text": "Research [GENEPIO:0100003]" - }, - "Clinical trial [GENEPIO:0100549]": { - "text": "Clinical trial [GENEPIO:0100549]", - "is_a": "Research [GENEPIO:0100003]" - }, - "Field experiment [GENEPIO:0100549]": { - "text": "Field experiment [GENEPIO:0100549]", - "is_a": "Research [GENEPIO:0100003]" - }, - "Surveillance [GENEPIO:0100004]": { - "text": "Surveillance [GENEPIO:0100004]" - } - } - }, - "sequencing_platform menu": { - "name": "sequencing_platform menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Illumina [GENEPIO:0001923]": { - "text": "Illumina [GENEPIO:0001923]" - }, - "Pacific Biosciences [GENEPIO:0001927]": { - "text": "Pacific Biosciences [GENEPIO:0001927]" - }, - "Ion Torrent [GENEPIO:0002683]": { - "text": "Ion Torrent [GENEPIO:0002683]" - }, - "Oxford Nanopore Technologies [OBI:0002755]": { - "text": "Oxford Nanopore Technologies [OBI:0002755]" - }, - "BGI Genomics [GENEPIO:0004324]": { - "text": "BGI Genomics [GENEPIO:0004324]" - }, - "MGI [GENEPIO:0004325]": { - "text": "MGI [GENEPIO:0004325]" - } - } - }, - "sequencing_instrument menu": { - "name": "sequencing_instrument menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Illumina [GENEPIO:0100105]": { - "text": "Illumina [GENEPIO:0100105]" - }, - "Illumina Genome Analyzer [GENEPIO:0100106]": { - "text": "Illumina Genome Analyzer [GENEPIO:0100106]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina Genome Analyzer II [OBI:0000703]": { - "text": "Illumina Genome Analyzer II [OBI:0000703]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina Genome Analyzer IIx [OBI:0002000]": { - "text": "Illumina Genome Analyzer IIx [OBI:0002000]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina HiScanSQ [GENEPIO:0100109]": { - "text": "Illumina HiScanSQ [GENEPIO:0100109]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina HiSeq [GENEPIO:0100110]": { - "text": "Illumina HiSeq [GENEPIO:0100110]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina HiSeq X [GENEPIO:0100111]": { - "text": "Illumina HiSeq X [GENEPIO:0100111]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq X Five [GENEPIO:0100112]": { - "text": "Illumina HiSeq X Five [GENEPIO:0100112]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq X Ten [GENEPIO:0100113]": { - "text": "Illumina HiSeq X Ten [GENEPIO:0100113]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq 1000 [OBI:0002022]": { - "text": "Illumina HiSeq 1000 [OBI:0002022]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq 1500 [GENEPIO:0100115]": { - "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq 2000 [OBI:0002001]": { - "text": "Illumina HiSeq 2000 [OBI:0002001]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq 2500 [OBI:0002002]": { - "text": "Illumina HiSeq 2500 [OBI:0002002]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq 3000 [OBI:0002048]": { - "text": "Illumina HiSeq 3000 [OBI:0002048]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina HiSeq 4000 [OBI:0002049]": { - "text": "Illumina HiSeq 4000 [OBI:0002049]", - "is_a": "Illumina HiSeq [GENEPIO:0100110]" - }, - "Illumina iSeq [GENEPIO:0100120]": { - "text": "Illumina iSeq [GENEPIO:0100120]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina iSeq 100 [GENEPIO:0100121]": { - "text": "Illumina iSeq 100 [GENEPIO:0100121]", - "is_a": "Illumina iSeq [GENEPIO:0100120]" - }, - "Illumina NovaSeq [GENEPIO:0100122]": { - "text": "Illumina NovaSeq [GENEPIO:0100122]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina NovaSeq 6000 [GENEPIO:0100123]": { - "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "is_a": "Illumina NovaSeq [GENEPIO:0100122]" - }, - "Illumina MiniSeq [GENEPIO:0100124]": { - "text": "Illumina MiniSeq [GENEPIO:0100124]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina MiSeq [OBI:0002003]": { - "text": "Illumina MiSeq [OBI:0002003]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina NextSeq [GENEPIO:0100126]": { - "text": "Illumina NextSeq [GENEPIO:0100126]", - "is_a": "Illumina [GENEPIO:0100105]" - }, - "Illumina NextSeq 500 [OBI:0002021]": { - "text": "Illumina NextSeq 500 [OBI:0002021]", - "is_a": "Illumina NextSeq [GENEPIO:0100126]" - }, - "Illumina NextSeq 550 [GENEPIO:0100128]": { - "text": "Illumina NextSeq 550 [GENEPIO:0100128]", - "is_a": "Illumina NextSeq [GENEPIO:0100126]" - }, - "Illumina NextSeq 2000 [GENEPIO:0100129]": { - "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", - "is_a": "Illumina NextSeq [GENEPIO:0100126]" - }, - "PacBio [GENEPIO:0100130]": { - "text": "PacBio [GENEPIO:0100130]" - }, - "PacBio RS [GENEPIO:0100131]": { - "text": "PacBio RS [GENEPIO:0100131]", - "is_a": "PacBio [GENEPIO:0100130]" - }, - "PacBio RS II [OBI:0002012]": { - "text": "PacBio RS II [OBI:0002012]", - "is_a": "PacBio [GENEPIO:0100130]" - }, - "PacBio Sequel [GENEPIO:0100133]": { - "text": "PacBio Sequel [GENEPIO:0100133]", - "is_a": "PacBio [GENEPIO:0100130]" - }, - "PacBio Sequel II [GENEPIO:0100134]": { - "text": "PacBio Sequel II [GENEPIO:0100134]", - "is_a": "PacBio [GENEPIO:0100130]" - }, - "Ion Torrent [GENEPIO:0100135]": { - "text": "Ion Torrent [GENEPIO:0100135]" - }, - "Ion Torrent PGM [GENEPIO:0100136]": { - "text": "Ion Torrent PGM [GENEPIO:0100136]", - "is_a": "Ion Torrent [GENEPIO:0100135]" - }, - "Ion Torrent Proton [GENEPIO:0100137]": { - "text": "Ion Torrent Proton [GENEPIO:0100137]", - "is_a": "Ion Torrent [GENEPIO:0100135]" - }, - "Ion Torrent S5 XL [GENEPIO:0100138]": { - "text": "Ion Torrent S5 XL [GENEPIO:0100138]", - "is_a": "Ion Torrent [GENEPIO:0100135]" - }, - "Ion Torrent S5 [GENEPIO:0100139]": { - "text": "Ion Torrent S5 [GENEPIO:0100139]", - "is_a": "Ion Torrent [GENEPIO:0100135]" - }, - "Oxford Nanopore [GENEPIO:0100140]": { - "text": "Oxford Nanopore [GENEPIO:0100140]" - }, - "Oxford Nanopore GridION [GENEPIO:0100141]": { - "text": "Oxford Nanopore GridION [GENEPIO:0100141]", - "is_a": "Oxford Nanopore [GENEPIO:0100140]" - }, - "Oxford Nanopore MinION [GENEPIO:0100142]": { - "text": "Oxford Nanopore MinION [GENEPIO:0100142]", - "is_a": "Oxford Nanopore [GENEPIO:0100140]" - }, - "Oxford Nanopore PromethION [GENEPIO:0100143]": { - "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", - "is_a": "Oxford Nanopore [GENEPIO:0100140]" - }, - "BGISEQ [GENEPIO:0100144]": { - "text": "BGISEQ [GENEPIO:0100144]" - }, - "BGISEQ-500 [GENEPIO:0100145]": { - "text": "BGISEQ-500 [GENEPIO:0100145]", - "is_a": "BGISEQ [GENEPIO:0100144]" - }, - "DNBSEQ [GENEPIO:0100146]": { - "text": "DNBSEQ [GENEPIO:0100146]" - }, - "DNBSEQ-T7 [GENEPIO:0100147]": { - "text": "DNBSEQ-T7 [GENEPIO:0100147]", - "is_a": "DNBSEQ [GENEPIO:0100146]" - }, - "DNBSEQ-G400 [GENEPIO:0100148]": { - "text": "DNBSEQ-G400 [GENEPIO:0100148]", - "is_a": "DNBSEQ [GENEPIO:0100146]" - }, - "DNBSEQ-G400 FAST [GENEPIO:0100149]": { - "text": "DNBSEQ-G400 FAST [GENEPIO:0100149]", - "is_a": "DNBSEQ [GENEPIO:0100146]" - }, - "DNBSEQ-G50 [GENEPIO:0100150]": { - "text": "DNBSEQ-G50 [GENEPIO:0100150]", - "is_a": "DNBSEQ [GENEPIO:0100146]" - } - } - }, - "sequence_submitted_by menu": { - "name": "sequence_submitted_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]" - }, - "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]" - } - } - }, - "attribute_package menu": { - "name": "attribute_package menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Pathogen.cl [GENEPIO:0001835]": { - "text": "Pathogen.cl [GENEPIO:0001835]" - }, - "Pathogen.env [GENEPIO:0100581]": { - "text": "Pathogen.env [GENEPIO:0100581]" - } - } - }, - "experimental_intervention menu": { - "name": "experimental_intervention menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Addition of substances to food/water [GENEPIO:0100536]": { - "text": "Addition of substances to food/water [GENEPIO:0100536]" - }, - "Antimicrobial pre-treatment [GENEPIO:0100537]": { - "text": "Antimicrobial pre-treatment [GENEPIO:0100537]" - }, - "Certified animal husbandry practices [GENEPIO:0100538]": { - "text": "Certified animal husbandry practices [GENEPIO:0100538]" - }, - "Certified organic farming practices [GENEPIO:0100539]": { - "text": "Certified organic farming practices [GENEPIO:0100539]" - }, - "Change in storage conditions [GENEPIO:0100540]": { - "text": "Change in storage conditions [GENEPIO:0100540]" - }, - "Cleaning/disinfection [GENEPIO:0100541]": { - "text": "Cleaning/disinfection [GENEPIO:0100541]" - }, - "Extended downtime between activities [GENEPIO:0100542]": { - "text": "Extended downtime between activities [GENEPIO:0100542]" - }, - "Fertilizer pre-treatment [GENEPIO:0100543]": { - "text": "Fertilizer pre-treatment [GENEPIO:0100543]" - }, - "Logistic slaughter [GENEPIO:0100545]": { - "text": "Logistic slaughter [GENEPIO:0100545]" - }, - "Microbial pre-treatment [GENEPIO:0100546]": { - "text": "Microbial pre-treatment [GENEPIO:0100546]" - }, - "Probiotic pre-treatment [GENEPIO:0100547]": { - "text": "Probiotic pre-treatment [GENEPIO:0100547]" - }, - "Vaccination [NCIT:C15346]": { - "text": "Vaccination [NCIT:C15346]" - } - } - }, - "AMR_testing_by menu": { - "name": "AMR_testing_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]" - }, - "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]" - } - } - }, - "antimicrobial_phenotype menu": { - "name": "antimicrobial_phenotype menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Antibiotic resistance not defined [GENEPIO:0002040]": { - "text": "Antibiotic resistance not defined [GENEPIO:0002040]" - }, - "Intermediate antimicrobial phenotype [ARO:3004300]": { - "text": "Intermediate antimicrobial phenotype [ARO:3004300]", - "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]" - }, - "Indeterminate antimicrobial phenotype [GENEPIO:0100585]": { - "text": "Indeterminate antimicrobial phenotype [GENEPIO:0100585]", - "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]" - }, - "Nonsusceptible antimicrobial phenotype [ARO:3004303]": { - "text": "Nonsusceptible antimicrobial phenotype [ARO:3004303]" - }, - "Resistant antimicrobial phenotype [ARO:3004301]": { - "text": "Resistant antimicrobial phenotype [ARO:3004301]" - }, - "Susceptible antimicrobial phenotype [ARO:3004302]": { - "text": "Susceptible antimicrobial phenotype [ARO:3004302]" - }, - "Susceptible dose dependent antimicrobial phenotype [ARO:3004304]": { - "text": "Susceptible dose dependent antimicrobial phenotype [ARO:3004304]" - } - } - }, - "antimicrobial_measurement_units menu": { - "name": "antimicrobial_measurement_units menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "milligram per litre (mg/L) [UO:0000273]": { - "text": "milligram per litre (mg/L) [UO:0000273]" - }, - "millimetre (mm) [UO:0000016]": { - "text": "millimetre (mm) [UO:0000016]" - }, - "microgram per millilitre (ug/mL) [UO:0000274]": { - "text": "microgram per millilitre (ug/mL) [UO:0000274]" - } - } - }, - "antimicrobial_measurement_sign menu": { - "name": "antimicrobial_measurement_sign menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "less than (<) [GENEPIO:0001002]": { - "text": "less than (<) [GENEPIO:0001002]" - }, - "less than or equal to (<=) [GENEPIO:0001003]": { - "text": "less than or equal to (<=) [GENEPIO:0001003]" - }, - "equal to (==) [GENEPIO:0001004]": { - "text": "equal to (==) [GENEPIO:0001004]" - }, - "greater than (>) [GENEPIO:0001006]": { - "text": "greater than (>) [GENEPIO:0001006]" - }, - "greater than or equal to (>=) [GENEPIO:0001005]": { - "text": "greater than or equal to (>=) [GENEPIO:0001005]" - } - } - }, - "antimicrobial_laboratory_typing_method menu": { - "name": "antimicrobial_laboratory_typing_method menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Agar diffusion [NCIT:85595]": { - "text": "Agar diffusion [NCIT:85595]" - }, - "Antimicrobial gradient (E-test) [NCIT:85596]": { - "text": "Antimicrobial gradient (E-test) [NCIT:85596]", - "is_a": "Agar diffusion [NCIT:85595]" - }, - "Agar dilution [ARO:3004411]": { - "text": "Agar dilution [ARO:3004411]" - }, - "Broth dilution [ARO:3004397]": { - "text": "Broth dilution [ARO:3004397]" - } - } - }, - "antimicrobial_laboratory_typing_platform menu": { - "name": "antimicrobial_laboratory_typing_platform menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "BIOMIC Microbiology System": { - "text": "BIOMIC Microbiology System" - }, - "Microscan [ARO:3004400]": { - "text": "Microscan [ARO:3004400]" - }, - "Phoenix [ARO:3004401]": { - "text": "Phoenix [ARO:3004401]" - }, - "Sensititre [ARO:3004402]": { - "text": "Sensititre [ARO:3004402]" - }, - "Vitek System [ARO:3004403]": { - "text": "Vitek System [ARO:3004403]" - } - } - }, - "antimicrobial_vendor_name": { - "name": "antimicrobial_vendor_name", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Becton Dickinson [ARO:3004405]": { - "text": "Becton Dickinson [ARO:3004405]" - }, - "bioMérieux [ARO:3004406]": { - "text": "bioMérieux [ARO:3004406]" - }, - "Omron [ARO:3004408]": { - "text": "Omron [ARO:3004408]" - }, - "Siemens [ARO:3004407]": { - "text": "Siemens [ARO:3004407]" - }, - "Trek [ARO:3004409]": { - "text": "Trek [ARO:3004409]" - } - } - }, - "antimicrobial_testing_standard menu": { - "name": "antimicrobial_testing_standard menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]": { - "text": "British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]" - }, - "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]": { - "text": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" - }, - "Deutsches Institut für Normung (DIN) [ARO:3004367]": { - "text": "Deutsches Institut für Normung (DIN) [ARO:3004367]" - }, - "European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]": { - "text": "European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]" - }, - "National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]": { - "text": "National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]" - }, - "National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]": { - "text": "National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]" - }, - "Société Française de Microbiologie (SFM) [ARO:3004369]": { - "text": "Société Française de Microbiologie (SFM) [ARO:3004369]" - }, - "Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]": { - "text": "Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]" - }, - "Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]": { - "text": "Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]" - } - } - } - }, - "slots": { - "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" - ], - "slot_uri": "GENEPIO:0001123", - "range": "WhitespaceMinimizedString", - "required": true - }, - "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", - "slot_uri": "GENEPIO:0100427", - "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" - ], - "slot_uri": "GENEPIO:0001153", - "required": true, - "any_of": [ - { - "range": "sample_collected_by menu" - }, - { - "range": "null value menu" - } - ] - }, - "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", - "slot_uri": "GENEPIO:0100428", - "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", - "slot_uri": "GENEPIO:0100429", - "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", - "slot_uri": "GENEPIO:0100430", - "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", - "slot_uri": "GENEPIO:0100431", - "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", - "slot_uri": "GENEPIO:0100432", - "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", - "slot_uri": "GENEPIO:0001156", - "range": "WhitespaceMinimizedString", - "required": true - }, - "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" - ], - "slot_uri": "GENEPIO:0001198", - "required": true, - "any_of": [ - { - "range": "purpose_of_sampling menu" - }, - { - "range": "null value menu" - } - ] - }, - "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", - "slot_uri": "GENEPIO:0100433", - "any_of": [ - { - "range": "presampling_activity menu" - }, - { - "range": "null value menu" - } - ] - }, - "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", - "slot_uri": "GENEPIO:0100434", - "range": "WhitespaceMinimizedString" - }, - "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", - "slot_uri": "GENEPIO:0100435", - "any_of": [ - { - "range": "specimen_processing menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 (country)" - ], - "slot_uri": "GENEPIO:0001181", - "required": true, - "any_of": [ - { - "range": "geo_loc_name (country) menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 (state/province/region)" - ], - "slot_uri": "GENEPIO:0001185", - "required": true, - "any_of": [ - { - "range": "geo_loc_name (state/province/region) menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 (site)" - ], - "slot_uri": "GENEPIO:0100436", - "range": "WhitespaceMinimizedString" - }, - "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", - "slot_uri": "GENEPIO:0100437", - "any_of": [ - { - "range": "geo_loc_name (country) menu" - }, - { - "range": "null value menu" - } - ] - }, - "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", - "slot_uri": "GENEPIO:0100438", - "any_of": [ - { - "range": "geo_loc_name (country) menu" - }, - { - "range": "null value menu" - } - ] - }, - "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", - "slot_uri": "GENEPIO:0100309", - "range": "WhitespaceMinimizedString" - }, - "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", - "slot_uri": "GENEPIO:0100310", - "range": "WhitespaceMinimizedString" - }, - "sample_collection_date": { - "name": "sample_collection_date", - "description": "The date on which the sample was collected.", - "title": "sample_collection_date", - "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." - ], - "examples": [ - { - "value": "2020-10-30" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:sample collection date" - ], - "slot_uri": "GENEPIO:0001174", - "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", - "slot_uri": "GENEPIO:0001177", - "range": "sample_collection_date_precision menu", - "required": true - }, - "sample_received_date": { - "name": "sample_received_date", - "description": "The date on which the sample was received.", - "title": "sample_received_date", - "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." - ], - "examples": [ - { - "value": "2020-11-15" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001179", - "range": "date" - }, - "original_sample_description": { - "name": "original_sample_description", - "description": "The original sample description provided by the sample collector.", - "title": "original_sample_description", - "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." - ], - "examples": [ - { - "value": "RTE Prosciutto from deli" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100439", - "range": "WhitespaceMinimizedString" - }, - "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": [ - "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": "Poultry hatchery [ENVO:01001874]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:environmental_site" - ], - "slot_uri": "GENEPIO:0001232", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "environmental_site menu" - }, - { - "range": "null value menu" - } - ] - }, - "water_depth": { - "name": "water_depth", - "description": "The depth of some water.", - "title": "water_depth", - "comments": [ - "Provide the depth of water with a value and unit." - ], - "examples": [ - { - "value": "5m" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100440", - "range": "WhitespaceMinimizedString" - }, - "sediment_depth": { - "name": "sediment_depth", - "description": "The depth of some water.", - "title": "sediment_depth", - "comments": [ - "Provide the depth of water with a value and unit." - ], - "examples": [ - { - "value": "5m" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100697", - "range": "WhitespaceMinimizedString" - }, - "air_temperature": { - "name": "air_temperature", - "description": "The temperature of some air.", - "title": "air_temperature", - "comments": [ - "Provide the temperature of the air with a value and unit. Do not provide a symbol for degree e.g. oC" - ], - "examples": [ - { - "value": "25C" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100441", - "range": "WhitespaceMinimizedString" - }, - "water_temperature": { - "name": "water_temperature", - "description": "The temperature of some water.", - "title": "water_temperature", - "comments": [ - "Provide the temperature of the water with a value and unit. Do not provide a symbol for degree e.g. oC" - ], - "examples": [ - { - "value": "4C" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100698", - "range": "WhitespaceMinimizedString" - }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", - "comments": [ - "Provide the weather conditions at the time of sample collection." - ], - "examples": [ - { - "value": "Rain [ENVO:01001564]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100442", - "multivalued": true, - "any_of": [ - { - "range": "weather_type menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "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": "Total coliform count data" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100690", - "multivalued": true, - "any_of": [ - { - "range": "available_data_types menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "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": "Turkey [NCBITaxon:9103]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100443", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "animal_or_plant_population menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 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": "Soil [ENVO:00001998]" - }, - { - "value": "Water [CHEBI:15377]" - }, - { - "value": "Wastewater [ENVO:00002001]" - }, - { - "value": "Broom [ENVO:03501377]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:environmental_material" - ], - "slot_uri": "GENEPIO:0001223", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "environmental_material menu" - }, - { - "range": "null value menu" - } - ] - }, - "anatomical_material": { - "name": "anatomical_material", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "title": "anatomical_material", - "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." - ], - "examples": [ - { - "value": "Tissue [UBERON:0000479]" - }, - { - "value": "Blood [UBERON:0000178]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:anatomical_material" - ], - "slot_uri": "GENEPIO:0001211", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "anatomical_material menu" - }, - { - "range": "null value menu" - } - ] - }, - "body_product": { - "name": "body_product", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "title": "body_product", - "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." - ], - "examples": [ - { - "value": "Feces [UBERON:0001988]" - }, - { - "value": "Urine [UBERON:0001088]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:body_product" - ], - "slot_uri": "GENEPIO:0001216", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "body_product menu" - }, - { - "range": "null value menu" - } - ] - }, - "anatomical_part": { - "name": "anatomical_part", - "description": "An anatomical part of an organism e.g. oropharynx.", - "title": "anatomical_part", - "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." - ], - "examples": [ - { - "value": "Snout [UBERON:0006333]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:anatomical_part" - ], - "slot_uri": "GENEPIO:0001214", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "anatomical_part menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "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": "Dorso-lateral region [BSPO:0000080]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100700", - "any_of": [ - { - "range": "anatomical_region menu" - }, - { - "range": "null value menu" - } - ] - }, - "food_product": { - "name": "food_product", - "description": "A material consumed and digested for nutritional value or enjoyment.", - "title": "food_product", - "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": "Feather meal [FOODON:00003927]" - }, - { - "value": "Bone meal [ENVO:02000054]" - }, - { - "value": "Chicken breast [FOODON:00002703]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_product" - ], - "slot_uri": "GENEPIO:0100444", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "food_product menu" - }, - { - "range": "null value menu" - } - ] - }, - "food_product_properties": { - "name": "food_product_properties", - "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", - "title": "food_product_properties", - "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)." - ], - "examples": [ - { - "value": "Food (chopped) [FOODON:00002777]" - }, - { - "value": "Ready-to-eat (RTE) [FOODON:03316636]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_product_properties" - ], - "slot_uri": "GENEPIO:0100445", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "food_product_properties menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma." - ], - "examples": [ - { - "value": "Chicken [NCBITaxon:9031]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100446", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "animal_source_of_food menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "Provide the name of the agricultural production stream from the picklist." - ], - "examples": [ - { - "value": "Beef cattle production stream [FOODON:03000452]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100699", - "any_of": [ - { - "range": "food_product_production_stream menu" - }, - { - "range": "null value menu" - } - ] - }, - "sample_storage_method": { - "name": "sample_storage_method", - "description": "The type of packaging used to contain a food product.", - "title": "sample_storage_method", - "comments": [ - "If known, provide information regarding how the food product was packaged." - ], - "examples": [ - { - "value": "Plastic tray or pan [FOODON:03490126]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100447", - "range": "WhitespaceMinimizedString" - }, - "sample_storage_medium": { - "name": "sample_storage_medium", - "description": "A specification of the way that a specimen is or was stored.", - "title": "sample_storage_medium", - "comments": [ - "Provide a description of how the same was stored." - ], - "examples": [ - { - "value": "Frozen at -20C" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100448", - "range": "WhitespaceMinimizedString" - }, - "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": "PBS + 20% glycerol" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:collection_device" - ], - "slot_uri": "GENEPIO:0001234", - "recommended": true, - "any_of": [ - { - "range": "collection_device menu" - }, - { - "range": "null value menu" - } - ] - }, - "collection_method": { - "name": "collection_method", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "title": "collection_method", - "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." - ], - "examples": [ - { - "value": "Drag swab [OBI:0002822]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:collection_method" - ], - "slot_uri": "GENEPIO:0001241", - "recommended": true, - "any_of": [ - { - "range": "collection_method menu" - }, - { - "range": "null value menu" - } - ] - }, - "food_packaging": { - "name": "food_packaging", - "description": "The type of packaging used to contain a food product.", - "title": "food_packaging", - "comments": [ - "If known, provide information regarding how the food product was packaged." - ], - "examples": [ - { - "value": "Rinsing for specimen collection [GENEPIO_0002116]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_packaging" - ], - "slot_uri": "GENEPIO:0100447", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "food_packaging menu" - }, - { - "range": "null value menu" - } - ] - }, - "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", - "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." - ], - "examples": [ - { - "value": "2020-05-25" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100615", - "range": "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", - "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." - ], - "examples": [ - { - "value": "2020-05-25" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100616", - "range": "date" - }, - "host (common name)": { - "name": "host (common name)", - "description": "The commonly used name of the host.", - "title": "host (common name)", - "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." - ], - "examples": [ - { - "value": "Cow [NCBITaxon:9913]" - }, - { - "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001386", - "recommended": true, - "any_of": [ - { - "range": "host (common name) menu" - }, - { - "range": "null value menu" - } - ] - }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", - "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." - ], - "examples": [ - { - "value": "Bos taurus [NCBITaxon:9913]" - }, - { - "value": "Homo sapiens [NCBITaxon:9103]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:host" - ], - "slot_uri": "GENEPIO:0001387", - "recommended": true, - "any_of": [ - { - "range": "host (scientific name) menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 name of the ecotype of the host organism." - ], - "examples": [ - { - "value": "Sea ecotype" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100450", - "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)", - "comments": [ - "Provide the name of the breed of the host organism." - ], - "examples": [ - { - "value": "Holstein" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:host_disease" - ], - "slot_uri": "GENEPIO:0100451", - "range": "WhitespaceMinimizedString" - }, - "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": [ - "Select the host's food production name from the pick list." - ], - "examples": [ - { - "value": "Calf [FOODON:03411349]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100452", - "any_of": [ - { - "range": "host (food production name) menu" - }, - { - "range": "null value menu" - } - ] - }, - "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", - "slot_uri": "GENEPIO:0001394", - "range": "host_age_bin menu" - }, - "host_disease": { - "name": "host_disease", - "description": "The name of the disease experienced by the host.", - "title": "host_disease", - "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”." - ], - "examples": [ - { - "value": "mastitis, gastroenteritis" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001391", - "range": "WhitespaceMinimizedString" - }, - "microbiological_method": { - "name": "microbiological_method", - "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", - "title": "microbiological_method", - "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." - ], - "examples": [ - { - "value": "MFHPB-30" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100454", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "strain": { - "name": "strain", - "description": "The strain identifier.", - "title": "strain", - "comments": [ - "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": "K12" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100455", - "range": "WhitespaceMinimizedString" - }, - "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 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": "SA20131043" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100456", - "range": "WhitespaceMinimizedString", - "required": true - }, - "alternative_isolate_ID": { - "name": "alternative_isolate_ID", - "description": "An alternative isolate_ID assigned to the isolate by another organization.", - "title": "alternative_isolate_ID", - "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." - ], - "examples": [ - { - "value": "GHIF3456[PHAC]" - }, - { - "value": "QWICK222[CFIA]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100457", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "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": [ - "If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID." - ], - "examples": [ - { - "value": "SUB_ON_1526" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100458", - "range": "WhitespaceMinimizedString" - }, - "IRIDA_isolate_ID": { - "name": "IRIDA_isolate_ID", - "description": "The identifier of the isolate in the IRIDA platform.", - "title": "IRIDA_isolate_ID", - "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." - ], - "examples": [ - { - "value": "GRDI_LL_12345" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100459", - "range": "WhitespaceMinimizedString", - "required": true - }, - "IRIDA_project_ID": { - "name": "IRIDA_project_ID", - "description": "The identifier of the Project in the iRIDA platform.", - "title": "IRIDA_project_ID", - "comments": [ - "Provide the IRIDA \"project ID\"." - ], - "examples": [ - { - "value": "666" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100460", - "range": "WhitespaceMinimizedString", - "required": true - }, - "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 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": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100461", - "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", - "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." - ], - "examples": [ - { - "value": "Topp Lab" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100462", - "range": "WhitespaceMinimizedString" - }, - "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 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": "Enterics Lab Manager" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100463", - "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", - "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." - ], - "examples": [ - { - "value": "enterics@lab.ca" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100464", - "range": "WhitespaceMinimizedString" - }, - "isolation_date": { - "name": "isolation_date", - "description": "The date on which the isolate was isolated from a sample.", - "title": "isolation_date", - "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." - ], - "examples": [ - { - "value": "2020-10-30" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100465", - "range": "date" - }, - "isolate_received_date": { - "name": "isolate_received_date", - "description": "The date on which the isolate was received by the laboratory.", - "title": "isolate_received_date", - "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." - ], - "examples": [ - { - "value": "2020-11-15" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100466", - "range": "WhitespaceMinimizedString" - }, - "organism": { - "name": "organism", - "description": "Taxonomic name of the organism.", - "title": "organism", - "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." - ], - "examples": [ - { - "value": "Salmonella enterica subsp. enterica [NCBITaxon:59201]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:organism" - ], - "slot_uri": "GENEPIO:0001191", - "required": true, - "any_of": [ - { - "range": "organism menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 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": "PCR assay [OBI:0002740]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100583", - "recommended": true, - "any_of": [ - { - "range": "taxonomic_identification_process menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "Briefly describe the taxonomic identififcation method details using free text." - ], - "examples": [ - { - "value": "Biolog instrument" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100584", - "range": "WhitespaceMinimizedString" - }, - "serovar": { - "name": "serovar", - "description": "The serovar of the organism.", - "title": "serovar", - "comments": [ - "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": "Heidelberg" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100467", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "serotyping_method": { - "name": "serotyping_method", - "description": "The method used to determine the serovar.", - "title": "serotyping_method", - "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." - ], - "examples": [ - { - "value": "SISTR 1.0.1" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100468", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "phagetype": { - "name": "phagetype", - "description": "The phagetype of the organism.", - "title": "phagetype", - "comments": [ - "Provide if known. If unknown, put “missing”." - ], - "examples": [ - { - "value": "47" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100469", - "range": "WhitespaceMinimizedString" - }, - "library_ID": { - "name": "library_ID", - "description": "The user-specified identifier for the library prepared for sequencing.", - "title": "library_ID", - "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." - ], - "examples": [ - { - "value": "LS_2010_NP_123446" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001448", - "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", - "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." - ], - "examples": [ - { - "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:sequenced_by" - ], - "slot_uri": "GENEPIO:0100416", - "required": true, - "any_of": [ - { - "range": "sequenced_by menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 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": "Topp Lab" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100470", - "range": "WhitespaceMinimizedString" - }, - "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 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": "Enterics Lab Manager" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100471", - "range": "WhitespaceMinimizedString" - }, - "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": [ - "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": "enterics@lab.ca" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100422", - "range": "WhitespaceMinimizedString", - "required": true - }, - "purpose_of_sequencing": { - "name": "purpose_of_sequencing", - "description": "The reason that the sample was sequenced.", - "title": "purpose_of_sequencing", - "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." - ], - "examples": [ - { - "value": "Research [GENEPIO:0100003]" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:purpose_of_sequencing" - ], - "slot_uri": "GENEPIO:0001445", - "multivalued": true, - "required": true, - "any_of": [ - { - "range": "purpose_of_sequencing menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 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": "AMR-GRDI (PA-1356)" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100472", - "range": "WhitespaceMinimizedString" - }, - "sequencing_platform": { - "name": "sequencing_platform", - "description": "The platform technology used to perform the sequencing.", - "title": "sequencing_platform", - "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." - ], - "examples": [ - { - "value": "Illumina [GENEPIO:0001923]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100473", - "any_of": [ - { - "range": "sequencing_platform menu" - }, - { - "range": "null value menu" - } - ] - }, - "sequencing_instrument": { - "name": "sequencing_instrument", - "description": "The model of the sequencing instrument used.", - "title": "sequencing_instrument", - "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." - ], - "examples": [ - { - "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001452", - "any_of": [ - { - "range": "sequencing_instrument menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "Provide the name of the library preparation kit used." - ], - "examples": [ - { - "value": "Nextera XT" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001450", - "range": "WhitespaceMinimizedString" - }, - "sequencing_protocol": { - "name": "sequencing_protocol", - "description": "The protocol or method used for sequencing.", - "title": "sequencing_protocol", - "comments": [ - "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": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001454", - "range": "WhitespaceMinimizedString" - }, - "r1_fastq_filename": { - "name": "r1_fastq_filename", - "description": "The user-specified filename of the r1 FASTQ file.", - "title": "r1_fastq_filename", - "comments": [ - "Provide the r1 FASTQ filename." - ], - "examples": [ - { - "value": "ABC123_S1_L001_R1_001.fastq.gz" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001476", - "range": "WhitespaceMinimizedString" - }, - "r2_fastq_filename": { - "name": "r2_fastq_filename", - "description": "The user-specified filename of the r2 FASTQ file.", - "title": "r2_fastq_filename", - "comments": [ - "Provide the r2 FASTQ filename." - ], - "examples": [ - { - "value": "ABC123_S1_L001_R2_001.fastq.gz" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001477", - "range": "WhitespaceMinimizedString" - }, - "fast5_filename": { - "name": "fast5_filename", - "description": "The user-specified filename of the FAST5 file.", - "title": "fast5_filename", - "comments": [ - "Provide the FAST5 filename." - ], - "examples": [ - { - "value": "batch1a_sequences.fast5" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001480", - "range": "WhitespaceMinimizedString" - }, - "assembly_filename": { - "name": "assembly_filename", - "description": "The user-defined filename of the FASTA file.", - "title": "assembly_filename", - "comments": [ - "Provide the FASTA filename." - ], - "examples": [ - { - "value": "pathogenassembly123.fasta" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001461", - "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", - "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)\"." - ], - "examples": [ - { - "value": "Environment Canada (EC)" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001159", - "any_of": [ - { - "range": "sequence_submitted_by menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 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": "Enterics Lab Manager" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100474", - "range": "WhitespaceMinimizedString" - }, - "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": [ - "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" - ], - "examples": [ - { - "value": "RespLab@lab.ca" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001165", - "range": "WhitespaceMinimizedString" - }, - "publication_ID": { - "name": "publication_ID", - "description": "The identifier for a publication.", - "title": "publication_ID", - "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." - ], - "examples": [ - { - "value": "PMID: 33205991" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100475", - "range": "WhitespaceMinimizedString" - }, - "attribute_package": { - "name": "attribute_package", - "description": "The attribute package used to structure metadata in an INSDC BioSample.", - "title": "attribute_package", - "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”." - ], - "examples": [ - { - "value": "Pathogen.env" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100476", - "any_of": [ - { - "range": "attribute_package menu" - }, - { - "range": "null value menu" - } - ] - }, - "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." - ], - "examples": [ - { - "value": "PRJNA12345" - } - ], - "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "BIOSAMPLE:bioproject_accession" - ], - "slot_uri": "GENEPIO:0001136", - "range": "WhitespaceMinimizedString" - }, - "biosample_accession": { - "name": "biosample_accession", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "title": "biosample_accession", - "comments": [ - "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": "SAMN14180202" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001139", - "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", - "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." - ], - "examples": [ - { - "value": "SRR11177792" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001142", - "range": "WhitespaceMinimizedString" - }, - "GenBank_accession": { - "name": "GenBank_accession", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "title": "GenBank_accession", - "comments": [ - "Store the accession returned from a GenBank/ENA/DDBJ submission." - ], - "examples": [ - { - "value": "MN908947.3" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001145", - "range": "WhitespaceMinimizedString" - }, - "prevalence_metrics": { - "name": "prevalence_metrics", - "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", - "title": "prevalence_metrics", - "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." - ], - "examples": [ - { - "value": "Number of total samples collected, Number of positive samples" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100480", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "prevalence_metrics_details": { - "name": "prevalence_metrics_details", - "description": "The details pertaining to the prevalence metrics from a surveillance project.", - "title": "prevalence_metrics_details", - "comments": [ - "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": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100481", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "stage_of_production": { - "name": "stage_of_production", - "description": "The stage of food production.", - "title": "stage_of_production", - "comments": [ - "Provide the stage of food production as free text." - ], - "examples": [ - { - "value": "Abattoir [ENVO:01000925]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100482", - "recommended": true, - "any_of": [ - { - "range": "stage_of_production menu" - }, - { - "range": "null value menu" - } - ] - }, - "experimental_intervention": { - "name": "experimental_intervention", - "description": "The category of the experimental intervention applied in the food production system.", - "title": "experimental_intervention", - "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." - ], - "examples": [ - { - "value": "Vaccination [NCIT:C15346]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100483", - "multivalued": true, - "recommended": true, - "any_of": [ - { - "range": "experimental_intervention menu" - }, - { - "range": "null value menu" - } - ] - }, - "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": [ - "If an experimental intervention was applied in the survey, provide details in this field as free text." - ], - "examples": [ - { - "value": "2% cranberry solution mixed in feed" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100484", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "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 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": "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100511", - "required": true, - "any_of": [ - { - "range": "AMR_testing_by menu" - }, - { - "range": "null value menu" - } - ] - }, - "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 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": "Topp Lab" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100512", - "range": "WhitespaceMinimizedString" - }, - "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 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", - "slot_uri": "GENEPIO:0100513", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "null value menu" - } - ] - }, - "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 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", - "slot_uri": "GENEPIO:0100514", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "null value menu" - } - ] - }, - "AMR_testing_date": { - "name": "AMR_testing_date", - "description": "The date the antimicrobial resistance testing was performed.", - "title": "AMR_testing_date", - "comments": [ - "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." - ], - "examples": [ - { - "value": "2022-04-03" - } - ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100515", - "range": "date" - }, - "antimicrobial_resistance_test_drug": { - "name": "antimicrobial_resistance_test_drug", - "description": "The antimicrobial drug being tested.", - "title": "antimicrobial_resistance_test_drug", - "examples": [ - { - "value": "amikacin" - } - ], - "from_schema": "https://example.com/GRDI", - "recommended": true, - "any_of": [ - { - "range": "antimicrobial_resistance_test_drug menu" - }, - { - "range": "null value menu" - } - ] - }, - "resistance_phenotype": { - "name": "resistance_phenotype", - "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "resistance_phenotype", - "comments": [ - "Select a phenotype from the pick list provided." - ], - "examples": [ - { - "value": "Susceptible antimicrobial phenotype [ARO:3004302]" - } - ], - "from_schema": "https://example.com/GRDI", - "recommended": true, - "any_of": [ - { - "range": "antimicrobial_phenotype menu" - }, - { - "range": "null value menu" - } - ] - }, - "measurement": { - "name": "measurement", - "description": "The measured value of resistance to given antibiotic.", - "title": "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", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "null value menu" - } - ] - }, - "measurement_units": { - "name": "measurement_units", - "description": "The units of the antimicrobial resistance measurement.", - "title": "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", - "required": true, - "any_of": [ - { - "range": "antimicrobial_measurement_units menu" - }, - { - "range": "null value menu" - } - ] - }, - "measurement_sign": { - "name": "measurement_sign", - "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "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", - "required": true, - "any_of": [ - { - "range": "antimicrobial_measurement_sign menu" - }, - { - "range": "null value menu" - } - ] - }, - "laboratory_typing_method": { - "name": "laboratory_typing_method", - "description": "The general method used for antimicrobial susceptibility testing.", - "title": "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", - "any_of": [ - { - "range": "antimicrobial_laboratory_typing_method menu" - }, - { - "range": "null value menu" - } - ] - }, - "laboratory_typing_platform": { - "name": "laboratory_typing_platform", - "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "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", - "any_of": [ - { - "range": "antimicrobial_laboratory_typing_platform menu" - }, - { - "range": "null value menu" - } - ] - }, - "laboratory_typing_platform_version": { - "name": "laboratory_typing_platform_version", - "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "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", - "range": "WhitespaceMinimizedString" - }, - "vendor_name": { - "name": "vendor_name", - "description": "The name of the vendor of the testing platform used.", - "title": "vendor_name", - "comments": [ - "Provide the full name of the company (avoid abbreviations)." - ], - "examples": [ - { - "value": "Sensititre" - } - ], - "from_schema": "https://example.com/GRDI", - "any_of": [ - { - "range": "antimicrobial_vendor_name" - }, - { - "range": "null value menu" - } - ] - }, - "testing_standard": { - "name": "testing_standard", - "description": "The testing standard used for determination of resistance phenotype", - "title": "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", - "recommended": true, - "any_of": [ - { - "range": "antimicrobial_testing_standard menu" - }, - { - "range": "null value menu" - } - ] - }, - "testing_standard_version": { - "name": "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": "testing_standard_version", - "comments": [ - "If applicable, include a version number for the testing standard used." - ], - "examples": [ - { - "value": "M100" - } - ], - "from_schema": "https://example.com/GRDI", - "range": "WhitespaceMinimizedString" - }, - "testing_standard_details": { - "name": "testing_standard_details", - "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "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", - "range": "WhitespaceMinimizedString" - }, - "susceptible_breakpoint": { - "name": "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": "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", - "range": "WhitespaceMinimizedString" - }, - "intermediate_breakpoint": { - "name": "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": "intermediate_breakpoint", - "examples": [ - { - "value": "16" - } - ], - "from_schema": "https://example.com/GRDI", - "range": "WhitespaceMinimizedString" - }, - "resistant_breakpoint": { - "name": "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": "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", - "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", - "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", - "range": "Provenance" - } - }, - "classes": { - "dh_interface": { - "name": "dh_interface", - "description": "A DataHarmonizer interface", - "from_schema": "https://example.com/GRDI" - }, - "GRDI_Sample": { - "name": "GRDI_Sample", - "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, - "identifier": true, - "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" - }, - "specimen_processing": { - "name": "specimen_processing", - "rank": 13, - "slot_group": "Sample collection and processing" - }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", - "rank": 14, - "slot_group": "Sample collection and processing" - }, - "geo_loc_name (state/province/region)": { - "name": "geo_loc_name (state/province/region)", - "rank": 15, - "slot_group": "Sample collection and processing" - }, - "geo_loc_name (site)": { - "name": "geo_loc_name (site)", - "rank": 16, - "slot_group": "Sample collection and processing" - }, - "food_product_origin_geo_loc_name (country)": { - "name": "food_product_origin_geo_loc_name (country)", - "rank": 17, - "slot_group": "Sample collection and processing" - }, - "host_origin_geo_loc_name (country)": { - "name": "host_origin_geo_loc_name (country)", - "rank": 18, - "slot_group": "Sample collection and processing" - }, - "geo_loc latitude": { - "name": "geo_loc latitude", - "rank": 19, - "slot_group": "Sample collection and processing" - }, - "geo_loc longitude": { - "name": "geo_loc longitude", - "rank": 20, - "slot_group": "Sample collection and processing" - }, - "sample_collection_date": { - "name": "sample_collection_date", - "rank": 21, - "slot_group": "Sample collection and processing" - }, - "sample_collection_date_precision": { - "name": "sample_collection_date_precision", - "rank": 22, - "slot_group": "Sample collection and processing" - }, - "sample_received_date": { - "name": "sample_received_date", - "rank": 23, - "slot_group": "Sample collection and processing" - }, - "original_sample_description": { - "name": "original_sample_description", - "rank": 24, - "slot_group": "Sample collection and processing" - }, - "environmental_site": { - "name": "environmental_site", - "rank": 25, - "slot_group": "Sample collection and processing" - }, - "water_depth": { - "name": "water_depth", - "rank": 26, - "slot_group": "Sample collection and processing" - }, - "sediment_depth": { - "name": "sediment_depth", - "rank": 27, - "slot_group": "Sample collection and processing" - }, - "air_temperature": { - "name": "air_temperature", - "rank": 28, - "slot_group": "Sample collection and processing" - }, - "water_temperature": { - "name": "water_temperature", - "rank": 29, - "slot_group": "Sample collection and processing" - }, - "weather_type": { - "name": "weather_type", - "rank": 30, - "slot_group": "Sample collection and processing" - }, - "available_data_types": { - "name": "available_data_types", - "rank": 31, - "slot_group": "Sample collection and processing" - }, - "animal_or_plant_population": { - "name": "animal_or_plant_population", - "rank": 32, - "slot_group": "Sample collection and processing" - }, - "environmental_material": { - "name": "environmental_material", - "rank": 33, - "slot_group": "Sample collection and processing" - }, - "anatomical_material": { - "name": "anatomical_material", - "rank": 34, - "slot_group": "Sample collection and processing" - }, - "body_product": { - "name": "body_product", - "rank": 35, - "slot_group": "Sample collection and processing" - }, - "anatomical_part": { - "name": "anatomical_part", - "rank": 36, - "slot_group": "Sample collection and processing" - }, - "anatomical_region": { - "name": "anatomical_region", - "rank": 37, - "slot_group": "Sample collection and processing" - }, - "food_product": { - "name": "food_product", - "rank": 38, - "slot_group": "Sample collection and processing" - }, - "food_product_properties": { - "name": "food_product_properties", - "rank": 39, - "slot_group": "Sample collection and processing" - }, - "animal_source_of_food": { - "name": "animal_source_of_food", - "rank": 40, - "slot_group": "Sample collection and processing" - }, - "food_product_production_stream": { - "name": "food_product_production_stream", - "rank": 41, - "slot_group": "Sample collection and processing" - }, - "sample_storage_method": { - "name": "sample_storage_method", - "rank": 42, - "slot_group": "Sample collection and processing" - }, - "sample_storage_medium": { - "name": "sample_storage_medium", - "rank": 43, - "slot_group": "Sample collection and processing" - }, - "collection_device": { - "name": "collection_device", - "rank": 44, - "slot_group": "Sample collection and processing" - }, - "collection_method": { - "name": "collection_method", - "rank": 45, - "slot_group": "Sample collection and processing" - }, - "food_packaging": { - "name": "food_packaging", - "rank": 46, - "slot_group": "Sample collection and processing" - }, - "food_quality_date": { - "name": "food_quality_date", - "rank": 47, - "slot_group": "Sample collection and processing" - }, - "food_packaging_date": { - "name": "food_packaging_date", - "rank": 48, - "slot_group": "Sample collection and processing" - }, - "host (common name)": { - "name": "host (common name)", - "rank": 49, - "slot_group": "Host information" - }, - "host (scientific name)": { - "name": "host (scientific name)", - "rank": 50, - "slot_group": "Host information" - }, - "host (ecotype)": { - "name": "host (ecotype)", - "rank": 51, - "slot_group": "Host information" - }, - "host (breed)": { - "name": "host (breed)", - "rank": 52, - "slot_group": "Host information" - }, - "host (food production name)": { - "name": "host (food production name)", - "rank": 53, - "slot_group": "Host information" - }, - "host_age_bin": { - "name": "host_age_bin", - "rank": 54, - "slot_group": "Host information" - }, - "host_disease": { - "name": "host_disease", - "rank": 55, - "slot_group": "Host information" - }, - "microbiological_method": { - "name": "microbiological_method", - "rank": 56, - "slot_group": "Strain and isolation information" - }, - "strain": { - "name": "strain", - "rank": 57, - "slot_group": "Strain and isolation information" - }, - "isolate_ID": { - "name": "isolate_ID", - "rank": 58, - "slot_group": "Strain and isolation information" - }, - "alternative_isolate_ID": { - "name": "alternative_isolate_ID", - "rank": 59, - "slot_group": "Strain and isolation information" - }, - "progeny_isolate_ID": { - "name": "progeny_isolate_ID", - "rank": 60, - "slot_group": "Strain and isolation information" - }, - "IRIDA_isolate_ID": { - "name": "IRIDA_isolate_ID", - "rank": 61, - "slot_group": "Strain and isolation information" - }, - "IRIDA_project_ID": { - "name": "IRIDA_project_ID", - "rank": 62, - "slot_group": "Strain and isolation information" - }, - "isolated_by": { - "name": "isolated_by", - "rank": 63, - "slot_group": "Strain and isolation information" - }, - "isolated_by_laboratory_name": { - "name": "isolated_by_laboratory_name", - "rank": 64, - "slot_group": "Strain and isolation information" - }, - "isolated_by_contact_name": { - "name": "isolated_by_contact_name", - "rank": 65, - "slot_group": "Strain and isolation information" - }, - "isolated_by_contact_email": { - "name": "isolated_by_contact_email", - "rank": 66, - "slot_group": "Strain and isolation information" - }, - "isolation_date": { - "name": "isolation_date", - "rank": 67, - "slot_group": "Strain and isolation information" - }, - "isolate_received_date": { - "name": "isolate_received_date", - "rank": 68, - "slot_group": "Strain and isolation information" - }, - "organism": { - "name": "organism", - "rank": 69, - "slot_group": "Strain and isolation information" - }, - "taxonomic_identification_process": { - "name": "taxonomic_identification_process", - "rank": 70, - "slot_group": "Strain and isolation information" - }, - "taxonomic_identification_process_details": { - "name": "taxonomic_identification_process_details", - "rank": 71, - "slot_group": "Strain and isolation information" - }, - "serovar": { - "name": "serovar", - "rank": 72, - "slot_group": "Strain and isolation information" - }, - "serotyping_method": { - "name": "serotyping_method", - "rank": 73, - "slot_group": "Strain and isolation information" - }, - "phagetype": { - "name": "phagetype", - "rank": 74, - "slot_group": "Strain and isolation information" - }, - "library_ID": { - "name": "library_ID", - "rank": 75, - "slot_group": "Sequence information" - }, - "sequenced_by": { - "name": "sequenced_by", - "rank": 76, - "slot_group": "Sequence information" - }, - "sequenced_by_laboratory_name": { - "name": "sequenced_by_laboratory_name", - "rank": 77, - "slot_group": "Sequence information" - }, - "sequenced_by_contact_name": { - "name": "sequenced_by_contact_name", - "rank": 78, - "slot_group": "Sequence information" - }, - "sequenced_by_contact_email": { - "name": "sequenced_by_contact_email", - "rank": 79, - "slot_group": "Sequence information" - }, - "purpose_of_sequencing": { - "name": "purpose_of_sequencing", - "rank": 80, - "slot_group": "Sequence information" - }, - "sequencing_project_name": { - "name": "sequencing_project_name", - "rank": 81, - "slot_group": "Sequence information" - }, - "sequencing_platform": { - "name": "sequencing_platform", - "rank": 82, - "slot_group": "Sequence information" - }, - "sequencing_instrument": { - "name": "sequencing_instrument", - "rank": 83, - "slot_group": "Sequence information" - }, - "library_preparation_kit": { - "name": "library_preparation_kit", - "rank": 84, - "slot_group": "Sequence information" - }, - "sequencing_protocol": { - "name": "sequencing_protocol", - "rank": 85, - "slot_group": "Sequence information" - }, - "r1_fastq_filename": { - "name": "r1_fastq_filename", - "rank": 86, - "slot_group": "Sequence information" - }, - "r2_fastq_filename": { - "name": "r2_fastq_filename", - "rank": 87, - "slot_group": "Sequence information" - }, - "fast5_filename": { - "name": "fast5_filename", - "rank": 88, - "slot_group": "Sequence information" - }, - "assembly_filename": { - "name": "assembly_filename", - "rank": 89, - "slot_group": "Sequence information" - }, - "sequence_submitted_by": { - "name": "sequence_submitted_by", - "rank": 90, - "slot_group": "Public repository information" - }, - "sequence_submitted_by_contact_name": { - "name": "sequence_submitted_by_contact_name", - "rank": 91, - "slot_group": "Public repository information" - }, - "sequence_submitted_by_contact_email": { - "name": "sequence_submitted_by_contact_email", - "rank": 92, - "slot_group": "Public repository information" - }, - "publication_ID": { - "name": "publication_ID", - "rank": 93, - "slot_group": "Public repository information" - }, - "attribute_package": { - "name": "attribute_package", - "rank": 94, - "slot_group": "Public repository information" - }, - "bioproject_accession": { - "name": "bioproject_accession", - "rank": 95, - "slot_group": "Public repository information" - }, - "biosample_accession": { - "name": "biosample_accession", - "rank": 96, - "slot_group": "Public repository information" - }, - "SRA_accession": { - "name": "SRA_accession", - "rank": 97, - "slot_group": "Public repository information" - }, - "GenBank_accession": { - "name": "GenBank_accession", - "rank": 98, - "slot_group": "Public repository information" - }, - "prevalence_metrics": { - "name": "prevalence_metrics", - "rank": 99, - "slot_group": "Risk assessment information" - }, - "prevalence_metrics_details": { - "name": "prevalence_metrics_details", - "rank": 100, - "slot_group": "Risk assessment information" - }, - "stage_of_production": { - "name": "stage_of_production", - "rank": 101, - "slot_group": "Risk assessment information" - }, - "experimental_intervention": { - "name": "experimental_intervention", - "rank": 102, - "slot_group": "Risk assessment information" - }, - "experiment_intervention_details": { - "name": "experiment_intervention_details", - "rank": 103, - "slot_group": "Risk assessment information" - }, - "AMR_testing_by": { - "name": "AMR_testing_by", - "rank": 104, - "slot_group": "Antimicrobial resistance" - }, - "AMR_testing_by_laboratory_name": { - "name": "AMR_testing_by_laboratory_name", - "rank": 105, - "slot_group": "Antimicrobial resistance" - }, - "AMR_testing_by_contact_name": { - "name": "AMR_testing_by_contact_name", - "rank": 106, - "slot_group": "Antimicrobial resistance" - }, - "AMR_testing_by_contact_email": { - "name": "AMR_testing_by_contact_email", - "rank": 107, - "slot_group": "Antimicrobial resistance" - }, - "AMR_testing_date": { - "name": "AMR_testing_date", - "rank": 108, - "slot_group": "Antimicrobial resistance" - }, - "authors": { - "name": "authors", - "rank": 711, - "slot_group": "Contributor acknowledgement" - }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "rank": 712, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "sample_collector_sample_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample", - "AMR_Test" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "required": true - }, - "alternative_sample_ID": { - "name": "alternative_sample_ID", - "description": "An alternative sample_ID assigned to the sample by another organization.", - "title": "alternative_sample_ID", - "from_schema": "https://example.com/GRDI", - "rank": 2, - "slot_uri": "GENEPIO:0100427", - "alias": "alternative_sample_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "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", - "from_schema": "https://example.com/GRDI", - "rank": 3, - "slot_uri": "GENEPIO:0001153", - "alias": "sample_collected_by", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "required": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 4, - "slot_uri": "GENEPIO:0100428", - "alias": "sample_collected_by_laboratory_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "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", - "from_schema": "https://example.com/GRDI", - "rank": 5, - "slot_uri": "GENEPIO:0100429", - "alias": "sample_collection_project_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "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", - "from_schema": "https://example.com/GRDI", - "rank": 6, - "slot_uri": "GENEPIO:0100430", - "alias": "sample_plan_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "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", - "from_schema": "https://example.com/GRDI", - "rank": 7, - "slot_uri": "GENEPIO:0100431", - "alias": "sample_plan_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "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", - "from_schema": "https://example.com/GRDI", - "rank": 8, - "slot_uri": "GENEPIO:0100432", - "alias": "sample_collector_contact_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "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", - "from_schema": "https://example.com/GRDI", - "rank": 9, - "slot_uri": "GENEPIO:0001156", - "alias": "sample_collector_contact_email", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "required": true - }, - "purpose_of_sampling": { - "name": "purpose_of_sampling", - "description": "The reason that the sample was collected.", - "title": "purpose_of_sampling", - "from_schema": "https://example.com/GRDI", - "rank": 10, - "slot_uri": "GENEPIO:0001198", - "alias": "purpose_of_sampling", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "required": true - }, - "presampling_activity": { - "name": "presampling_activity", - "description": "The experimental activities or variables that affected the sample collected.", - "title": "presampling_activity", - "from_schema": "https://example.com/GRDI", - "rank": 11, - "slot_uri": "GENEPIO:0100433", - "alias": "presampling_activity", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 12, - "slot_uri": "GENEPIO:0100434", - "alias": "presampling_activity_details", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "specimen_processing": { - "name": "specimen_processing", - "description": "The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures.", - "title": "specimen_processing", - "from_schema": "https://example.com/GRDI", - "rank": 13, - "slot_uri": "GENEPIO:0100435", - "alias": "specimen_processing", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", - "description": "The country of origin of the sample.", - "title": "geo_loc_name (country)", - "from_schema": "https://example.com/GRDI", - "rank": 14, - "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "required": true - }, - "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)", - "from_schema": "https://example.com/GRDI", - "rank": 15, - "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/region)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "required": true - }, - "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)", - "from_schema": "https://example.com/GRDI", - "rank": 16, - "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_(site)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "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)", - "from_schema": "https://example.com/GRDI", - "rank": 17, - "slot_uri": "GENEPIO:0100437", - "alias": "food_product_origin_geo_loc_name_(country)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "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)", - "from_schema": "https://example.com/GRDI", - "rank": 18, - "slot_uri": "GENEPIO:0100438", - "alias": "host_origin_geo_loc_name_(country)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "geo_loc latitude": { - "name": "geo_loc latitude", - "description": "The latitude coordinates of the geographical location of sample collection.", - "title": "geo_loc latitude", - "from_schema": "https://example.com/GRDI", - "rank": 19, - "slot_uri": "GENEPIO:0100309", - "alias": "geo_loc_latitude", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "geo_loc longitude": { - "name": "geo_loc longitude", - "description": "The longitude coordinates of the geographical location of sample collection.", - "title": "geo_loc longitude", - "from_schema": "https://example.com/GRDI", - "rank": 20, - "slot_uri": "GENEPIO:0100310", - "alias": "geo_loc_longitude", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sample_collection_date": { - "name": "sample_collection_date", - "description": "The date on which the sample was collected.", - "title": "sample_collection_date", - "from_schema": "https://example.com/GRDI", - "rank": 21, - "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "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", - "from_schema": "https://example.com/GRDI", - "rank": 22, - "slot_uri": "GENEPIO:0001177", - "alias": "sample_collection_date_precision", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "sample_collection_date_precision menu", - "required": true - }, - "sample_received_date": { - "name": "sample_received_date", - "description": "The date on which the sample was received.", - "title": "sample_received_date", - "from_schema": "https://example.com/GRDI", - "rank": 23, - "slot_uri": "GENEPIO:0001179", - "alias": "sample_received_date", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "date" - }, - "original_sample_description": { - "name": "original_sample_description", - "description": "The original sample description provided by the sample collector.", - "title": "original_sample_description", - "from_schema": "https://example.com/GRDI", - "rank": 24, - "slot_uri": "GENEPIO:0100439", - "alias": "original_sample_description", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 25, - "slot_uri": "GENEPIO:0001232", - "multivalued": true, - "alias": "environmental_site", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "water_depth": { - "name": "water_depth", - "description": "The depth of some water.", - "title": "water_depth", - "from_schema": "https://example.com/GRDI", - "rank": 26, - "slot_uri": "GENEPIO:0100440", - "alias": "water_depth", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sediment_depth": { - "name": "sediment_depth", - "description": "The depth of some water.", - "title": "sediment_depth", - "from_schema": "https://example.com/GRDI", - "rank": 27, - "slot_uri": "GENEPIO:0100697", - "alias": "sediment_depth", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "air_temperature": { - "name": "air_temperature", - "description": "The temperature of some air.", - "title": "air_temperature", - "from_schema": "https://example.com/GRDI", - "rank": 28, - "slot_uri": "GENEPIO:0100441", - "alias": "air_temperature", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "water_temperature": { - "name": "water_temperature", - "description": "The temperature of some water.", - "title": "water_temperature", - "from_schema": "https://example.com/GRDI", - "rank": 29, - "slot_uri": "GENEPIO:0100698", - "alias": "water_temperature", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", - "from_schema": "https://example.com/GRDI", - "rank": 30, - "slot_uri": "GENEPIO:0100442", - "multivalued": true, - "alias": "weather_type", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 31, - "slot_uri": "GENEPIO:0100690", - "multivalued": true, - "alias": "available_data_types", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 32, - "slot_uri": "GENEPIO:0100443", - "multivalued": true, - "alias": "animal_or_plant_population", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 33, - "slot_uri": "GENEPIO:0001223", - "multivalued": true, - "alias": "environmental_material", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "anatomical_material": { - "name": "anatomical_material", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "title": "anatomical_material", - "from_schema": "https://example.com/GRDI", - "rank": 34, - "slot_uri": "GENEPIO:0001211", - "multivalued": true, - "alias": "anatomical_material", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "body_product": { - "name": "body_product", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "title": "body_product", - "from_schema": "https://example.com/GRDI", - "rank": 35, - "slot_uri": "GENEPIO:0001216", - "multivalued": true, - "alias": "body_product", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "anatomical_part": { - "name": "anatomical_part", - "description": "An anatomical part of an organism e.g. oropharynx.", - "title": "anatomical_part", - "from_schema": "https://example.com/GRDI", - "rank": 36, - "slot_uri": "GENEPIO:0001214", - "multivalued": true, - "alias": "anatomical_part", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 37, - "slot_uri": "GENEPIO:0100700", - "alias": "anatomical_region", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "food_product": { - "name": "food_product", - "description": "A material consumed and digested for nutritional value or enjoyment.", - "title": "food_product", - "from_schema": "https://example.com/GRDI", - "rank": 38, - "slot_uri": "GENEPIO:0100444", - "multivalued": true, - "alias": "food_product", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "food_product_properties": { - "name": "food_product_properties", - "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", - "title": "food_product_properties", - "from_schema": "https://example.com/GRDI", - "rank": 39, - "slot_uri": "GENEPIO:0100445", - "multivalued": true, - "alias": "food_product_properties", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "animal_source_of_food": { - "name": "animal_source_of_food", - "description": "The animal from which the food product was derived.", - "title": "animal_source_of_food", - "from_schema": "https://example.com/GRDI", - "rank": 40, - "slot_uri": "GENEPIO:0100446", - "multivalued": true, - "alias": "animal_source_of_food", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 41, - "slot_uri": "GENEPIO:0100699", - "alias": "food_product_production_stream", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing" - }, - "sample_storage_method": { - "name": "sample_storage_method", - "description": "The type of packaging used to contain a food product.", - "title": "sample_storage_method", - "from_schema": "https://example.com/GRDI", - "rank": 42, - "slot_uri": "GENEPIO:0100447", - "alias": "sample_storage_method", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sample_storage_medium": { - "name": "sample_storage_medium", - "description": "A specification of the way that a specimen is or was stored.", - "title": "sample_storage_medium", - "from_schema": "https://example.com/GRDI", - "rank": 43, - "slot_uri": "GENEPIO:0100448", - "alias": "sample_storage_medium", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "collection_device": { - "name": "collection_device", - "description": "The instrument or container used to collect the sample e.g. swab.", - "title": "collection_device", - "from_schema": "https://example.com/GRDI", - "rank": 44, - "slot_uri": "GENEPIO:0001234", - "alias": "collection_device", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "collection_method": { - "name": "collection_method", - "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", - "title": "collection_method", - "from_schema": "https://example.com/GRDI", - "rank": 45, - "slot_uri": "GENEPIO:0001241", - "alias": "collection_method", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "food_packaging": { - "name": "food_packaging", - "description": "The type of packaging used to contain a food product.", - "title": "food_packaging", - "from_schema": "https://example.com/GRDI", - "rank": 46, - "slot_uri": "GENEPIO:0100447", - "multivalued": true, - "alias": "food_packaging", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "recommended": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 47, - "slot_uri": "GENEPIO:0100615", - "alias": "food_quality_date", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "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", - "from_schema": "https://example.com/GRDI", - "rank": 48, - "slot_uri": "GENEPIO:0100616", - "alias": "food_packaging_date", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sample collection and processing", - "range": "date" - }, - "host (common name)": { - "name": "host (common name)", - "description": "The commonly used name of the host.", - "title": "host (common name)", - "from_schema": "https://example.com/GRDI", - "rank": 49, - "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Host information", - "recommended": true - }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", - "from_schema": "https://example.com/GRDI", - "rank": 50, - "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Host information", - "recommended": true - }, - "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)", - "from_schema": "https://example.com/GRDI", - "rank": 51, - "slot_uri": "GENEPIO:0100450", - "alias": "host_(ecotype)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Host 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)", - "from_schema": "https://example.com/GRDI", - "rank": 52, - "slot_uri": "GENEPIO:0100451", - "alias": "host_(breed)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Host information", - "range": "WhitespaceMinimizedString" - }, - "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)", - "from_schema": "https://example.com/GRDI", - "rank": 53, - "slot_uri": "GENEPIO:0100452", - "alias": "host_(food_production_name)", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Host information" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 54, - "slot_uri": "GENEPIO:0001394", - "alias": "host_age_bin", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Host information", - "range": "host_age_bin menu" - }, - "host_disease": { - "name": "host_disease", - "description": "The name of the disease experienced by the host.", - "title": "host_disease", - "from_schema": "https://example.com/GRDI", - "rank": 55, - "slot_uri": "GENEPIO:0001391", - "alias": "host_disease", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Host information", - "range": "WhitespaceMinimizedString" - }, - "microbiological_method": { - "name": "microbiological_method", - "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", - "title": "microbiological_method", - "from_schema": "https://example.com/GRDI", - "rank": 56, - "slot_uri": "GENEPIO:0100454", - "alias": "microbiological_method", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "strain": { - "name": "strain", - "description": "The strain identifier.", - "title": "strain", - "from_schema": "https://example.com/GRDI", - "rank": 57, - "slot_uri": "GENEPIO:0100455", - "alias": "strain", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 58, - "slot_uri": "GENEPIO:0100456", - "alias": "isolate_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "required": true - }, - "alternative_isolate_ID": { - "name": "alternative_isolate_ID", - "description": "An alternative isolate_ID assigned to the isolate by another organization.", - "title": "alternative_isolate_ID", - "from_schema": "https://example.com/GRDI", - "rank": 59, - "slot_uri": "GENEPIO:0100457", - "alias": "alternative_isolate_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 60, - "slot_uri": "GENEPIO:0100458", - "alias": "progeny_isolate_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" - }, - "IRIDA_isolate_ID": { - "name": "IRIDA_isolate_ID", - "description": "The identifier of the isolate in the IRIDA platform.", - "title": "IRIDA_isolate_ID", - "from_schema": "https://example.com/GRDI", - "rank": 61, - "slot_uri": "GENEPIO:0100459", - "alias": "IRIDA_isolate_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "required": true - }, - "IRIDA_project_ID": { - "name": "IRIDA_project_ID", - "description": "The identifier of the Project in the iRIDA platform.", - "title": "IRIDA_project_ID", - "from_schema": "https://example.com/GRDI", - "rank": 62, - "slot_uri": "GENEPIO:0100460", - "alias": "IRIDA_project_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "required": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 63, - "slot_uri": "GENEPIO:0100461", - "alias": "isolated_by", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation 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", - "from_schema": "https://example.com/GRDI", - "rank": 64, - "slot_uri": "GENEPIO:0100462", - "alias": "isolated_by_laboratory_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 65, - "slot_uri": "GENEPIO:0100463", - "alias": "isolated_by_contact_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation 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", - "from_schema": "https://example.com/GRDI", - "rank": 66, - "slot_uri": "GENEPIO:0100464", - "alias": "isolated_by_contact_email", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" - }, - "isolation_date": { - "name": "isolation_date", - "description": "The date on which the isolate was isolated from a sample.", - "title": "isolation_date", - "from_schema": "https://example.com/GRDI", - "rank": 67, - "slot_uri": "GENEPIO:0100465", - "alias": "isolation_date", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "date" - }, - "isolate_received_date": { - "name": "isolate_received_date", - "description": "The date on which the isolate was received by the laboratory.", - "title": "isolate_received_date", - "from_schema": "https://example.com/GRDI", - "rank": 68, - "slot_uri": "GENEPIO:0100466", - "alias": "isolate_received_date", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" - }, - "organism": { - "name": "organism", - "description": "Taxonomic name of the organism.", - "title": "organism", - "from_schema": "https://example.com/GRDI", - "rank": 69, - "slot_uri": "GENEPIO:0001191", - "alias": "organism", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "required": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 70, - "slot_uri": "GENEPIO:0100583", - "alias": "taxonomic_identification_process", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "recommended": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 71, - "slot_uri": "GENEPIO:0100584", - "alias": "taxonomic_identification_process_details", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" - }, - "serovar": { - "name": "serovar", - "description": "The serovar of the organism.", - "title": "serovar", - "from_schema": "https://example.com/GRDI", - "rank": 72, - "slot_uri": "GENEPIO:0100467", - "alias": "serovar", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "serotyping_method": { - "name": "serotyping_method", - "description": "The method used to determine the serovar.", - "title": "serotyping_method", - "from_schema": "https://example.com/GRDI", - "rank": 73, - "slot_uri": "GENEPIO:0100468", - "alias": "serotyping_method", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "phagetype": { - "name": "phagetype", - "description": "The phagetype of the organism.", - "title": "phagetype", - "from_schema": "https://example.com/GRDI", - "rank": 74, - "slot_uri": "GENEPIO:0100469", - "alias": "phagetype", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" - }, - "library_ID": { - "name": "library_ID", - "description": "The user-specified identifier for the library prepared for sequencing.", - "title": "library_ID", - "from_schema": "https://example.com/GRDI", - "rank": 75, - "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "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", - "from_schema": "https://example.com/GRDI", - "rank": 76, - "slot_uri": "GENEPIO:0100416", - "alias": "sequenced_by", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "required": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 77, - "slot_uri": "GENEPIO:0100470", - "alias": "sequenced_by_laboratory_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 78, - "slot_uri": "GENEPIO:0100471", - "alias": "sequenced_by_contact_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 79, - "slot_uri": "GENEPIO:0100422", - "alias": "sequenced_by_contact_email", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString", - "required": true - }, - "purpose_of_sequencing": { - "name": "purpose_of_sequencing", - "description": "The reason that the sample was sequenced.", - "title": "purpose_of_sequencing", - "from_schema": "https://example.com/GRDI", - "rank": 80, - "slot_uri": "GENEPIO:0001445", - "multivalued": true, - "alias": "purpose_of_sequencing", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "required": true - }, - "sequencing_project_name": { - "name": "sequencing_project_name", - "description": "The name of the project/initiative/program for which sequencing was performed.", - "title": "sequencing_project_name", - "from_schema": "https://example.com/GRDI", - "rank": 81, - "slot_uri": "GENEPIO:0100472", - "alias": "sequencing_project_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "sequencing_platform": { - "name": "sequencing_platform", - "description": "The platform technology used to perform the sequencing.", - "title": "sequencing_platform", - "from_schema": "https://example.com/GRDI", - "rank": 82, - "slot_uri": "GENEPIO:0100473", - "alias": "sequencing_platform", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information" - }, - "sequencing_instrument": { - "name": "sequencing_instrument", - "description": "The model of the sequencing instrument used.", - "title": "sequencing_instrument", - "from_schema": "https://example.com/GRDI", - "rank": 83, - "slot_uri": "GENEPIO:0001452", - "alias": "sequencing_instrument", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 84, - "slot_uri": "GENEPIO:0001450", - "alias": "library_preparation_kit", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "sequencing_protocol": { - "name": "sequencing_protocol", - "description": "The protocol or method used for sequencing.", - "title": "sequencing_protocol", - "from_schema": "https://example.com/GRDI", - "rank": 85, - "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "r1_fastq_filename": { - "name": "r1_fastq_filename", - "description": "The user-specified filename of the r1 FASTQ file.", - "title": "r1_fastq_filename", - "from_schema": "https://example.com/GRDI", - "rank": 86, - "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "r2_fastq_filename": { - "name": "r2_fastq_filename", - "description": "The user-specified filename of the r2 FASTQ file.", - "title": "r2_fastq_filename", - "from_schema": "https://example.com/GRDI", - "rank": 87, - "slot_uri": "GENEPIO:0001477", - "alias": "r2_fastq_filename", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "fast5_filename": { - "name": "fast5_filename", - "description": "The user-specified filename of the FAST5 file.", - "title": "fast5_filename", - "from_schema": "https://example.com/GRDI", - "rank": 88, - "slot_uri": "GENEPIO:0001480", - "alias": "fast5_filename", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, - "assembly_filename": { - "name": "assembly_filename", - "description": "The user-defined filename of the FASTA file.", - "title": "assembly_filename", - "from_schema": "https://example.com/GRDI", - "rank": 89, - "slot_uri": "GENEPIO:0001461", - "alias": "assembly_filename", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Sequence information", - "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", - "from_schema": "https://example.com/GRDI", - "rank": 90, - "slot_uri": "GENEPIO:0001159", - "alias": "sequence_submitted_by", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 91, - "slot_uri": "GENEPIO:0100474", - "alias": "sequence_submitted_by_contact_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 92, - "slot_uri": "GENEPIO:0001165", - "alias": "sequence_submitted_by_contact_email", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" - }, - "publication_ID": { - "name": "publication_ID", - "description": "The identifier for a publication.", - "title": "publication_ID", - "from_schema": "https://example.com/GRDI", - "rank": 93, - "slot_uri": "GENEPIO:0100475", - "alias": "publication_ID", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" - }, - "attribute_package": { - "name": "attribute_package", - "description": "The attribute package used to structure metadata in an INSDC BioSample.", - "title": "attribute_package", - "from_schema": "https://example.com/GRDI", - "rank": 94, - "slot_uri": "GENEPIO:0100476", - "alias": "attribute_package", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information" - }, - "bioproject_accession": { - "name": "bioproject_accession", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "title": "bioproject_accession", - "from_schema": "https://example.com/GRDI", - "rank": 95, - "slot_uri": "GENEPIO:0001136", - "alias": "bioproject_accession", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" - }, - "biosample_accession": { - "name": "biosample_accession", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "title": "biosample_accession", - "from_schema": "https://example.com/GRDI", - "rank": 96, - "slot_uri": "GENEPIO:0001139", - "alias": "biosample_accession", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information", - "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", - "from_schema": "https://example.com/GRDI", - "rank": 97, - "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" - }, - "GenBank_accession": { - "name": "GenBank_accession", - "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", - "title": "GenBank_accession", - "from_schema": "https://example.com/GRDI", - "rank": 98, - "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Public repository information", - "range": "WhitespaceMinimizedString" - }, - "prevalence_metrics": { - "name": "prevalence_metrics", - "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", - "title": "prevalence_metrics", - "from_schema": "https://example.com/GRDI", - "rank": 99, - "slot_uri": "GENEPIO:0100480", - "alias": "prevalence_metrics", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Risk assessment information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "prevalence_metrics_details": { - "name": "prevalence_metrics_details", - "description": "The details pertaining to the prevalence metrics from a surveillance project.", - "title": "prevalence_metrics_details", - "from_schema": "https://example.com/GRDI", - "rank": 100, - "slot_uri": "GENEPIO:0100481", - "alias": "prevalence_metrics_details", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Risk assessment information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "stage_of_production": { - "name": "stage_of_production", - "description": "The stage of food production.", - "title": "stage_of_production", - "from_schema": "https://example.com/GRDI", - "rank": 101, - "slot_uri": "GENEPIO:0100482", - "alias": "stage_of_production", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Risk assessment information", - "recommended": true - }, - "experimental_intervention": { - "name": "experimental_intervention", - "description": "The category of the experimental intervention applied in the food production system.", - "title": "experimental_intervention", - "from_schema": "https://example.com/GRDI", - "rank": 102, - "slot_uri": "GENEPIO:0100483", - "multivalued": true, - "alias": "experimental_intervention", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Risk assessment information", - "recommended": true - }, - "experiment_intervention_details": { - "name": "experiment_intervention_details", - "description": "The details of the experimental intervention applied in the food production system.", - "title": "experiment_intervention_details", - "from_schema": "https://example.com/GRDI", - "rank": 103, - "slot_uri": "GENEPIO:0100484", - "alias": "experiment_intervention_details", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Risk assessment information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "AMR_testing_by": { - "name": "AMR_testing_by", - "description": "The name of the organization that performed the antimicrobial resistance testing.", - "title": "AMR_testing_by", - "from_schema": "https://example.com/GRDI", - "rank": 104, - "slot_uri": "GENEPIO:0100511", - "alias": "AMR_testing_by", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Antimicrobial resistance", - "required": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 105, - "slot_uri": "GENEPIO:0100512", - "alias": "AMR_testing_by_laboratory_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Antimicrobial resistance", - "range": "WhitespaceMinimizedString" - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 106, - "slot_uri": "GENEPIO:0100513", - "alias": "AMR_testing_by_contact_name", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Antimicrobial resistance", - "required": true - }, - "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", - "from_schema": "https://example.com/GRDI", - "rank": 107, - "slot_uri": "GENEPIO:0100514", - "alias": "AMR_testing_by_contact_email", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Antimicrobial resistance", - "required": true - }, - "AMR_testing_date": { - "name": "AMR_testing_date", - "description": "The date the antimicrobial resistance testing was performed.", - "title": "AMR_testing_date", - "from_schema": "https://example.com/GRDI", - "rank": 108, - "slot_uri": "GENEPIO:0100515", - "alias": "AMR_testing_date", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Antimicrobial resistance", - "range": "date" - }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", - "from_schema": "https://example.com/GRDI", - "rank": 711, - "slot_uri": "GENEPIO:0001517", - "alias": "authors", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Contributor acknowledgement", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", - "from_schema": "https://example.com/GRDI", - "rank": 712, - "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", - "owner": "GRDI_Sample", - "domain_of": [ - "GRDI_Sample" - ], - "slot_group": "Contributor acknowledgement", - "range": "Provenance" - } - } - }, - "AMR_Test": { - "name": "AMR_Test", - "description": "Antimicrobial test result", - "from_schema": "https://example.com/GRDI", - "is_a": "dh_interface", - "slot_usage": { - "sample_collector_sample_ID": { - "name": "sample_collector_sample_ID", - "rank": 1, - "multivalued": false, - "range": "GRDI_Sample", - "inlined": false - }, - "antimicrobial_resistance_test_drug": { - "name": "antimicrobial_resistance_test_drug", - "rank": 2 - }, - "resistance_phenotype": { - "name": "resistance_phenotype", - "rank": 3 - }, - "measurement": { - "name": "measurement", - "rank": 4 - }, - "measurement_units": { - "name": "measurement_units", - "rank": 5 - }, - "measurement_sign": { - "name": "measurement_sign", - "rank": 6 - }, - "laboratory_typing_method": { - "name": "laboratory_typing_method", - "rank": 7 - }, - "laboratory_typing_platform": { - "name": "laboratory_typing_platform", - "rank": 8 - }, - "laboratory_typing_platform_version": { - "name": "laboratory_typing_platform_version", - "rank": 9 - }, - "vendor_name": { - "name": "vendor_name", - "rank": 10 - }, - "testing_standard": { - "name": "testing_standard", - "rank": 11 - }, - "testing_standard_version": { - "name": "testing_standard_version", - "rank": 12 - }, - "testing_standard_details": { - "name": "testing_standard_details", - "rank": 13 - }, - "susceptible_breakpoint": { - "name": "susceptible_breakpoint", - "rank": 14 - }, - "intermediate_breakpoint": { - "name": "intermediate_breakpoint", - "rank": 15 - }, - "resistant_breakpoint": { - "name": "resistant_breakpoint", - "rank": 16 - } - }, - "attributes": { - "sample_collector_sample_ID": { - "name": "sample_collector_sample_ID", - "description": "The user-defined name for the sample.", - "title": "sample_collector_sample_ID", - "from_schema": "https://example.com/GRDI", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "multivalued": false, - "alias": "sample_collector_sample_ID", - "owner": "AMR_Test", - "domain_of": [ - "GRDI_Sample", - "AMR_Test" - ], - "range": "GRDI_Sample", - "required": true, - "inlined": false - }, - "antimicrobial_resistance_test_drug": { - "name": "antimicrobial_resistance_test_drug", - "description": "The antimicrobial drug being tested.", - "title": "antimicrobial_resistance_test_drug", - "from_schema": "https://example.com/GRDI", - "rank": 2, - "alias": "antimicrobial_resistance_test_drug", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "recommended": true - }, - "resistance_phenotype": { - "name": "resistance_phenotype", - "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", - "title": "resistance_phenotype", - "from_schema": "https://example.com/GRDI", - "rank": 3, - "alias": "resistance_phenotype", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "recommended": true - }, - "measurement": { - "name": "measurement", - "description": "The measured value of resistance to given antibiotic.", - "title": "measurement", - "from_schema": "https://example.com/GRDI", - "rank": 4, - "alias": "measurement", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "required": true - }, - "measurement_units": { - "name": "measurement_units", - "description": "The units of the antimicrobial resistance measurement.", - "title": "measurement_units", - "from_schema": "https://example.com/GRDI", - "rank": 5, - "alias": "measurement_units", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "required": true - }, - "measurement_sign": { - "name": "measurement_sign", - "description": "The qualifier associated with the antimicrobial resistance measurement", - "title": "measurement_sign", - "from_schema": "https://example.com/GRDI", - "rank": 6, - "alias": "measurement_sign", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "required": true - }, - "laboratory_typing_method": { - "name": "laboratory_typing_method", - "description": "The general method used for antimicrobial susceptibility testing.", - "title": "laboratory_typing_method", - "from_schema": "https://example.com/GRDI", - "rank": 7, - "alias": "laboratory_typing_method", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ] - }, - "laboratory_typing_platform": { - "name": "laboratory_typing_platform", - "description": "The brand/platform used for antimicrobial susceptibility testing.", - "title": "laboratory_typing_platform", - "from_schema": "https://example.com/GRDI", - "rank": 8, - "alias": "laboratory_typing_platform", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ] - }, - "laboratory_typing_platform_version": { - "name": "laboratory_typing_platform_version", - "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", - "title": "laboratory_typing_platform_version", - "from_schema": "https://example.com/GRDI", - "rank": 9, - "alias": "laboratory_typing_platform_version", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "range": "WhitespaceMinimizedString" - }, - "vendor_name": { - "name": "vendor_name", - "description": "The name of the vendor of the testing platform used.", - "title": "vendor_name", - "from_schema": "https://example.com/GRDI", - "rank": 10, - "alias": "vendor_name", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ] - }, - "testing_standard": { - "name": "testing_standard", - "description": "The testing standard used for determination of resistance phenotype", - "title": "testing_standard", - "from_schema": "https://example.com/GRDI", - "rank": 11, - "alias": "testing_standard", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "recommended": true - }, - "testing_standard_version": { - "name": "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": "testing_standard_version", - "from_schema": "https://example.com/GRDI", - "rank": 12, - "alias": "testing_standard_version", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "range": "WhitespaceMinimizedString" - }, - "testing_standard_details": { - "name": "testing_standard_details", - "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", - "title": "testing_standard_details", - "from_schema": "https://example.com/GRDI", - "rank": 13, - "alias": "testing_standard_details", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "range": "WhitespaceMinimizedString" - }, - "susceptible_breakpoint": { - "name": "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": "susceptible_breakpoint", - "from_schema": "https://example.com/GRDI", - "rank": 14, - "alias": "susceptible_breakpoint", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "range": "WhitespaceMinimizedString" - }, - "intermediate_breakpoint": { - "name": "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": "intermediate_breakpoint", - "from_schema": "https://example.com/GRDI", - "rank": 15, - "alias": "intermediate_breakpoint", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "range": "WhitespaceMinimizedString" - }, - "resistant_breakpoint": { - "name": "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": "resistant_breakpoint", - "from_schema": "https://example.com/GRDI", - "rank": 16, - "alias": "resistant_breakpoint", - "owner": "AMR_Test", - "domain_of": [ - "AMR_Test" - ], - "range": "WhitespaceMinimizedString" - } - } - }, - "Container": { - "name": "Container", - "from_schema": "https://example.com/GRDI", - "attributes": { - "GRDI_samples": { - "name": "GRDI_samples", - "from_schema": "https://example.com/GRDI", - "multivalued": true, - "alias": "GRDI_samples", - "owner": "Container", - "domain_of": [ - "Container" - ], - "range": "GRDI_Sample", - "inlined_as_list": true - }, - "AMR_Tests": { - "name": "AMR_Tests", - "from_schema": "https://example.com/GRDI", - "multivalued": true, - "alias": "AMR_Tests", - "owner": "Container", - "domain_of": [ - "Container" - ], - "range": "AMR_Test", - "inlined_as_list": true - } - }, - "tree_root": true - } - }, - "source_file": "schema_1m.yaml", - "settings": { - "Title_Case": { - "setting_key": "Title_Case", - "setting_value": "(((?<=\\b)[^a-z\\W]\\w*?|[\\W])+)" - }, - "UPPER_CASE": { - "setting_key": "UPPER_CASE", - "setting_value": "[A-Z\\W\\d_]*" - }, - "lower_case": { - "setting_key": "lower_case", - "setting_value": "[a-z\\W\\d_]*" - } - }, - "@type": "SchemaDefinition" -} \ No newline at end of file diff --git a/web/templates/grdi/schema_1m.yaml b/web/templates/grdi/schema_1m.yaml deleted file mode 100644 index 2548bc22..00000000 --- a/web/templates/grdi/schema_1m.yaml +++ /dev/null @@ -1,5654 +0,0 @@ -id: https://example.com/GRDI -name: GRDI -description: '' -version: 8.9.8 -imports: -- linkml:types -prefixes: - linkml: https://w3id.org/linkml/ - GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ -classes: - dh_interface: - name: dh_interface - description: A DataHarmonizer interface - from_schema: https://example.com/GRDI - - GRDI_Sample: - name: GRDI_Sample - description: Specification for GRDI virus biosample data gathering - is_a: dh_interface - slots: - - sample_collector_sample_ID - - alternative_sample_ID - - sample_collected_by - - sample_collected_by_laboratory_name - - sample_collection_project_name - - sample_plan_name - - sample_plan_ID - - sample_collector_contact_name - - sample_collector_contact_email - - purpose_of_sampling - - presampling_activity - - presampling_activity_details - - specimen_processing - - geo_loc_name (country) - - geo_loc_name (state/province/region) - - geo_loc_name (site) - - food_product_origin_geo_loc_name (country) - - host_origin_geo_loc_name (country) - - geo_loc latitude - - geo_loc longitude - - sample_collection_date - - sample_collection_date_precision - - sample_received_date - - original_sample_description - - environmental_site - - water_depth - - sediment_depth - - air_temperature - - water_temperature - - weather_type - - available_data_types - - animal_or_plant_population - - environmental_material - - anatomical_material - - body_product - - anatomical_part - - anatomical_region - - food_product - - food_product_properties - - animal_source_of_food - - food_product_production_stream - - sample_storage_method - - sample_storage_medium - - collection_device - - collection_method - - food_packaging - - food_quality_date - - food_packaging_date - - host (common name) - - host (scientific name) - - host (ecotype) - - host (breed) - - host (food production name) - - host_age_bin - - host_disease - - microbiological_method - - strain - - isolate_ID - - alternative_isolate_ID - - progeny_isolate_ID - - IRIDA_isolate_ID - - IRIDA_project_ID - - isolated_by - - isolated_by_laboratory_name - - isolated_by_contact_name - - isolated_by_contact_email - - isolation_date - - isolate_received_date - - organism - - taxonomic_identification_process - - taxonomic_identification_process_details - - serovar - - serotyping_method - - phagetype - - library_ID - - sequenced_by - - sequenced_by_laboratory_name - - sequenced_by_contact_name - - sequenced_by_contact_email - - purpose_of_sequencing - - sequencing_project_name - - sequencing_platform - - sequencing_instrument - - library_preparation_kit - - sequencing_protocol - - r1_fastq_filename - - r2_fastq_filename - - fast5_filename - - assembly_filename - - sequence_submitted_by - - sequence_submitted_by_contact_name - - sequence_submitted_by_contact_email - - publication_ID - - attribute_package - - bioproject_accession - - biosample_accession - - SRA_accession - - GenBank_accession - - prevalence_metrics - - prevalence_metrics_details - - stage_of_production - - experimental_intervention - - experiment_intervention_details - - AMR_testing_by - - AMR_testing_by_laboratory_name - - AMR_testing_by_contact_name - - AMR_testing_by_contact_email - - AMR_testing_date - - authors - - DataHarmonizer provenance - slot_usage: - sample_collector_sample_ID: - rank: 1 - identifier: true - slot_group: Sample collection and processing - alternative_sample_ID: - rank: 2 - slot_group: Sample collection and processing - sample_collected_by: - rank: 3 - slot_group: Sample collection and processing - sample_collected_by_laboratory_name: - rank: 4 - slot_group: Sample collection and processing - sample_collection_project_name: - rank: 5 - slot_group: Sample collection and processing - sample_plan_name: - rank: 6 - slot_group: Sample collection and processing - sample_plan_ID: - rank: 7 - slot_group: Sample collection and processing - sample_collector_contact_name: - rank: 8 - slot_group: Sample collection and processing - sample_collector_contact_email: - rank: 9 - slot_group: Sample collection and processing - purpose_of_sampling: - rank: 10 - slot_group: Sample collection and processing - presampling_activity: - rank: 11 - slot_group: Sample collection and processing - presampling_activity_details: - rank: 12 - slot_group: Sample collection and processing - specimen_processing: - rank: 13 - slot_group: Sample collection and processing - geo_loc_name (country): - rank: 14 - slot_group: Sample collection and processing - geo_loc_name (state/province/region): - rank: 15 - slot_group: Sample collection and processing - geo_loc_name (site): - rank: 16 - slot_group: Sample collection and processing - food_product_origin_geo_loc_name (country): - rank: 17 - slot_group: Sample collection and processing - host_origin_geo_loc_name (country): - rank: 18 - slot_group: Sample collection and processing - geo_loc latitude: - rank: 19 - slot_group: Sample collection and processing - geo_loc longitude: - rank: 20 - slot_group: Sample collection and processing - sample_collection_date: - rank: 21 - slot_group: Sample collection and processing - sample_collection_date_precision: - rank: 22 - slot_group: Sample collection and processing - sample_received_date: - rank: 23 - slot_group: Sample collection and processing - original_sample_description: - rank: 24 - slot_group: Sample collection and processing - environmental_site: - rank: 25 - slot_group: Sample collection and processing - water_depth: - rank: 26 - slot_group: Sample collection and processing - sediment_depth: - rank: 27 - slot_group: Sample collection and processing - air_temperature: - rank: 28 - slot_group: Sample collection and processing - water_temperature: - rank: 29 - slot_group: Sample collection and processing - weather_type: - rank: 30 - slot_group: Sample collection and processing - available_data_types: - rank: 31 - slot_group: Sample collection and processing - animal_or_plant_population: - rank: 32 - slot_group: Sample collection and processing - environmental_material: - rank: 33 - slot_group: Sample collection and processing - anatomical_material: - rank: 34 - slot_group: Sample collection and processing - body_product: - rank: 35 - slot_group: Sample collection and processing - anatomical_part: - rank: 36 - slot_group: Sample collection and processing - anatomical_region: - rank: 37 - slot_group: Sample collection and processing - food_product: - rank: 38 - slot_group: Sample collection and processing - food_product_properties: - rank: 39 - slot_group: Sample collection and processing - animal_source_of_food: - rank: 40 - slot_group: Sample collection and processing - food_product_production_stream: - rank: 41 - slot_group: Sample collection and processing - sample_storage_method: - rank: 42 - slot_group: Sample collection and processing - sample_storage_medium: - rank: 43 - slot_group: Sample collection and processing - collection_device: - rank: 44 - slot_group: Sample collection and processing - collection_method: - rank: 45 - slot_group: Sample collection and processing - food_packaging: - rank: 46 - slot_group: Sample collection and processing - food_quality_date: - rank: 47 - slot_group: Sample collection and processing - food_packaging_date: - rank: 48 - slot_group: Sample collection and processing - host (common name): - rank: 49 - slot_group: Host information - host (scientific name): - rank: 50 - slot_group: Host information - host (ecotype): - rank: 51 - slot_group: Host information - host (breed): - rank: 52 - slot_group: Host information - host (food production name): - rank: 53 - slot_group: Host information - host_age_bin: - rank: 54 - slot_group: Host information - host_disease: - rank: 55 - slot_group: Host information - microbiological_method: - rank: 56 - slot_group: Strain and isolation information - strain: - rank: 57 - slot_group: Strain and isolation information - isolate_ID: - rank: 58 - slot_group: Strain and isolation information - alternative_isolate_ID: - rank: 59 - slot_group: Strain and isolation information - progeny_isolate_ID: - rank: 60 - slot_group: Strain and isolation information - IRIDA_isolate_ID: - rank: 61 - slot_group: Strain and isolation information - IRIDA_project_ID: - rank: 62 - slot_group: Strain and isolation information - isolated_by: - rank: 63 - slot_group: Strain and isolation information - isolated_by_laboratory_name: - rank: 64 - slot_group: Strain and isolation information - isolated_by_contact_name: - rank: 65 - slot_group: Strain and isolation information - isolated_by_contact_email: - rank: 66 - slot_group: Strain and isolation information - isolation_date: - rank: 67 - slot_group: Strain and isolation information - isolate_received_date: - rank: 68 - slot_group: Strain and isolation information - organism: - rank: 69 - slot_group: Strain and isolation information - taxonomic_identification_process: - rank: 70 - slot_group: Strain and isolation information - taxonomic_identification_process_details: - rank: 71 - slot_group: Strain and isolation information - serovar: - rank: 72 - slot_group: Strain and isolation information - serotyping_method: - rank: 73 - slot_group: Strain and isolation information - phagetype: - rank: 74 - slot_group: Strain and isolation information - library_ID: - rank: 75 - slot_group: Sequence information - sequenced_by: - rank: 76 - slot_group: Sequence information - sequenced_by_laboratory_name: - rank: 77 - slot_group: Sequence information - sequenced_by_contact_name: - rank: 78 - slot_group: Sequence information - sequenced_by_contact_email: - rank: 79 - slot_group: Sequence information - purpose_of_sequencing: - rank: 80 - slot_group: Sequence information - sequencing_project_name: - rank: 81 - slot_group: Sequence information - sequencing_platform: - rank: 82 - slot_group: Sequence information - sequencing_instrument: - rank: 83 - slot_group: Sequence information - library_preparation_kit: - rank: 84 - slot_group: Sequence information - sequencing_protocol: - rank: 85 - slot_group: Sequence information - r1_fastq_filename: - rank: 86 - slot_group: Sequence information - r2_fastq_filename: - rank: 87 - slot_group: Sequence information - fast5_filename: - rank: 88 - slot_group: Sequence information - assembly_filename: - rank: 89 - slot_group: Sequence information - sequence_submitted_by: - rank: 90 - slot_group: Public repository information - sequence_submitted_by_contact_name: - rank: 91 - slot_group: Public repository information - sequence_submitted_by_contact_email: - rank: 92 - slot_group: Public repository information - publication_ID: - rank: 93 - slot_group: Public repository information - attribute_package: - rank: 94 - slot_group: Public repository information - bioproject_accession: - rank: 95 - slot_group: Public repository information - biosample_accession: - rank: 96 - slot_group: Public repository information - SRA_accession: - rank: 97 - slot_group: Public repository information - GenBank_accession: - rank: 98 - slot_group: Public repository information - prevalence_metrics: - rank: 99 - slot_group: Risk assessment information - prevalence_metrics_details: - rank: 100 - slot_group: Risk assessment information - stage_of_production: - rank: 101 - slot_group: Risk assessment information - experimental_intervention: - rank: 102 - slot_group: Risk assessment information - experiment_intervention_details: - rank: 103 - slot_group: Risk assessment information - AMR_testing_by: - rank: 104 - slot_group: Antimicrobial resistance - AMR_testing_by_laboratory_name: - rank: 105 - slot_group: Antimicrobial resistance - AMR_testing_by_contact_name: - rank: 106 - slot_group: Antimicrobial resistance - AMR_testing_by_contact_email: - rank: 107 - slot_group: Antimicrobial resistance - AMR_testing_date: - rank: 108 - slot_group: Antimicrobial resistance - authors: - rank: 711 - slot_group: Contributor acknowledgement - DataHarmonizer provenance: - rank: 712 - slot_group: Contributor acknowledgement - - AMR_Test: - name: AMR_Test - description: Antimicrobial test result - is_a: dh_interface - slots: - - sample_collector_sample_ID - - antimicrobial_resistance_test_drug - - resistance_phenotype - - measurement - - measurement_units - - measurement_sign - - laboratory_typing_method - - laboratory_typing_platform - - laboratory_typing_platform_version - - vendor_name - - testing_standard - - testing_standard_version - - testing_standard_details - - susceptible_breakpoint - - intermediate_breakpoint - - resistant_breakpoint - slot_usage: - sample_collector_sample_ID: - range: GRDI_Sample - multivalued: false - inlined: false - rank: 1 - antimicrobial_resistance_test_drug: - rank: 2 - resistance_phenotype: - rank: 3 - measurement: - rank: 4 - measurement_units: - rank: 5 - measurement_sign: - rank: 6 - laboratory_typing_method: - rank: 7 - laboratory_typing_platform: - rank: 8 - laboratory_typing_platform_version: - rank: 9 - vendor_name: - rank: 10 - testing_standard: - rank: 11 - testing_standard_version: - rank: 12 - testing_standard_details: - rank: 13 - susceptible_breakpoint: - rank: 14 - intermediate_breakpoint: - rank: 15 - resistant_breakpoint: - rank: 16 - - Container: - tree_root: true - attributes: - GRDI_samples: - range: GRDI_Sample - multivalued: true - inlined_as_list: true - AMR_Tests: - range: AMR_Test - multivalued: true - inlined_as_list: true - - -slots: - sample_collector_sample_ID: - name: sample_collector_sample_ID - title: sample_collector_sample_ID - description: The user-defined name for the sample. - 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 - slot_uri: GENEPIO:0001123 - range: WhitespaceMinimizedString - required: true - exact_mappings: - - BIOSAMPLE:sample_name - alternative_sample_ID: - name: alternative_sample_ID - title: alternative_sample_ID - description: An alternative sample_ID assigned to the sample by another organization. - 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\u2019s 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] - slot_uri: GENEPIO:0100427 - range: WhitespaceMinimizedString - required: true - sample_collected_by: - name: sample_collected_by - title: sample_collected_by - description: The name of the agency, organization or institution with which the - sample collector is affiliated. - 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] - slot_uri: GENEPIO:0001153 - any_of: - - range: sample_collected_by menu - - range: null value menu - required: true - exact_mappings: - - BIOSAMPLE:collected_by - sample_collected_by_laboratory_name: - name: sample_collected_by_laboratory_name - title: sample_collected_by_laboratory_name - description: The specific laboratory affiliation of the sample collector. - 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 - slot_uri: GENEPIO:0100428 - range: WhitespaceMinimizedString - sample_collection_project_name: - name: sample_collection_project_name - title: sample_collection_project_name - description: The name of the project/initiative/program for which the sample was - collected. - 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) - slot_uri: GENEPIO:0100429 - range: WhitespaceMinimizedString - sample_plan_name: - name: sample_plan_name - title: sample_plan_name - description: The name of the study design for a surveillance project. - 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 - slot_uri: GENEPIO:0100430 - range: WhitespaceMinimizedString - recommended: true - sample_plan_ID: - name: sample_plan_ID - title: sample_plan_ID - description: The identifier of the study design for a surveillance project. - 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 - slot_uri: GENEPIO:0100431 - range: WhitespaceMinimizedString - recommended: true - sample_collector_contact_name: - name: sample_collector_contact_name - title: sample_collector_contact_name - description: The name or job title of the contact responsible for follow-up regarding - the sample. - 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 - slot_uri: GENEPIO:0100432 - range: WhitespaceMinimizedString - sample_collector_contact_email: - name: sample_collector_contact_email - title: sample_collector_contact_email - description: The email address of the contact responsible for follow-up regarding - the sample. - 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 - slot_uri: GENEPIO:0001156 - range: WhitespaceMinimizedString - required: true - purpose_of_sampling: - name: purpose_of_sampling - title: purpose_of_sampling - description: The reason that the sample was collected. - 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] - slot_uri: GENEPIO:0001198 - any_of: - - range: purpose_of_sampling menu - - range: null value menu - required: true - exact_mappings: - - BIOSAMPLE:purpose_of_sampling - presampling_activity: - name: presampling_activity - title: presampling_activity - description: The experimental activities or variables that affected the sample - collected. - 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] - slot_uri: GENEPIO:0100433 - any_of: - - range: presampling_activity menu - - range: null value menu - presampling_activity_details: - name: presampling_activity_details - title: presampling_activity_details - description: The details of the experimental activities or variables that affected - the sample collected. - 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. - slot_uri: GENEPIO:0100434 - range: WhitespaceMinimizedString - specimen_processing: - name: specimen_processing - title: specimen_processing - description: The processing applied to samples post-collection, prior to further - testing, characterization, or isolation procedures. - 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] - slot_uri: GENEPIO:0100435 - any_of: - - range: specimen_processing menu - - range: null value menu - geo_loc_name (country): - name: geo_loc_name (country) - title: geo_loc_name (country) - description: The country of origin of the sample. - 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] - slot_uri: GENEPIO:0001181 - any_of: - - range: geo_loc_name (country) menu - - range: null value menu - required: true - exact_mappings: - - BIOSAMPLE:geo_loc_name - - BIOSAMPLE:geo_loc_name (country) - geo_loc_name (state/province/region): - name: geo_loc_name (state/province/region) - title: geo_loc_name (state/province/region) - description: The state/province/territory of origin of the sample. - 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] - slot_uri: GENEPIO:0001185 - any_of: - - range: geo_loc_name (state/province/region) menu - - range: null value menu - required: true - exact_mappings: - - BIOSAMPLE:geo_loc_name - - BIOSAMPLE:geo_loc_name (state/province/region) - geo_loc_name (site): - name: geo_loc_name (site) - title: geo_loc_name (site) - description: The name of a specific geographical location e.g. Credit River (rather - than river). - 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 - slot_uri: GENEPIO:0100436 - range: WhitespaceMinimizedString - exact_mappings: - - BIOSAMPLE:geo_loc_name - - BIOSAMPLE:geo_loc_name (site) - food_product_origin_geo_loc_name (country): - name: food_product_origin_geo_loc_name (country) - title: food_product_origin_geo_loc_name (country) - description: The country of origin of a food product. - 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] - slot_uri: GENEPIO:0100437 - any_of: - - range: geo_loc_name (country) menu - - range: null value menu - host_origin_geo_loc_name (country): - name: host_origin_geo_loc_name (country) - title: host_origin_geo_loc_name (country) - description: The country of origin of the host. - 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] - slot_uri: GENEPIO:0100438 - any_of: - - range: geo_loc_name (country) menu - - range: null value menu - geo_loc latitude: - name: geo_loc latitude - title: geo_loc latitude - description: The latitude coordinates of the geographical location of sample collection. - 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 - slot_uri: GENEPIO:0100309 - range: WhitespaceMinimizedString - geo_loc longitude: - name: geo_loc longitude - title: geo_loc longitude - description: The longitude coordinates of the geographical location of sample - collection. - 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 - slot_uri: GENEPIO:0100310 - range: WhitespaceMinimizedString - sample_collection_date: - name: sample_collection_date - title: sample_collection_date - description: The date on which the sample was collected. - comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" - or "YYYY". - examples: - - value: '2020-10-30' - slot_uri: GENEPIO:0001174 - range: date - required: true - exact_mappings: - - BIOSAMPLE:sample collection date - sample_collection_date_precision: - name: sample_collection_date_precision - title: sample_collection_date_precision - description: The precision to which the "sample collection date" was provided. - 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] - slot_uri: GENEPIO:0001177 - range: sample_collection_date_precision menu - required: true - sample_received_date: - name: sample_received_date - title: sample_received_date - description: The date on which the sample was received. - comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" - or "YYYY". - examples: - - value: '2020-11-15' - slot_uri: GENEPIO:0001179 - range: date - original_sample_description: - name: original_sample_description - title: original_sample_description - description: The original sample description provided by the sample collector. - 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. - examples: - - value: RTE Prosciutto from deli - slot_uri: GENEPIO:0100439 - range: WhitespaceMinimizedString - environmental_site: - name: environmental_site - title: environmental_site - description: An environmental location may describe a site in the natural or built - environment e.g. hospital, wet market, bat cave. - 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. - examples: - - value: Poultry hatchery [ENVO:01001874] - slot_uri: GENEPIO:0001232 - any_of: - - range: environmental_site menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:environmental_site - water_depth: - name: water_depth - title: water_depth - description: The depth of some water. - comments: Provide the depth of water with a value and unit. - examples: - - value: 5m - slot_uri: GENEPIO:0100440 - range: WhitespaceMinimizedString - sediment_depth: - name: sediment_depth - title: sediment_depth - description: The depth of some water. - comments: Provide the depth of water with a value and unit. - examples: - - value: 5m - slot_uri: GENEPIO:0100697 - range: WhitespaceMinimizedString - air_temperature: - name: air_temperature - title: air_temperature - description: The temperature of some air. - comments: Provide the temperature of the air with a value and unit. Do not provide - a symbol for degree e.g. oC - examples: - - value: 25C - slot_uri: GENEPIO:0100441 - range: WhitespaceMinimizedString - water_temperature: - name: water_temperature - title: water_temperature - description: The temperature of some water. - comments: Provide the temperature of the water with a value and unit. Do not provide - a symbol for degree e.g. oC - examples: - - value: 4C - slot_uri: GENEPIO:0100698 - range: WhitespaceMinimizedString - weather_type: - name: weather_type - title: weather_type - description: The state of the atmosphere at a place and time as regards heat, - dryness, sunshine, wind, rain, etc. - comments: Provide the weather conditions at the time of sample collection. - examples: - - value: Rain [ENVO:01001564] - slot_uri: GENEPIO:0100442 - any_of: - - range: weather_type menu - - range: null value menu - multivalued: true - available_data_types: - name: available_data_types - title: available_data_types - description: The type of data that is available, that may or may not require permission - to access. - 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. - examples: - - value: Total coliform count data - slot_uri: GENEPIO:0100690 - any_of: - - range: available_data_types menu - - range: null value menu - multivalued: true - animal_or_plant_population: - name: animal_or_plant_population - title: animal_or_plant_population - description: The type of animal or plant population inhabiting an area. - 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.' - examples: - - value: Turkey [NCBITaxon:9103] - slot_uri: GENEPIO:0100443 - any_of: - - range: animal_or_plant_population menu - - range: null value menu - multivalued: true - recommended: true - environmental_material: - name: environmental_material - title: environmental_material - description: A substance obtained from the natural or man-made environment e.g. - soil, water, sewage, door handle, bed handrail, face mask. - 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. - examples: - - value: Soil [ENVO:00001998] - - value: Water [CHEBI:15377] - - value: Wastewater [ENVO:00002001] - - value: Broom [ENVO:03501377] - slot_uri: GENEPIO:0001223 - any_of: - - range: environmental_material menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:environmental_material - anatomical_material: - name: anatomical_material - title: anatomical_material - description: A substance obtained from an anatomical part of an organism e.g. - tissue, blood. - 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. - examples: - - value: Tissue [UBERON:0000479] - - value: Blood [UBERON:0000178] - slot_uri: GENEPIO:0001211 - any_of: - - range: anatomical_material menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:anatomical_material - body_product: - name: body_product - title: body_product - description: A substance excreted/secreted from an organism e.g. feces, urine, - sweat. - 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. - examples: - - value: Feces [UBERON:0001988] - - value: Urine [UBERON:0001088] - slot_uri: GENEPIO:0001216 - any_of: - - range: body_product menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:body_product - anatomical_part: - name: anatomical_part - title: anatomical_part - description: An anatomical part of an organism e.g. oropharynx. - 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. - examples: - - value: Snout [UBERON:0006333] - slot_uri: GENEPIO:0001214 - any_of: - - range: anatomical_part menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:anatomical_part - anatomical_region: - name: anatomical_region - title: anatomical_region - description: A 3D region in space without well-defined compartmental boundaries; - for example, the dorsal region of an ectoderm. - 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. - examples: - - value: Dorso-lateral region [BSPO:0000080] - slot_uri: GENEPIO:0100700 - any_of: - - range: anatomical_region menu - - range: null value menu - food_product: - name: food_product - title: food_product - description: A material consumed and digested for nutritional value or enjoyment. - 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: Feather meal [FOODON:00003927] - - value: Bone meal [ENVO:02000054] - - value: Chicken breast [FOODON:00002703] - slot_uri: GENEPIO:0100444 - any_of: - - range: food_product menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:food_product - food_product_properties: - name: food_product_properties - title: food_product_properties - description: Any characteristic of the food product pertaining to its state, processing, - a label claim, or implications for consumers. - 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). - examples: - - value: Food (chopped) [FOODON:00002777] - - value: Ready-to-eat (RTE) [FOODON:03316636] - slot_uri: GENEPIO:0100445 - any_of: - - range: food_product_properties menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:food_product_properties - animal_source_of_food: - name: animal_source_of_food - title: animal_source_of_food - description: The animal from which the food product was derived. - comments: Provide the common name of the animal. If not applicable, leave blank. - Multiple entries can be provided, separated by a comma. - examples: - - value: Chicken [NCBITaxon:9031] - slot_uri: GENEPIO:0100446 - any_of: - - range: animal_source_of_food menu - - range: null value menu - multivalued: true - recommended: true - food_product_production_stream: - name: food_product_production_stream - title: 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. - comments: Provide the name of the agricultural production stream from the picklist. - examples: - - value: Beef cattle production stream [FOODON:03000452] - slot_uri: GENEPIO:0100699 - any_of: - - range: food_product_production_stream menu - - range: null value menu - sample_storage_method: - name: sample_storage_method - title: sample_storage_method - description: The type of packaging used to contain a food product. - comments: If known, provide information regarding how the food product was packaged. - examples: - - value: Plastic tray or pan [FOODON:03490126] - slot_uri: GENEPIO:0100447 - range: WhitespaceMinimizedString - sample_storage_medium: - name: sample_storage_medium - title: sample_storage_medium - description: A specification of the way that a specimen is or was stored. - comments: Provide a description of how the same was stored. - examples: - - value: Frozen at -20C - slot_uri: GENEPIO:0100448 - range: WhitespaceMinimizedString - collection_device: - name: collection_device - title: collection_device - description: The instrument or container used to collect the sample e.g. swab. - 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: PBS + 20% glycerol - slot_uri: GENEPIO:0001234 - any_of: - - range: collection_device menu - - range: null value menu - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:collection_device - collection_method: - name: collection_method - title: collection_method - description: The process used to collect the sample e.g. phlebotomy, necropsy. - 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. - examples: - - value: Drag swab [OBI:0002822] - slot_uri: GENEPIO:0001241 - any_of: - - range: collection_method menu - - range: null value menu - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:collection_method - food_packaging: - name: food_packaging - title: food_packaging - description: The type of packaging used to contain a food product. - comments: If known, provide information regarding how the food product was packaged. - examples: - - value: Rinsing for specimen collection [GENEPIO_0002116] - slot_uri: GENEPIO:0100447 - any_of: - - range: food_packaging menu - - range: null value menu - multivalued: true - recommended: true - exact_mappings: - - BIOSAMPLE:isolation_source - - BIOSAMPLE:food_packaging - food_quality_date: - name: food_quality_date - title: 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. - 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. - examples: - - value: '2020-05-25' - slot_uri: GENEPIO:0100615 - range: date - food_packaging_date: - name: food_packaging_date - title: food_packaging_date - description: A food product's packaging date as marked by a food manufacturer - or retailer. - 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. - examples: - - value: '2020-05-25' - slot_uri: GENEPIO:0100616 - range: date - host (common name): - name: host (common name) - title: host (common name) - description: The commonly used name of the host. - 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. - examples: - - value: Cow [NCBITaxon:9913] - - value: Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] - slot_uri: GENEPIO:0001386 - any_of: - - range: host (common name) menu - - range: null value menu - recommended: true - host (scientific name): - name: host (scientific name) - title: host (scientific name) - description: The taxonomic, or scientific name of the host. - 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. - examples: - - value: Bos taurus [NCBITaxon:9913] - - value: Homo sapiens [NCBITaxon:9103] - slot_uri: GENEPIO:0001387 - any_of: - - range: host (scientific name) menu - - range: null value menu - recommended: true - exact_mappings: - - BIOSAMPLE:host - host (ecotype): - name: host (ecotype) - title: host (ecotype) - description: The biotype resulting from selection in a particular habitat, e.g. - the A. thaliana Ecotype Ler. - comments: Provide the name of the ecotype of the host organism. - examples: - - value: Sea ecotype - slot_uri: GENEPIO:0100450 - range: WhitespaceMinimizedString - host (breed): - name: host (breed) - title: 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. - comments: Provide the name of the breed of the host organism. - examples: - - value: Holstein - slot_uri: GENEPIO:0100451 - range: WhitespaceMinimizedString - exact_mappings: - - BIOSAMPLE:host_disease - host (food production name): - name: host (food production name) - title: 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. - comments: Select the host's food production name from the pick list. - examples: - - value: Calf [FOODON:03411349] - slot_uri: GENEPIO:0100452 - any_of: - - range: host (food production name) menu - - range: null value menu - host_age_bin: - name: host_age_bin - title: host_age_bin - description: Age of host at the time of sampling, expressed as an age group. - 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. - slot_uri: GENEPIO:0001394 - range: host_age_bin menu - host_disease: - name: host_disease - title: host_disease - description: The name of the disease experienced by the host. - 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 \u201Cmissing\u201D." - examples: - - value: mastitis, gastroenteritis - slot_uri: GENEPIO:0001391 - range: WhitespaceMinimizedString - microbiological_method: - name: microbiological_method - title: microbiological_method - description: The laboratory method used to grow, prepare, and/or isolate the microbial - isolate. - 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. - examples: - - value: MFHPB-30 - slot_uri: GENEPIO:0100454 - range: WhitespaceMinimizedString - recommended: true - strain: - name: strain - title: strain - description: The strain identifier. - comments: 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: K12 - slot_uri: GENEPIO:0100455 - range: WhitespaceMinimizedString - isolate_ID: - name: isolate_ID - title: isolate_ID - description: The user-defined identifier for the isolate, as provided by the laboratory - that originally isolated the isolate. - 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. - examples: - - value: SA20131043 - slot_uri: GENEPIO:0100456 - range: WhitespaceMinimizedString - required: true - alternative_isolate_ID: - name: alternative_isolate_ID - title: alternative_isolate_ID - description: An alternative isolate_ID assigned to the isolate by another organization. - 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\u2019s agency\ - \ name i.e. ID[short organization code]. Agency short forms include the following:\n\ - Public Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\n\ - Agriculture 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: GHIF3456[PHAC] - - value: QWICK222[CFIA] - slot_uri: GENEPIO:0100457 - range: WhitespaceMinimizedString - recommended: true - progeny_isolate_ID: - name: progeny_isolate_ID - title: progeny_isolate_ID - description: The identifier assigned to a progenitor isolate derived from an isolate - that was directly obtained from a sample. - comments: If your sequence data pertains to progeny of an original isolate, provide - the progeny_isolate_ID. - examples: - - value: SUB_ON_1526 - slot_uri: GENEPIO:0100458 - range: WhitespaceMinimizedString - IRIDA_isolate_ID: - name: IRIDA_isolate_ID - title: IRIDA_isolate_ID - description: The identifier of the isolate in the IRIDA platform. - 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. - examples: - - value: GRDI_LL_12345 - slot_uri: GENEPIO:0100459 - range: WhitespaceMinimizedString - required: true - IRIDA_project_ID: - name: IRIDA_project_ID - title: IRIDA_project_ID - description: The identifier of the Project in the iRIDA platform. - comments: Provide the IRIDA "project ID". - examples: - - value: '666' - slot_uri: GENEPIO:0100460 - range: WhitespaceMinimizedString - required: true - isolated_by: - name: isolated_by - title: isolated_by - description: The name of the agency, organization or institution with which the - individual who performed the isolation procedure is affiliated. - 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. - examples: - - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - slot_uri: GENEPIO:0100461 - range: WhitespaceMinimizedString - isolated_by_laboratory_name: - name: isolated_by_laboratory_name - title: isolated_by_laboratory_name - description: The specific laboratory affiliation of the individual who performed - the isolation procedure. - 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. - examples: - - value: Topp Lab - slot_uri: GENEPIO:0100462 - range: WhitespaceMinimizedString - isolated_by_contact_name: - name: isolated_by_contact_name - title: isolated_by_contact_name - description: The name or title of the contact responsible for follow-up regarding - the isolate. - 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. - examples: - - value: Enterics Lab Manager - slot_uri: GENEPIO:0100463 - range: WhitespaceMinimizedString - isolated_by_contact_email: - name: isolated_by_contact_email - title: isolated_by_contact_email - description: The email address of the contact responsible for follow-up regarding - the isolate. - 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. - examples: - - value: enterics@lab.ca - slot_uri: GENEPIO:0100464 - range: WhitespaceMinimizedString - isolation_date: - name: isolation_date - title: isolation_date - description: The date on which the isolate was isolated from a sample. - comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" - or "YYYY". - examples: - - value: '2020-10-30' - slot_uri: GENEPIO:0100465 - range: date - isolate_received_date: - name: isolate_received_date - title: isolate_received_date - description: The date on which the isolate was received by the laboratory. - comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" - or "YYYY". - examples: - - value: '2020-11-15' - slot_uri: GENEPIO:0100466 - range: WhitespaceMinimizedString - organism: - name: organism - title: organism - description: Taxonomic name of the organism. - 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.' - examples: - - value: Salmonella enterica subsp. enterica [NCBITaxon:59201] - slot_uri: GENEPIO:0001191 - any_of: - - range: organism menu - - range: null value menu - required: true - exact_mappings: - - BIOSAMPLE:organism - taxonomic_identification_process: - name: taxonomic_identification_process - title: taxonomic_identification_process - description: The type of planned process by which an organismal entity is associated - with a taxon or taxa. - 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. - examples: - - value: PCR assay [OBI:0002740] - slot_uri: GENEPIO:0100583 - any_of: - - range: taxonomic_identification_process menu - - range: null value menu - recommended: true - taxonomic_identification_process_details: - name: taxonomic_identification_process_details - title: taxonomic_identification_process_details - description: The details of the process used to determine the taxonomic identification - of an organism. - comments: Briefly describe the taxonomic identififcation method details using - free text. - examples: - - value: Biolog instrument - slot_uri: GENEPIO:0100584 - range: WhitespaceMinimizedString - serovar: - name: serovar - title: serovar - description: The serovar of the organism. - comments: 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: Heidelberg - slot_uri: GENEPIO:0100467 - range: WhitespaceMinimizedString - recommended: true - serotyping_method: - name: serotyping_method - title: serotyping_method - description: The method used to determine the serovar. - comments: "If the serovar was determined via traditional serotyping methods, put\ - \ \u201CTraditional serotyping\u201D. If the serovar was determined via in silico\ - \ methods, provide the name and version number of the software." - examples: - - value: SISTR 1.0.1 - slot_uri: GENEPIO:0100468 - range: WhitespaceMinimizedString - recommended: true - phagetype: - name: phagetype - title: phagetype - description: The phagetype of the organism. - comments: "Provide if known. If unknown, put \u201Cmissing\u201D." - examples: - - value: '47' - slot_uri: GENEPIO:0100469 - range: WhitespaceMinimizedString - library_ID: - name: library_ID - title: library_ID - description: The user-specified identifier for the library prepared for sequencing. - 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. - examples: - - value: LS_2010_NP_123446 - slot_uri: GENEPIO:0001448 - range: WhitespaceMinimizedString - sequenced_by: - name: sequenced_by - title: sequenced_by - description: The name of the agency, organization or institution responsible for - sequencing the isolate's genome. - 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. - examples: - - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - slot_uri: GENEPIO:0100416 - any_of: - - range: sequenced_by menu - - range: null value menu - required: true - exact_mappings: - - BIOSAMPLE:sequenced_by - sequenced_by_laboratory_name: - name: sequenced_by_laboratory_name - title: sequenced_by_laboratory_name - description: The specific laboratory affiliation of the responsible for sequencing - the isolate's genome. - 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. - examples: - - value: Topp Lab - slot_uri: GENEPIO:0100470 - range: WhitespaceMinimizedString - sequenced_by_contact_name: - name: sequenced_by_contact_name - title: sequenced_by_contact_name - description: The name or title of the contact responsible for follow-up regarding - the sequence. - 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. - examples: - - value: Enterics Lab Manager - slot_uri: GENEPIO:0100471 - range: WhitespaceMinimizedString - sequenced_by_contact_email: - name: sequenced_by_contact_email - title: sequenced_by_contact_email - description: The email address of the contact responsible for follow-up regarding - the sequence. - 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. - examples: - - value: enterics@lab.ca - slot_uri: GENEPIO:0100422 - range: WhitespaceMinimizedString - required: true - purpose_of_sequencing: - name: purpose_of_sequencing - title: purpose_of_sequencing - description: The reason that the sample was sequenced. - 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.' - examples: - - value: Research [GENEPIO:0100003] - slot_uri: GENEPIO:0001445 - any_of: - - range: purpose_of_sequencing menu - - range: null value menu - multivalued: true - required: true - exact_mappings: - - BIOSAMPLE:purpose_of_sequencing - sequencing_project_name: - name: sequencing_project_name - title: sequencing_project_name - description: The name of the project/initiative/program for which sequencing was - performed. - 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: AMR-GRDI (PA-1356) - slot_uri: GENEPIO:0100472 - range: WhitespaceMinimizedString - sequencing_platform: - name: sequencing_platform - title: sequencing_platform - description: The platform technology used to perform the sequencing. - 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. - examples: - - value: Illumina [GENEPIO:0001923] - slot_uri: GENEPIO:0100473 - any_of: - - range: sequencing_platform menu - - range: null value menu - sequencing_instrument: - name: sequencing_instrument - title: sequencing_instrument - description: The model of the sequencing instrument used. - 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. - examples: - - value: Illumina HiSeq 2500 [GENEPIO:0100117] - slot_uri: GENEPIO:0001452 - any_of: - - range: sequencing_instrument menu - - range: null value menu - library_preparation_kit: - name: library_preparation_kit - title: library_preparation_kit - description: The name of the DNA library preparation kit used to generate the - library being sequenced. - comments: Provide the name of the library preparation kit used. - examples: - - value: Nextera XT - slot_uri: GENEPIO:0001450 - range: WhitespaceMinimizedString - sequencing_protocol: - name: sequencing_protocol - title: sequencing_protocol - description: The protocol or method used for sequencing. - comments: 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: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no - slot_uri: GENEPIO:0001454 - range: WhitespaceMinimizedString - r1_fastq_filename: - name: r1_fastq_filename - title: r1_fastq_filename - description: The user-specified filename of the r1 FASTQ file. - comments: Provide the r1 FASTQ filename. - examples: - - value: ABC123_S1_L001_R1_001.fastq.gz - slot_uri: GENEPIO:0001476 - range: WhitespaceMinimizedString - r2_fastq_filename: - name: r2_fastq_filename - title: r2_fastq_filename - description: The user-specified filename of the r2 FASTQ file. - comments: Provide the r2 FASTQ filename. - examples: - - value: ABC123_S1_L001_R2_001.fastq.gz - slot_uri: GENEPIO:0001477 - range: WhitespaceMinimizedString - fast5_filename: - name: fast5_filename - title: fast5_filename - description: The user-specified filename of the FAST5 file. - comments: Provide the FAST5 filename. - examples: - - value: batch1a_sequences.fast5 - slot_uri: GENEPIO:0001480 - range: WhitespaceMinimizedString - assembly_filename: - name: assembly_filename - title: assembly_filename - description: The user-defined filename of the FASTA file. - comments: Provide the FASTA filename. - examples: - - value: pathogenassembly123.fasta - slot_uri: GENEPIO:0001461 - range: WhitespaceMinimizedString - sequence_submitted_by: - name: sequence_submitted_by - title: sequence_submitted_by - description: The name of the agency that submitted the sequence to a database. - 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)". - examples: - - value: Environment Canada (EC) - slot_uri: GENEPIO:0001159 - any_of: - - range: sequence_submitted_by menu - - range: null value menu - sequence_submitted_by_contact_name: - name: sequence_submitted_by_contact_name - title: 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. - 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. - examples: - - value: Enterics Lab Manager - slot_uri: GENEPIO:0100474 - range: WhitespaceMinimizedString - sequence_submitted_by_contact_email: - name: sequence_submitted_by_contact_email - title: sequence_submitted_by_contact_email - description: The email address of the agency responsible for submission of the - sequence. - comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, - or RespLab@lab.ca - examples: - - value: RespLab@lab.ca - slot_uri: GENEPIO:0001165 - range: WhitespaceMinimizedString - publication_ID: - name: publication_ID - title: publication_ID - description: The identifier for a publication. - 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. - examples: - - value: 'PMID: 33205991' - slot_uri: GENEPIO:0100475 - range: WhitespaceMinimizedString - attribute_package: - name: attribute_package - title: attribute_package - description: The attribute package used to structure metadata in an INSDC BioSample. - comments: "If the sample is from a specific human or animal, put \u201CPathogen.cl\u201D\ - . If the sample is from an environmental sample including food, feed, production\ - \ facility, farm, water source, manure etc, put \u201CPathogen.env\u201D." - examples: - - value: Pathogen.env - slot_uri: GENEPIO:0100476 - any_of: - - range: attribute_package menu - - range: null value menu - bioproject_accession: - name: bioproject_accession - title: bioproject_accession - description: The INSDC accession number of the BioProject(s) to which the BioSample - belongs. - 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. - examples: - - value: PRJNA12345 - slot_uri: GENEPIO:0001136 - range: WhitespaceMinimizedString - exact_mappings: - - BIOSAMPLE:bioproject_accession - biosample_accession: - name: biosample_accession - title: biosample_accession - description: The identifier assigned to a BioSample in INSDC archives. - comments: 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: SAMN14180202 - slot_uri: GENEPIO:0001139 - range: WhitespaceMinimizedString - SRA_accession: - name: SRA_accession - title: 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. - 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. - examples: - - value: SRR11177792 - slot_uri: GENEPIO:0001142 - range: WhitespaceMinimizedString - GenBank_accession: - name: GenBank_accession - title: GenBank_accession - description: The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC - archives. - comments: Store the accession returned from a GenBank/ENA/DDBJ submission. - examples: - - value: MN908947.3 - slot_uri: GENEPIO:0001145 - range: WhitespaceMinimizedString - prevalence_metrics: - name: prevalence_metrics - title: prevalence_metrics - description: Metrics regarding the prevalence of the pathogen of interest obtained - from a surveillance project. - 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. - examples: - - value: Number of total samples collected, Number of positive samples - slot_uri: GENEPIO:0100480 - range: WhitespaceMinimizedString - recommended: true - prevalence_metrics_details: - name: prevalence_metrics_details - title: prevalence_metrics_details - description: The details pertaining to the prevalence metrics from a surveillance - project. - comments: 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: Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. - slot_uri: GENEPIO:0100481 - range: WhitespaceMinimizedString - recommended: true - stage_of_production: - name: stage_of_production - title: stage_of_production - description: The stage of food production. - comments: Provide the stage of food production as free text. - examples: - - value: Abattoir [ENVO:01000925] - slot_uri: GENEPIO:0100482 - any_of: - - range: stage_of_production menu - - range: null value menu - recommended: true - experimental_intervention: - name: experimental_intervention - title: experimental_intervention - description: The category of the experimental intervention applied in the food - production system. - 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. - examples: - - value: Vaccination [NCIT:C15346] - slot_uri: GENEPIO:0100483 - any_of: - - range: experimental_intervention menu - - range: null value menu - multivalued: true - recommended: true - experiment_intervention_details: - name: experiment_intervention_details - title: experiment_intervention_details - description: The details of the experimental intervention applied in the food - production system. - comments: If an experimental intervention was applied in the survey, provide details - in this field as free text. - examples: - - value: 2% cranberry solution mixed in feed - slot_uri: GENEPIO:0100484 - range: WhitespaceMinimizedString - recommended: true - AMR_testing_by: - name: AMR_testing_by - title: AMR_testing_by - description: The name of the organization that performed the antimicrobial resistance - testing. - 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. - examples: - - value: Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - slot_uri: GENEPIO:0100511 - any_of: - - range: AMR_testing_by menu - - range: null value menu - required: true - AMR_testing_by_laboratory_name: - name: AMR_testing_by_laboratory_name - title: AMR_testing_by_laboratory_name - description: The name of the lab within the organization that performed the antimicrobial - resistance testing. - 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. - examples: - - value: Topp Lab - slot_uri: GENEPIO:0100512 - range: WhitespaceMinimizedString - AMR_testing_by_contact_name: - name: AMR_testing_by_contact_name - title: 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. - 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 - slot_uri: GENEPIO:0100513 - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - required: true - AMR_testing_by_contact_email: - name: AMR_testing_by_contact_email - title: 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. - 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 - slot_uri: GENEPIO:0100514 - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - required: true - AMR_testing_date: - name: AMR_testing_date - title: AMR_testing_date - description: The date the antimicrobial resistance testing was performed. - comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" - or "YYYY". - examples: - - value: '2022-04-03' - slot_uri: GENEPIO:0100515 - range: date - - antimicrobial_resistance_test_drug: - name: antimicrobial_resistance_test_drug - title: antimicrobial_resistance_test_drug - description: The antimicrobial drug being tested. - examples: - - value: amikacin - any_of: - - range: antimicrobial_resistance_test_drug menu - - range: null value menu - recommended: true - resistance_phenotype: - name: resistance_phenotype - title: 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. - examples: - - value: Susceptible antimicrobial phenotype [ARO:3004302] - any_of: - - range: antimicrobial_phenotype menu - - range: null value menu - recommended: true - measurement: - name: measurement - title: measurement - description: The measured value of resistance to given antibiotic. - comments: This field should only contain a number (either an integer or a number - with decimals). - examples: - - value: '4' - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - required: true - measurement_units: - name: measurement_units - title: 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. - examples: - - value: ug/mL [UO:0000274] - any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu - required: true - measurement_sign: - name: measurement_sign - title: 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. - examples: - - value: greater than (>) [GENEPIO:0001006] - any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu - required: true - laboratory_typing_method: - name: laboratory_typing_method - title: 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. - examples: - - value: Broth dilution [ARO:3004397] - any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu - laboratory_typing_platform: - name: laboratory_typing_platform - title: 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. - examples: - - value: Sensitire [ARO:3004402] - any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu - laboratory_typing_platform_version: - name: laboratory_typing_platform_version - title: 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. - examples: - - value: CMV3AGNF - range: WhitespaceMinimizedString - vendor_name: - name: vendor_name - title: vendor_name - description: The name of the vendor of the testing platform used. - comments: Provide the full name of the company (avoid abbreviations). - examples: - - value: Sensititre - any_of: - - range: antimicrobial_vendor_name - - range: null value menu - testing_standard: - name: testing_standard - title: testing_standard - description: The testing standard used for determination of resistance phenotype - comments: Select a testing standard from the pick list provided. - examples: - - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu - recommended: true - testing_standard_version: - name: testing_standard_version - title: 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. - examples: - - value: M100 - range: WhitespaceMinimizedString - testing_standard_details: - name: testing_standard_details - title: 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. - examples: - - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - - value: '2017.' - range: WhitespaceMinimizedString - susceptible_breakpoint: - name: susceptible_breakpoint - title: 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." - examples: - - value: '8' - range: WhitespaceMinimizedString - intermediate_breakpoint: - name: intermediate_breakpoint - title: 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." - examples: - - value: '16' - range: WhitespaceMinimizedString - resistant_breakpoint: - name: resistant_breakpoint - title: 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." - examples: - - value: '32' - range: WhitespaceMinimizedString - - authors: - name: authors - title: authors - description: Names of individuals contributing to the processes of sample collection, - sequence generation, analysis, and data submission. - 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 - slot_uri: GENEPIO:0001517 - range: WhitespaceMinimizedString - recommended: true - DataHarmonizer provenance: - name: DataHarmonizer provenance - title: DataHarmonizer provenance - description: The DataHarmonizer software and template version 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 - slot_uri: GENEPIO:0001518 - range: Provenance -enums: - null value menu: - name: null value menu - permissible_values: - Not Applicable [GENEPIO:0001619]: - text: Not Applicable [GENEPIO:0001619] - Missing [GENEPIO:0001618]: - text: Missing [GENEPIO:0001618] - Not Collected [GENEPIO:0001620]: - text: Not Collected [GENEPIO:0001620] - Not Provided [GENEPIO:0001668]: - text: Not Provided [GENEPIO:0001668] - Restricted Access [GENEPIO:0001810]: - text: Restricted Access [GENEPIO:0001810] - sample_collected_by menu: - name: 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] - 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] - University of Manitoba (UM) [GENEPIO:0004434]: - text: University of Manitoba (UM) [GENEPIO:0004434] - purpose_of_sampling menu: - name: purpose_of_sampling menu - permissible_values: - Cluster/Outbreak investigation [GENEPIO:0100001]: - text: Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100002]: - text: Diagnostic testing [GENEPIO:0100002] - Environmental testing [GENEPIO:0100548]: - text: Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003]: - text: Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549]: - text: Clinical trial [GENEPIO:0100549] - is_a: Research [GENEPIO:0100003] - Field experiment [GENEPIO:0100550]: - text: Field experiment [GENEPIO:0100550] - is_a: Research [GENEPIO:0100003] - Survey study [GENEPIO:0100582]: - text: Survey study [GENEPIO:0100582] - is_a: Research [GENEPIO:0100003] - Surveillance [GENEPIO:0100004]: - text: Surveillance [GENEPIO:0100004] - presampling_activity menu: - name: presampling_activity menu - permissible_values: - Addition of substances to food/water [GENEPIO:0100536]: - text: Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537]: - text: Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538]: - text: Certified animal husbandry practices [GENEPIO:0100538] - Certified humane animal husbandry practices [GENEPIO:0100894]: - text: Certified humane animal husbandry practices [GENEPIO:0100894] - is_a: Certified animal husbandry practices [GENEPIO:0100538] - Certified organic farming practices [GENEPIO:0100539]: - text: Certified organic farming practices [GENEPIO:0100539] - Conventional farming practices [GENEPIO:0100895]: - text: Conventional farming practices [GENEPIO:0100895] - Change in storage conditions [GENEPIO:0100540]: - text: Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541]: - text: Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542]: - text: Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543]: - text: Fertilizer pre-treatment [GENEPIO:0100543] - Genetic mutation [GENEPIO:0100544[: - text: Genetic mutation [GENEPIO:0100544[ - Logistic slaughter [GENEPIO:0100545]: - text: Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546]: - text: Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547]: - text: Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346]: - text: Vaccination [NCIT:C15346] - specimen_processing menu: - name: specimen_processing menu - permissible_values: - Biological replicate [OBI:0000198]: - text: Biological replicate [OBI:0000198] - Samples pooled [OBI:0600016]: - text: Samples pooled [OBI:0600016] - Technical replicate [OBI:0000249]: - text: Technical replicate [OBI:0000249] - Isolated from single source [GENEPIO:0100926]: - text: Isolated from single source [GENEPIO:0100926] - geo_loc_name (country) menu: - name: geo_loc_name (country) menu - permissible_values: - Afghanistan [GAZ:00006882]: - text: Afghanistan [GAZ:00006882] - Albania [GAZ:00002953]: - text: Albania [GAZ:00002953] - Algeria [GAZ:00000563]: - text: Algeria [GAZ:00000563] - American Samoa [GAZ:00003957]: - text: American Samoa [GAZ:00003957] - Andorra [GAZ:00002948]: - text: Andorra [GAZ:00002948] - Angola [GAZ:00001095]: - text: Angola [GAZ:00001095] - Anguilla [GAZ:00009159]: - text: Anguilla [GAZ:00009159] - Antarctica [GAZ:00000462]: - text: Antarctica [GAZ:00000462] - Antigua and Barbuda [GAZ:00006883]: - text: Antigua and Barbuda [GAZ:00006883] - Argentina [GAZ:00002928]: - text: Argentina [GAZ:00002928] - Armenia [GAZ:00004094]: - text: Armenia [GAZ:00004094] - Aruba [GAZ:00004025]: - text: Aruba [GAZ:00004025] - Ashmore and Cartier Islands [GAZ:00005901]: - text: Ashmore and Cartier Islands [GAZ:00005901] - Australia [GAZ:00000463]: - text: Australia [GAZ:00000463] - Austria [GAZ:00002942]: - text: Austria [GAZ:00002942] - Azerbaijan [GAZ:00004941]: - text: Azerbaijan [GAZ:00004941] - Bahamas [GAZ:00002733]: - text: Bahamas [GAZ:00002733] - Bahrain [GAZ:00005281]: - text: Bahrain [GAZ:00005281] - Baker Island [GAZ:00007117]: - text: Baker Island [GAZ:00007117] - Bangladesh [GAZ:00003750]: - text: Bangladesh [GAZ:00003750] - Barbados [GAZ:00001251]: - text: Barbados [GAZ:00001251] - Bassas da India [GAZ:00005810]: - text: Bassas da India [GAZ:00005810] - Belarus [GAZ:00006886]: - text: Belarus [GAZ:00006886] - Belgium [GAZ:00002938]: - text: Belgium [GAZ:00002938] - Belize [GAZ:00002934]: - text: Belize [GAZ:00002934] - Benin [GAZ:00000904]: - text: Benin [GAZ:00000904] - Bermuda [GAZ:00001264]: - text: Bermuda [GAZ:00001264] - Bhutan [GAZ:00003920]: - text: Bhutan [GAZ:00003920] - Bolivia [GAZ:00002511]: - text: Bolivia [GAZ:00002511] - Borneo [GAZ:00025355]: - text: Borneo [GAZ:00025355] - Bosnia and Herzegovina [GAZ:00006887]: - text: Bosnia and Herzegovina [GAZ:00006887] - Botswana [GAZ:00001097]: - text: Botswana [GAZ:00001097] - Bouvet Island [GAZ:00001453]: - text: Bouvet Island [GAZ:00001453] - Brazil [GAZ:00002828]: - text: Brazil [GAZ:00002828] - British Virgin Islands [GAZ:00003961]: - text: British Virgin Islands [GAZ:00003961] - Brunei [GAZ:00003901]: - text: Brunei [GAZ:00003901] - Bulgaria [GAZ:00002950]: - text: Bulgaria [GAZ:00002950] - Burkina Faso [GAZ:00000905]: - text: Burkina Faso [GAZ:00000905] - Burundi [GAZ:00001090]: - text: Burundi [GAZ:00001090] - Cambodia [GAZ:00006888]: - text: Cambodia [GAZ:00006888] - Cameroon [GAZ:00001093]: - text: Cameroon [GAZ:00001093] - Canada [GAZ:00002560]: - text: Canada [GAZ:00002560] - Cape Verde [GAZ:00001227]: - text: Cape Verde [GAZ:00001227] - Cayman Islands [GAZ:00003986]: - text: Cayman Islands [GAZ:00003986] - Central African Republic [GAZ:00001089]: - text: Central African Republic [GAZ:00001089] - Chad [GAZ:00000586]: - text: Chad [GAZ:00000586] - Chile [GAZ:00002825]: - text: Chile [GAZ:00002825] - China [GAZ:00002845]: - text: China [GAZ:00002845] - Christmas Island [GAZ:00005915]: - text: Christmas Island [GAZ:00005915] - Clipperton Island [GAZ:00005838]: - text: Clipperton Island [GAZ:00005838] - Cocos Islands [GAZ:00009721]: - text: Cocos Islands [GAZ:00009721] - Colombia [GAZ:00002929]: - text: Colombia [GAZ:00002929] - Comoros [GAZ:00005820]: - text: Comoros [GAZ:00005820] - Cook Islands [GAZ:00053798]: - text: Cook Islands [GAZ:00053798] - Coral Sea Islands [GAZ:00005917]: - text: Coral Sea Islands [GAZ:00005917] - Costa Rica [GAZ:00002901]: - text: Costa Rica [GAZ:00002901] - Cote d'Ivoire [GAZ:00000906]: - text: Cote d'Ivoire [GAZ:00000906] - Croatia [GAZ:00002719]: - text: Croatia [GAZ:00002719] - Cuba [GAZ:00003762]: - text: Cuba [GAZ:00003762] - Curacao [GAZ:00012582]: - text: Curacao [GAZ:00012582] - Cyprus [GAZ:00004006]: - text: Cyprus [GAZ:00004006] - Czech Republic [GAZ:00002954]: - text: Czech Republic [GAZ:00002954] - Democratic Republic of the Congo [GAZ:00001086]: - text: Democratic Republic of the Congo [GAZ:00001086] - Denmark [GAZ:00005852]: - text: Denmark [GAZ:00005852] - Djibouti [GAZ:00000582]: - text: Djibouti [GAZ:00000582] - Dominica [GAZ:00006890]: - text: Dominica [GAZ:00006890] - Dominican Republic [GAZ:00003952]: - text: Dominican Republic [GAZ:00003952] - Ecuador [GAZ:00002912]: - text: Ecuador [GAZ:00002912] - Egypt [GAZ:00003934]: - text: Egypt [GAZ:00003934] - El Salvador [GAZ:00002935]: - text: El Salvador [GAZ:00002935] - Equatorial Guinea [GAZ:00001091]: - text: Equatorial Guinea [GAZ:00001091] - Eritrea [GAZ:00000581]: - text: Eritrea [GAZ:00000581] - Estonia [GAZ:00002959]: - text: Estonia [GAZ:00002959] - Eswatini [GAZ:00001099]: - text: Eswatini [GAZ:00001099] - Ethiopia [GAZ:00000567]: - text: Ethiopia [GAZ:00000567] - Europa Island [GAZ:00005811]: - text: Europa Island [GAZ:00005811] - Falkland Islands (Islas Malvinas) [GAZ:00001412]: - text: Falkland Islands (Islas Malvinas) [GAZ:00001412] - Faroe Islands [GAZ:00059206]: - text: Faroe Islands [GAZ:00059206] - Fiji [GAZ:00006891]: - text: Fiji [GAZ:00006891] - Finland [GAZ:00002937]: - text: Finland [GAZ:00002937] - France [GAZ:00003940]: - text: France [GAZ:00003940] - French Guiana [GAZ:00002516]: - text: French Guiana [GAZ:00002516] - French Polynesia [GAZ:00002918]: - text: French Polynesia [GAZ:00002918] - French Southern and Antarctic Lands [GAZ:00003753]: - text: French Southern and Antarctic Lands [GAZ:00003753] - Gabon [GAZ:00001092]: - text: Gabon [GAZ:00001092] - Gambia [GAZ:00000907]: - text: Gambia [GAZ:00000907] - Gaza Strip [GAZ:00009571]: - text: Gaza Strip [GAZ:00009571] - Georgia [GAZ:00004942]: - text: Georgia [GAZ:00004942] - Germany [GAZ:00002646]: - text: Germany [GAZ:00002646] - Ghana [GAZ:00000908]: - text: Ghana [GAZ:00000908] - Gibraltar [GAZ:00003987]: - text: Gibraltar [GAZ:00003987] - Glorioso Islands [GAZ:00005808]: - text: Glorioso Islands [GAZ:00005808] - Greece [GAZ:00002945]: - text: Greece [GAZ:00002945] - Greenland [GAZ:00001507]: - text: Greenland [GAZ:00001507] - Grenada [GAZ:02000573]: - text: Grenada [GAZ:02000573] - Guadeloupe [GAZ:00067142]: - text: Guadeloupe [GAZ:00067142] - Guam [GAZ:00003706]: - text: Guam [GAZ:00003706] - Guatemala [GAZ:00002936]: - text: Guatemala [GAZ:00002936] - Guernsey [GAZ:00001550]: - text: Guernsey [GAZ:00001550] - Guinea [GAZ:00000909]: - text: Guinea [GAZ:00000909] - Guinea-Bissau [GAZ:00000910]: - text: Guinea-Bissau [GAZ:00000910] - Guyana [GAZ:00002522]: - text: Guyana [GAZ:00002522] - Haiti [GAZ:00003953]: - text: Haiti [GAZ:00003953] - Heard Island and McDonald Islands [GAZ:00009718]: - text: Heard Island and McDonald Islands [GAZ:00009718] - Honduras [GAZ:00002894]: - text: Honduras [GAZ:00002894] - Hong Kong [GAZ:00003203]: - text: Hong Kong [GAZ:00003203] - Howland Island [GAZ:00007120]: - text: Howland Island [GAZ:00007120] - Hungary [GAZ:00002952]: - text: Hungary [GAZ:00002952] - Iceland [GAZ:00000843]: - text: Iceland [GAZ:00000843] - India [GAZ:00002839]: - text: India [GAZ:00002839] - Indonesia [GAZ:00003727]: - text: Indonesia [GAZ:00003727] - Iran [GAZ:00004474]: - text: Iran [GAZ:00004474] - Iraq [GAZ:00004483]: - text: Iraq [GAZ:00004483] - Ireland [GAZ:00002943]: - text: Ireland [GAZ:00002943] - Isle of Man [GAZ:00052477]: - text: Isle of Man [GAZ:00052477] - Israel [GAZ:00002476]: - text: Israel [GAZ:00002476] - Italy [GAZ:00002650]: - text: Italy [GAZ:00002650] - Jamaica [GAZ:00003781]: - text: Jamaica [GAZ:00003781] - Jan Mayen [GAZ:00005853]: - text: Jan Mayen [GAZ:00005853] - Japan [GAZ:00002747]: - text: Japan [GAZ:00002747] - Jarvis Island [GAZ:00007118]: - text: Jarvis Island [GAZ:00007118] - Jersey [GAZ:00001551]: - text: Jersey [GAZ:00001551] - Johnston Atoll [GAZ:00007114]: - text: Johnston Atoll [GAZ:00007114] - Jordan [GAZ:00002473]: - text: Jordan [GAZ:00002473] - Juan de Nova Island [GAZ:00005809]: - text: Juan de Nova Island [GAZ:00005809] - Kazakhstan [GAZ:00004999]: - text: Kazakhstan [GAZ:00004999] - Kenya [GAZ:00001101]: - text: Kenya [GAZ:00001101] - Kerguelen Archipelago [GAZ:00005682]: - text: Kerguelen Archipelago [GAZ:00005682] - Kingman Reef [GAZ:00007116]: - text: Kingman Reef [GAZ:00007116] - Kiribati [GAZ:00006894]: - text: Kiribati [GAZ:00006894] - Kosovo [GAZ:00011337]: - text: Kosovo [GAZ:00011337] - Kuwait [GAZ:00005285]: - text: Kuwait [GAZ:00005285] - Kyrgyzstan [GAZ:00006893]: - text: Kyrgyzstan [GAZ:00006893] - Laos [GAZ:00006889]: - text: Laos [GAZ:00006889] - Latvia [GAZ:00002958]: - text: Latvia [GAZ:00002958] - Lebanon [GAZ:00002478]: - text: Lebanon [GAZ:00002478] - Lesotho [GAZ:00001098]: - text: Lesotho [GAZ:00001098] - Liberia [GAZ:00000911]: - text: Liberia [GAZ:00000911] - Libya [GAZ:00000566]: - text: Libya [GAZ:00000566] - Liechtenstein [GAZ:00003858]: - text: Liechtenstein [GAZ:00003858] - Line Islands [GAZ:00007144]: - text: Line Islands [GAZ:00007144] - Lithuania [GAZ:00002960]: - text: Lithuania [GAZ:00002960] - Luxembourg [GAZ:00002947]: - text: Luxembourg [GAZ:00002947] - Macau [GAZ:00003202]: - text: Macau [GAZ:00003202] - Madagascar [GAZ:00001108]: - text: Madagascar [GAZ:00001108] - Malawi [GAZ:00001105]: - text: Malawi [GAZ:00001105] - Malaysia [GAZ:00003902]: - text: Malaysia [GAZ:00003902] - Maldives [GAZ:00006924]: - text: Maldives [GAZ:00006924] - Mali [GAZ:00000584]: - text: Mali [GAZ:00000584] - Malta [GAZ:00004017]: - text: Malta [GAZ:00004017] - Marshall Islands [GAZ:00007161]: - text: Marshall Islands [GAZ:00007161] - Martinique [GAZ:00067143]: - text: Martinique [GAZ:00067143] - Mauritania [GAZ:00000583]: - text: Mauritania [GAZ:00000583] - Mauritius [GAZ:00003745]: - text: Mauritius [GAZ:00003745] - Mayotte [GAZ:00003943]: - text: Mayotte [GAZ:00003943] - Mexico [GAZ:00002852]: - text: Mexico [GAZ:00002852] - Micronesia [GAZ:00005862]: - text: Micronesia [GAZ:00005862] - Midway Islands [GAZ:00007112]: - text: Midway Islands [GAZ:00007112] - Moldova [GAZ:00003897]: - text: Moldova [GAZ:00003897] - Monaco [GAZ:00003857]: - text: Monaco [GAZ:00003857] - Mongolia [GAZ:00008744]: - text: Mongolia [GAZ:00008744] - Montenegro [GAZ:00006898]: - text: Montenegro [GAZ:00006898] - Montserrat [GAZ:00003988]: - text: Montserrat [GAZ:00003988] - Morocco [GAZ:00000565]: - text: Morocco [GAZ:00000565] - Mozambique [GAZ:00001100]: - text: Mozambique [GAZ:00001100] - Myanmar [GAZ:00006899]: - text: Myanmar [GAZ:00006899] - Namibia [GAZ:00001096]: - text: Namibia [GAZ:00001096] - Nauru [GAZ:00006900]: - text: Nauru [GAZ:00006900] - Navassa Island [GAZ:00007119]: - text: Navassa Island [GAZ:00007119] - Nepal [GAZ:00004399]: - text: Nepal [GAZ:00004399] - Netherlands [GAZ:00002946]: - text: Netherlands [GAZ:00002946] - New Caledonia [GAZ:00005206]: - text: New Caledonia [GAZ:00005206] - New Zealand [GAZ:00000469]: - text: New Zealand [GAZ:00000469] - Nicaragua [GAZ:00002978]: - text: Nicaragua [GAZ:00002978] - Niger [GAZ:00000585]: - text: Niger [GAZ:00000585] - Nigeria [GAZ:00000912]: - text: Nigeria [GAZ:00000912] - Niue [GAZ:00006902]: - text: Niue [GAZ:00006902] - Norfolk Island [GAZ:00005908]: - text: Norfolk Island [GAZ:00005908] - North Korea [GAZ:00002801]: - text: North Korea [GAZ:00002801] - North Macedonia [GAZ:00006895]: - text: North Macedonia [GAZ:00006895] - North Sea [GAZ:00002284]: - text: North Sea [GAZ:00002284] - Northern Mariana Islands [GAZ:00003958]: - text: Northern Mariana Islands [GAZ:00003958] - Norway [GAZ:00002699]: - text: Norway [GAZ:00002699] - Oman [GAZ:00005283]: - text: Oman [GAZ:00005283] - Pakistan [GAZ:00005246]: - text: Pakistan [GAZ:00005246] - Palau [GAZ:00006905]: - text: Palau [GAZ:00006905] - Panama [GAZ:00002892]: - text: Panama [GAZ:00002892] - Papua New Guinea [GAZ:00003922]: - text: Papua New Guinea [GAZ:00003922] - Paracel Islands [GAZ:00010832]: - text: Paracel Islands [GAZ:00010832] - Paraguay [GAZ:00002933]: - text: Paraguay [GAZ:00002933] - Peru [GAZ:00002932]: - text: Peru [GAZ:00002932] - Philippines [GAZ:00004525]: - text: Philippines [GAZ:00004525] - Pitcairn Islands [GAZ:00005867]: - text: Pitcairn Islands [GAZ:00005867] - Poland [GAZ:00002939]: - text: Poland [GAZ:00002939] - Portugal [GAZ:00004126]: - text: Portugal [GAZ:00004126] - Puerto Rico [GAZ:00006935]: - text: Puerto Rico [GAZ:00006935] - Qatar [GAZ:00005286]: - text: Qatar [GAZ:00005286] - Republic of the Congo [GAZ:00001088]: - text: Republic of the Congo [GAZ:00001088] - Reunion [GAZ:00003945]: - text: Reunion [GAZ:00003945] - Romania [GAZ:00002951]: - text: Romania [GAZ:00002951] - Ross Sea [GAZ:00023304]: - text: Ross Sea [GAZ:00023304] - Russia [GAZ:00002721]: - text: Russia [GAZ:00002721] - Rwanda [GAZ:00001087]: - text: Rwanda [GAZ:00001087] - Saint Helena [GAZ:00000849]: - text: Saint Helena [GAZ:00000849] - Saint Kitts and Nevis [GAZ:00006906]: - text: Saint Kitts and Nevis [GAZ:00006906] - Saint Lucia [GAZ:00006909]: - text: Saint Lucia [GAZ:00006909] - Saint Pierre and Miquelon [GAZ:00003942]: - text: Saint Pierre and Miquelon [GAZ:00003942] - Saint Martin [GAZ:00005841]: - text: Saint Martin [GAZ:00005841] - Saint Vincent and the Grenadines [GAZ:02000565]: - text: Saint Vincent and the Grenadines [GAZ:02000565] - Samoa [GAZ:00006910]: - text: Samoa [GAZ:00006910] - San Marino [GAZ:00003102]: - text: San Marino [GAZ:00003102] - Sao Tome and Principe [GAZ:00006927]: - text: Sao Tome and Principe [GAZ:00006927] - Saudi Arabia [GAZ:00005279]: - text: Saudi Arabia [GAZ:00005279] - Senegal [GAZ:00000913]: - text: Senegal [GAZ:00000913] - Serbia [GAZ:00002957]: - text: Serbia [GAZ:00002957] - Seychelles [GAZ:00006922]: - text: Seychelles [GAZ:00006922] - Sierra Leone [GAZ:00000914]: - text: Sierra Leone [GAZ:00000914] - Singapore [GAZ:00003923]: - text: Singapore [GAZ:00003923] - Sint Maarten [GAZ:00012579]: - text: Sint Maarten [GAZ:00012579] - Slovakia [GAZ:00002956]: - text: Slovakia [GAZ:00002956] - Slovenia [GAZ:00002955]: - text: Slovenia [GAZ:00002955] - Solomon Islands [GAZ:00005275]: - text: Solomon Islands [GAZ:00005275] - Somalia [GAZ:00001104]: - text: Somalia [GAZ:00001104] - South Africa [GAZ:00001094]: - text: South Africa [GAZ:00001094] - South Georgia and the South Sandwich Islands [GAZ:00003990]: - text: South Georgia and the South Sandwich Islands [GAZ:00003990] - South Korea [GAZ:00002802]: - text: South Korea [GAZ:00002802] - South Sudan [GAZ:00233439]: - text: South Sudan [GAZ:00233439] - Spain [GAZ:00003936]: - text: Spain [GAZ:00003936] - Spratly Islands [GAZ:00010831]: - text: Spratly Islands [GAZ:00010831] - Sri Lanka [GAZ:00003924]: - text: Sri Lanka [GAZ:00003924] - State of Palestine [GAZ:00002475]: - text: State of Palestine [GAZ:00002475] - Sudan [GAZ:00000560]: - text: Sudan [GAZ:00000560] - Suriname [GAZ:00002525]: - text: Suriname [GAZ:00002525] - Svalbard [GAZ:00005396]: - text: Svalbard [GAZ:00005396] - Swaziland [GAZ:00001099]: - text: Swaziland [GAZ:00001099] - Sweden [GAZ:00002729]: - text: Sweden [GAZ:00002729] - Switzerland [GAZ:00002941]: - text: Switzerland [GAZ:00002941] - Syria [GAZ:00002474]: - text: Syria [GAZ:00002474] - Taiwan [GAZ:00005341]: - text: Taiwan [GAZ:00005341] - Tajikistan [GAZ:00006912]: - text: Tajikistan [GAZ:00006912] - Tanzania [GAZ:00001103]: - text: Tanzania [GAZ:00001103] - Thailand [GAZ:00003744]: - text: Thailand [GAZ:00003744] - Timor-Leste [GAZ:00006913]: - text: Timor-Leste [GAZ:00006913] - Togo [GAZ:00000915]: - text: Togo [GAZ:00000915] - Tokelau [GAZ:00260188]: - text: Tokelau [GAZ:00260188] - Tonga [GAZ:00006916]: - text: Tonga [GAZ:00006916] - Trinidad and Tobago [GAZ:00003767]: - text: Trinidad and Tobago [GAZ:00003767] - Tromelin Island [GAZ:00005812]: - text: Tromelin Island [GAZ:00005812] - Tunisia [GAZ:00000562]: - text: Tunisia [GAZ:00000562] - Turkey [GAZ:00000558]: - text: Turkey [GAZ:00000558] - Turkmenistan [GAZ:00005018]: - text: Turkmenistan [GAZ:00005018] - Turks and Caicos Islands [GAZ:00003955]: - text: Turks and Caicos Islands [GAZ:00003955] - Tuvalu [GAZ:00009715]: - text: Tuvalu [GAZ:00009715] - United States of America [GAZ:00002459]: - text: United States of America [GAZ:00002459] - Uganda [GAZ:00001102]: - text: Uganda [GAZ:00001102] - Ukraine [GAZ:00002724]: - text: Ukraine [GAZ:00002724] - United Arab Emirates [GAZ:00005282]: - text: United Arab Emirates [GAZ:00005282] - United Kingdom [GAZ:00002637]: - text: United Kingdom [GAZ:00002637] - Uruguay [GAZ:00002930]: - text: Uruguay [GAZ:00002930] - Uzbekistan [GAZ:00004979]: - text: Uzbekistan [GAZ:00004979] - Vanuatu [GAZ:00006918]: - text: Vanuatu [GAZ:00006918] - Venezuela [GAZ:00002931]: - text: Venezuela [GAZ:00002931] - Viet Nam [GAZ:00003756]: - text: Viet Nam [GAZ:00003756] - Virgin Islands [GAZ:00003959]: - text: Virgin Islands [GAZ:00003959] - Wake Island [GAZ:00007111]: - text: Wake Island [GAZ:00007111] - Wallis and Futuna [GAZ:00007191]: - text: Wallis and Futuna [GAZ:00007191] - West Bank [GAZ:00009572]: - text: West Bank [GAZ:00009572] - Western Sahara [GAZ:00000564]: - text: Western Sahara [GAZ:00000564] - Yemen [GAZ:00005284]: - text: Yemen [GAZ:00005284] - Zambia [GAZ:00001107]: - text: Zambia [GAZ:00001107] - Zimbabwe [GAZ:00001106]: - text: Zimbabwe [GAZ:00001106] - geo_loc_name (state/province/region) menu: - name: geo_loc_name (state/province/region) menu - permissible_values: - Atlantic region (Canada) [wikidata:Q246972]: - text: Atlantic region (Canada) [wikidata:Q246972] - New Brunswick [GAZ:00002570]: - text: New Brunswick [GAZ:00002570] - is_a: Atlantic region (Canada) [wikidata:Q246972] - Newfoundland & Labrador [GAZ:00002567]: - text: Newfoundland & Labrador [GAZ:00002567] - is_a: Atlantic region (Canada) [wikidata:Q246972] - Nova Scotia [GAZ:00002565]: - text: Nova Scotia [GAZ:00002565] - is_a: Atlantic region (Canada) [wikidata:Q246972] - Prince Edward Island [GAZ:00002572]: - text: Prince Edward Island [GAZ:00002572] - is_a: Atlantic region (Canada) [wikidata:Q246972] - Central region (Canada) [wikidata:Q1048064]: - text: Central region (Canada) [wikidata:Q1048064] - Ontario [GAZ:00002563]: - text: Ontario [GAZ:00002563] - is_a: Central region (Canada) [wikidata:Q1048064] - Quebec [GAZ:00002569]: - text: Quebec [GAZ:00002569] - is_a: Central region (Canada) [wikidata:Q1048064] - Northern region (Canada) [wikidata:Q764146]: - text: Northern region (Canada) [wikidata:Q764146] - Northwest Territories [GAZ:00002575]: - text: Northwest Territories [GAZ:00002575] - is_a: Northern region (Canada) [wikidata:Q764146] - Nunuvut [GAZ:00002574]: - text: Nunuvut [GAZ:00002574] - is_a: Northern region (Canada) [wikidata:Q764146] - Yukon [GAZ:00002576]: - text: Yukon [GAZ:00002576] - is_a: Northern region (Canada) [wikidata:Q764146] - Pacific region (Canada) [wikidata:Q122953299]: - text: Pacific region (Canada) [wikidata:Q122953299] - British Columbia [GAZ:00002562]: - text: British Columbia [GAZ:00002562] - is_a: Pacific region (Canada) [wikidata:Q122953299] - Prairie region (Canada) [wikidata:Q1364746]: - text: Prairie region (Canada) [wikidata:Q1364746] - Alberta [GAZ:00002566]: - text: Alberta [GAZ:00002566] - is_a: Prairie region (Canada) [wikidata:Q1364746] - Manitoba [GAZ:00002571]: - text: Manitoba [GAZ:00002571] - is_a: Prairie region (Canada) [wikidata:Q1364746] - Saskatchewan [GAZ:00002564]: - text: Saskatchewan [GAZ:00002564] - is_a: Prairie region (Canada) [wikidata:Q1364746] - sample_collection_date_precision menu: - name: sample_collection_date_precision menu - permissible_values: - year [UO:0000036]: - text: year [UO:0000036] - month [UO:0000035]: - text: month [UO:0000035] - day [UO:0000033]: - text: day [UO:0000033] - environmental_site menu: - name: environmental_site menu - permissible_values: - Abattoir [ENVO:01000925]: - text: Abattoir [ENVO:01000925] - Agricultural Field [ENVO:00000114]: - text: Agricultural Field [ENVO:00000114] - Alluvial fan [ENVO:00000314]: - text: Alluvial fan [ENVO:00000314] - Animal cage [ENVO:01000922]: - text: Animal cage [ENVO:01000922] - Aquarium [ENVO:00002196]: - text: Aquarium [ENVO:00002196] - Artificial wetland [ENVO:03501406]: - text: Artificial wetland [ENVO:03501406] - Breeding ground [ENVO:03501441]: - text: Breeding ground [ENVO:03501441] - Building [ENVO:00000073]: - text: Building [ENVO:00000073] - Barn [EOL:0001898]: - text: Barn [EOL:0001898] - is_a: Building [ENVO:00000073] - Breeder barn [ENVO:03501383]: - text: Breeder barn [ENVO:03501383] - is_a: Barn [EOL:0001898] - Broiler barn [ENVO:03501386]: - text: Broiler barn [ENVO:03501386] - is_a: Barn [EOL:0001898] - Sheep barn [ENVO:03501385]: - text: Sheep barn [ENVO:03501385] - is_a: Barn [EOL:0001898] - Biodome [ENVO:03501397]: - text: Biodome [ENVO:03501397] - is_a: Building [ENVO:00000073] - Cottage [ENVO:03501393]: - text: Cottage [ENVO:03501393] - is_a: Building [ENVO:00000073] - Dairy [ENVO:00003862]: - text: Dairy [ENVO:00003862] - is_a: Building [ENVO:00000073] - Hospital [ENVO:00002173]: - text: Hospital [ENVO:00002173] - is_a: Building [ENVO:00000073] - Laboratory facility [ENVO:01001406]: - text: Laboratory facility [ENVO:01001406] - is_a: Building [ENVO:00000073] - Pigsty [ENVO:03501413]: - text: Pigsty [ENVO:03501413] - is_a: Building [ENVO:00000073] - Building part (organizational term): - text: Building part (organizational term) - Air intake [ENVO:03501380]: - text: Air intake [ENVO:03501380] - is_a: Building part (organizational term) - Animal pen [ENVO:03501387]: - text: Animal pen [ENVO:03501387] - is_a: Building part (organizational term) - Building floor [ENVO:01000486]: - text: Building floor [ENVO:01000486] - is_a: Building part (organizational term) - Building wall [ENVO:01000465]: - text: Building wall [ENVO:01000465] - is_a: Building part (organizational term) - Countertop [ENVO:03501404]: - text: Countertop [ENVO:03501404] - is_a: Building part (organizational term) - Shelf [ENVO:03501403]: - text: Shelf [ENVO:03501403] - is_a: Building part (organizational term) - Stall [EOL:0001903]: - text: Stall [EOL:0001903] - is_a: Building part (organizational term) - Window sill [ENVO:03501381]: - text: Window sill [ENVO:03501381] - is_a: Building part (organizational term) - Creek [ENVO:03501405]: - text: Creek [ENVO:03501405] - Farm [ENVO:00000078]: - text: Farm [ENVO:00000078] - Beef farm [ENVO:03501443]: - text: Beef farm [ENVO:03501443] - is_a: Farm [ENVO:00000078] - Breeder farm [ENVO:03501384]: - text: Breeder farm [ENVO:03501384] - is_a: Farm [ENVO:00000078] - Dairy farm [ENVO:03501416]: - text: Dairy farm [ENVO:03501416] - is_a: Farm [ENVO:00000078] - Feedlot [ENVO:01000627]: - text: Feedlot [ENVO:01000627] - is_a: Farm [ENVO:00000078] - Beef cattle feedlot [ENVO:03501444]: - text: Beef cattle feedlot [ENVO:03501444] - is_a: Feedlot [ENVO:01000627] - Fish farm [ENVO:00000294]: - text: Fish farm [ENVO:00000294] - is_a: Farm [ENVO:00000078] - Research farm [ENVO:03501417]: - text: Research farm [ENVO:03501417] - is_a: Farm [ENVO:00000078] - Central Experimental Farm [GAZ:00004603]: - text: Central Experimental Farm [GAZ:00004603] - is_a: Farm [ENVO:00000078] - Freshwater environment [ENVO:01000306]: - text: Freshwater environment [ENVO:01000306] - Hatchery [ENVO:01001873]: - text: Hatchery [ENVO:01001873] - Poultry hatchery [ENVO:01001874]: - text: Poultry hatchery [ENVO:01001874] - is_a: Hatchery [ENVO:01001873] - Lake [ENVO:00000020]: - text: Lake [ENVO:00000020] - Manure digester facility [ENVO:03501422]: - text: Manure digester facility [ENVO:03501422] - Manure lagoon (Anaerobic lagoon) [ENVO:03501423]: - text: Manure lagoon (Anaerobic lagoon) [ENVO:03501423] - Manure pit [ENVO:01001872]: - text: Manure pit [ENVO:01001872] - Marine environment [ENVO:01000320]: - text: Marine environment [ENVO:01000320] - Benthic zone [ENVO:03501440]: - text: Benthic zone [ENVO:03501440] - is_a: Marine environment [ENVO:01000320] - Pelagic zone [ENVO:00000208]: - text: Pelagic zone [ENVO:00000208] - is_a: Marine environment [ENVO:01000320] - Park [ENVO:00000562]: - text: Park [ENVO:00000562] - Pond [ENVO:00000033]: - text: Pond [ENVO:00000033] - Reservoir [ENVO:00000025]: - text: Reservoir [ENVO:00000025] - Irrigation reservoir [ENVO:00000450]: - text: Irrigation reservoir [ENVO:00000450] - is_a: Reservoir [ENVO:00000025] - Retail environment [ENVO:01001448]: - text: Retail environment [ENVO:01001448] - Shop [ENVO:00002221]: - text: Shop [ENVO:00002221] - is_a: Retail environment [ENVO:01001448] - Butcher shop [ENVO:03501396]: - text: Butcher shop [ENVO:03501396] - is_a: Shop [ENVO:00002221] - Pet store [ENVO:03501395]: - text: Pet store [ENVO:03501395] - is_a: Shop [ENVO:00002221] - Supermarket [ENVO:01000984]: - text: Supermarket [ENVO:01000984] - is_a: Shop [ENVO:00002221] - River [ENVO:00000022]: - text: River [ENVO:00000022] - Roost (bird) [ENVO:03501439]: - text: Roost (bird) [ENVO:03501439] - Rural area [ENVO:01000772]: - text: Rural area [ENVO:01000772] - Slough [ENVO:03501438]: - text: Slough [ENVO:03501438] - Stream [ENVO:00000023]: - text: Stream [ENVO:00000023] - Trailer [ENVO:03501394]: - text: Trailer [ENVO:03501394] - Tributary [ENVO:00000495]: - text: Tributary [ENVO:00000495] - Truck [ENVO:01000602]: - text: Truck [ENVO:01000602] - Urban area [ENVO:03501437]: - text: Urban area [ENVO:03501437] - Water surface [ENVO:01001191]: - text: Water surface [ENVO:01001191] - Woodland area [ENVO:00000109]: - text: Woodland area [ENVO:00000109] - Zoo [ENVO:00010625]: - text: Zoo [ENVO:00010625] - antimicrobial_resistance_test_drug menu: - name: antimicrobial_resistance_test_drug menu - permissible_values: - amikacin: - text: amikacin - amoxicillin-clavulanic_acid: - text: amoxicillin-clavulanic_acid - ampicillin: - text: ampicillin - azithromycin: - text: azithromycin - cefazolin: - text: cefazolin - cefepime: - text: cefepime - cefotaxime: - text: cefotaxime - cefotaxime-clavulanic_acid: - text: cefotaxime-clavulanic_acid - cefoxitin: - text: cefoxitin - cefpodoxime: - text: cefpodoxime - ceftazidime: - text: ceftazidime - ceftazidime-clavulanic_acid: - text: ceftazidime-clavulanic_acid - ceftiofur: - text: ceftiofur - ceftriaxone: - text: ceftriaxone - cephalothin: - text: cephalothin - chloramphenicol: - text: chloramphenicol - ciprofloxacin: - text: ciprofloxacin - clindamycin: - text: clindamycin - doxycycline: - text: doxycycline - enrofloxacin: - text: enrofloxacin - erythromycin: - text: erythromycin - florfenicol: - text: florfenicol - gentamicin: - text: gentamicin - imipenem: - text: imipenem - kanamycin: - text: kanamycin - levofloxacin: - text: levofloxacin - linezolid: - text: linezolid - meropenem: - text: meropenem - nalidixic_acid: - text: nalidixic_acid - nitrofurantoin: - text: nitrofurantoin - norfloxacin: - text: norfloxacin - oxolinic-acid: - text: oxolinic-acid - oxytetracycline: - text: oxytetracycline - piperacillin: - text: piperacillin - piperacillin-tazobactam: - text: piperacillin-tazobactam - polymyxin-b: - text: polymyxin-b - quinupristin-dalfopristin: - text: quinupristin-dalfopristin - streptomycin: - text: streptomycin - sulfisoxazole: - text: sulfisoxazole - telithromycin: - text: telithromycin - tetracycline: - text: tetracycline - tigecycline: - text: tigecycline - trimethoprim-sulfamethoxazole: - text: trimethoprim-sulfamethoxazole - available_data_types menu: - name: available_data_types menu - permissible_values: - Documentation [GENEPIO:0100702]: - text: Documentation [GENEPIO:0100702] - Experimental parameters documentation [GENEPIO:0100703]: - text: Experimental parameters documentation [GENEPIO:0100703] - is_a: Documentation [GENEPIO:0100702] - Feed history [GENEPIO:0100704]: - text: Feed history [GENEPIO:0100704] - is_a: Documentation [GENEPIO:0100702] - Land use information [GENEPIO:0100705]: - text: Land use information [GENEPIO:0100705] - is_a: Documentation [GENEPIO:0100702] - Therapeutic administration history [GENEPIO:0100706]: - text: Therapeutic administration history [GENEPIO:0100706] - is_a: Documentation [GENEPIO:0100702] - Chemical characterization [GENEPIO:0100707]: - text: Chemical characterization [GENEPIO:0100707] - pH measurement [GENEPIO:0100708]: - text: pH measurement [GENEPIO:0100708] - is_a: Chemical characterization [GENEPIO:0100707] - Dissolved oxygen measurement [GENEPIO:0100709]: - text: Dissolved oxygen measurement [GENEPIO:0100709] - is_a: Chemical characterization [GENEPIO:0100707] - Nitrate measurement [GENEPIO:0100710]: - text: Nitrate measurement [GENEPIO:0100710] - is_a: Chemical characterization [GENEPIO:0100707] - Nitrite measurement [GENEPIO:0100711]: - text: Nitrite measurement [GENEPIO:0100711] - is_a: Chemical characterization [GENEPIO:0100707] - Phosphorous measurement [GENEPIO:0100712]: - text: Phosphorous measurement [GENEPIO:0100712] - is_a: Chemical characterization [GENEPIO:0100707] - Salinity measurement [GENEPIO:0100713]: - text: Salinity measurement [GENEPIO:0100713] - is_a: Chemical characterization [GENEPIO:0100707] - Microbiological characterization [GENEPIO:0100714]: - text: Microbiological characterization [GENEPIO:0100714] - Microbiological identification [GENEPIO:0100715]: - text: Microbiological identification [GENEPIO:0100715] - is_a: Microbiological characterization [GENEPIO:0100714] - Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]: - text: Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] - is_a: Microbiological identification [GENEPIO:0100715] - "Microbiological identification (bioM\xE9rieux API) [GENEPIO:0100717]": - text: "Microbiological identification (bioM\xE9rieux API) [GENEPIO:0100717]" - is_a: Microbiological identification [GENEPIO:0100715] - Microbiological identification (Biolog) [GENEPIO:0100718]: - text: Microbiological identification (Biolog) [GENEPIO:0100718] - is_a: Microbiological identification [GENEPIO:0100715] - Microbiological identification (FAME) [GENEPIO:0100719]: - text: Microbiological identification (FAME) [GENEPIO:0100719] - is_a: Microbiological identification [GENEPIO:0100715] - Microbiological identification (Sensititre) [GENEPIO:0100720]: - text: Microbiological identification (Sensititre) [GENEPIO:0100720] - is_a: Microbiological identification [GENEPIO:0100715] - Microbiological identification (ViTek) [GENEPIO:0100721]: - text: Microbiological identification (ViTek) [GENEPIO:0100721] - is_a: Microbiological identification [GENEPIO:0100715] - Phage type [GENEPIO:0100722]: - text: Phage type [GENEPIO:0100722] - is_a: Microbiological identification [GENEPIO:0100715] - Serotype [GENEPIO:0100723]: - text: Serotype [GENEPIO:0100723] - is_a: Microbiological identification [GENEPIO:0100715] - Phenotypic microbiological characterization [GENEPIO:0100724]: - text: Phenotypic microbiological characterization [GENEPIO:0100724] - is_a: Microbiological characterization [GENEPIO:0100714] - AMR phenotypic testing [GENEPIO:0100725]: - text: AMR phenotypic testing [GENEPIO:0100725] - is_a: Phenotypic microbiological characterization [GENEPIO:0100724] - Biolog phenotype microarray [GENEPIO:0100726]: - text: Biolog phenotype microarray [GENEPIO:0100726] - is_a: Phenotypic microbiological characterization [GENEPIO:0100724] - Microbiological quantification [GENEPIO:0100727]: - text: Microbiological quantification [GENEPIO:0100727] - Colony count [GENEPIO:0100728]: - text: Colony count [GENEPIO:0100728] - is_a: Microbiological quantification [GENEPIO:0100727] - Total coliform count [GENEPIO:0100729]: - text: Total coliform count [GENEPIO:0100729] - is_a: Colony count [GENEPIO:0100728] - Total fecal coliform count [GENEPIO:0100730]: - text: Total fecal coliform count [GENEPIO:0100730] - is_a: Colony count [GENEPIO:0100728] - Infectivity assay [GENEPIO:0100731]: - text: Infectivity assay [GENEPIO:0100731] - is_a: Microbiological quantification [GENEPIO:0100727] - ELISA toxin binding [GENEPIO:0100732]: - text: ELISA toxin binding [GENEPIO:0100732] - is_a: Microbiological quantification [GENEPIO:0100727] - Molecular characterization [GENEPIO:0100733]: - text: Molecular characterization [GENEPIO:0100733] - 16S rRNA Sanger sequencing [GENEPIO:0100734]: - text: 16S rRNA Sanger sequencing [GENEPIO:0100734] - is_a: Molecular characterization [GENEPIO:0100733] - PCR marker detection [GENEPIO:0100735]: - text: PCR marker detection [GENEPIO:0100735] - is_a: Molecular characterization [GENEPIO:0100733] - BOX PCR fingerprint [GENEPIO:0100736]: - text: BOX PCR fingerprint [GENEPIO:0100736] - is_a: PCR marker detection [GENEPIO:0100735] - ERIC PCR fingerprint [GENEPIO:0100737]: - text: ERIC PCR fingerprint [GENEPIO:0100737] - is_a: PCR marker detection [GENEPIO:0100735] - Plasmid type [GENEPIO:0100738]: - text: Plasmid type [GENEPIO:0100738] - is_a: Molecular characterization [GENEPIO:0100733] - Ribotype [GENEPIO:0100739]: - text: Ribotype [GENEPIO:0100739] - is_a: Molecular characterization [GENEPIO:0100733] - Molecular quantification [GENEPIO:0100740]: - text: Molecular quantification [GENEPIO:0100740] - qPCR marker organism quantification [GENEPIO:0100741]: - text: qPCR marker organism quantification [GENEPIO:0100741] - is_a: Molecular quantification [GENEPIO:0100740] - Physical characterization [GENEPIO:0100742]: - text: Physical characterization [GENEPIO:0100742] - Conductivity measurement [GENEPIO:0100743]: - text: Conductivity measurement [GENEPIO:0100743] - is_a: Physical characterization [GENEPIO:0100742] - Mollusc shell measurement [GENEPIO:0100744]: - text: Mollusc shell measurement [GENEPIO:0100744] - is_a: Physical characterization [GENEPIO:0100742] - Mollusc shell length [GENEPIO:0100745]: - text: Mollusc shell length [GENEPIO:0100745] - is_a: Mollusc shell measurement [GENEPIO:0100744] - Matter compostion [GENEPIO:0100746]: - text: Matter compostion [GENEPIO:0100746] - is_a: Physical characterization [GENEPIO:0100742] - Dry matter composition [GENEPIO:0100747]: - text: Dry matter composition [GENEPIO:0100747] - is_a: Matter compostion [GENEPIO:0100746] - Organic matter composition [GENEPIO:0100748]: - text: Organic matter composition [GENEPIO:0100748] - is_a: Matter compostion [GENEPIO:0100746] - Turbidity measurement [GENEPIO:0100749]: - text: Turbidity measurement [GENEPIO:0100749] - is_a: Physical characterization [GENEPIO:0100742] - weather_type menu: - name: weather_type menu - permissible_values: - Cloudy/Overcast [ENVO:03501418]: - text: Cloudy/Overcast [ENVO:03501418] - Partially cloudy [ENVO:03501419]: - text: Partially cloudy [ENVO:03501419] - is_a: Cloudy/Overcast [ENVO:03501418] - Drizzle [ENVO:03501420]: - text: Drizzle [ENVO:03501420] - Fog [ENVO:01000844]: - text: Fog [ENVO:01000844] - Rain [ENVO:01001564]: - text: Rain [ENVO:01001564] - Snow [ENVO:01000406]: - text: Snow [ENVO:01000406] - Storm [ENVO:01000876]: - text: Storm [ENVO:01000876] - Sunny/Clear [ENVO:03501421]: - text: Sunny/Clear [ENVO:03501421] - animal_or_plant_population menu: - name: animal_or_plant_population menu - permissible_values: - Algae [FOODON:03411301]: - text: Algae [FOODON:03411301] - Algal bloom [ENVO:2000004]: - text: Algal bloom [ENVO:2000004] - is_a: Algae [FOODON:03411301] - Cattle [FOODON:03411161]: - text: Cattle [FOODON:03411161] - Beef cattle [HSO:0000022]: - text: Beef cattle [HSO:0000022] - is_a: Cattle [FOODON:03411161] - Dairy cattle [FOODON:00002505]: - text: Dairy cattle [FOODON:00002505] - is_a: Cattle [FOODON:03411161] - Chicken [NCBITaxon:9031]: - text: Chicken [NCBITaxon:9031] - Crop [AGRO:00000325]: - text: Crop [AGRO:00000325] - Fish [FOODON:03411222]: - text: Fish [FOODON:03411222] - Pig [NCBITaxon:9823]: - text: Pig [NCBITaxon:9823] - Poultry [FOODON:00004298]: - text: Poultry [FOODON:00004298] - Sheep [NCBITaxon:9940]: - text: Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433]: - text: Shellfish [FOODON:03411433] - Crustacean [FOODON:03411374]: - text: Crustacean [FOODON:03411374] - is_a: Shellfish [FOODON:03411433] - Mollusc [FOODON:03412112]: - text: Mollusc [FOODON:03412112] - is_a: Shellfish [FOODON:03411433] - Tropical fish [FOODON:00004283]: - text: Tropical fish [FOODON:00004283] - Turkey [NCBITaxon:9103]: - text: Turkey [NCBITaxon:9103] - Wildlife [FOODON:00004503]: - text: Wildlife [FOODON:00004503] - Wild bird [FOODON:00004505]: - text: Wild bird [FOODON:00004505] - is_a: Wildlife [FOODON:00004503] - Seabird [FOODON:00004504]: - text: Seabird [FOODON:00004504] - is_a: Wild bird [FOODON:00004505] - environmental_material menu: - name: environmental_material menu - permissible_values: - Air [ENVO:00002005]: - text: Air [ENVO:00002005] - Alluvium [ENVO:01001202]: - text: Alluvium [ENVO:01001202] - Animal feeding equipment [AGRO:00000675]: - text: Animal feeding equipment [AGRO:00000675] - Animal feeder [AGRO:00000679]: - text: Animal feeder [AGRO:00000679] - is_a: Animal feeding equipment [AGRO:00000675] - Animal drinker [AGRO:00000680]: - text: Animal drinker [AGRO:00000680] - is_a: Animal feeding equipment [AGRO:00000675] - Feed pan [AGRO:00000676]: - text: Feed pan [AGRO:00000676] - is_a: Animal feeding equipment [AGRO:00000675] - Watering bowl [AGRO:00000677]: - text: Watering bowl [AGRO:00000677] - is_a: Animal feeding equipment [AGRO:00000675] - Animal transportation equipment [AGRO:00000671]: - text: Animal transportation equipment [AGRO:00000671] - Dead haul trailer [GENEPIO:0100896]: - text: Dead haul trailer [GENEPIO:0100896] - is_a: Animal transportation equipment [AGRO:00000671] - Dead haul truck [AGRO:00000673]: - text: Dead haul truck [AGRO:00000673] - is_a: Animal transportation equipment [AGRO:00000671] - Live haul trailer [GENEPIO:0100897]: - text: Live haul trailer [GENEPIO:0100897] - is_a: Animal transportation equipment [AGRO:00000671] - Live haul truck [AGRO:00000674]: - text: Live haul truck [AGRO:00000674] - is_a: Animal transportation equipment [AGRO:00000671] - Belt [NCIT:C49844]: - text: Belt [NCIT:C49844] - Biosolids [ENVO:00002059]: - text: Biosolids [ENVO:00002059] - Boot [GSSO:012935]: - text: Boot [GSSO:012935] - Boot cover [OBI:0002806]: - text: Boot cover [OBI:0002806] - is_a: Boot [GSSO:012935] - Broom [ENVO:03501377]: - text: Broom [ENVO:03501377] - Bulk tank [ENVO:03501379]: - text: Bulk tank [ENVO:03501379] - Chick box [AGRO:00000678]: - text: Chick box [AGRO:00000678] - Chick pad [AGRO:00000672]: - text: Chick pad [AGRO:00000672] - Cleaning equipment [ENVO:03501376]: - text: Cleaning equipment [ENVO:03501376] - Compost [ENVO:00002170]: - text: Compost [ENVO:00002170] - Contaminated water [ENVO:00002186]: - text: Contaminated water [ENVO:00002186] - Fecal slurry [ENVO:03501436]: - text: Fecal slurry [ENVO:03501436] - is_a: Contaminated water [ENVO:00002186] - Fluid from meat rinse [GENEPIO:0004323]: - text: Fluid from meat rinse [GENEPIO:0004323] - is_a: Contaminated water [ENVO:00002186] - Effluent [ENVO:03501407]: - text: Effluent [ENVO:03501407] - is_a: Contaminated water [ENVO:00002186] - Influent [ENVO:03501442]: - text: Influent [ENVO:03501442] - is_a: Contaminated water [ENVO:00002186] - Surface runoff [ENVO:03501408]: - text: Surface runoff [ENVO:03501408] - is_a: Contaminated water [ENVO:00002186] - Poultry plucking water [AGRO_00000693]: - text: Poultry plucking water [AGRO_00000693] - is_a: Contaminated water [ENVO:00002186] - Wastewater [ENVO:00002001]: - text: Wastewater [ENVO:00002001] - is_a: Contaminated water [ENVO:00002186] - Weep fluid [AGRO_00000692]: - text: Weep fluid [AGRO_00000692] - is_a: Contaminated water [ENVO:00002186] - Crate [ENVO:03501372]: - text: Crate [ENVO:03501372] - Dumpster [ENVO:03501400]: - text: Dumpster [ENVO:03501400] - Dust [ENVO:00002008]: - text: Dust [ENVO:00002008] - Egg belt [AGRO:00000670]: - text: Egg belt [AGRO:00000670] - Fan [NCIT:C49947]: - text: Fan [NCIT:C49947] - Freezer [ENVO:03501415]: - text: Freezer [ENVO:03501415] - Freezer handle [ENVO:03501414]: - text: Freezer handle [ENVO:03501414] - is_a: Freezer [ENVO:03501415] - Manure [ENVO:00003031]: - text: Manure [ENVO:00003031] - Animal manure [AGRO:00000079]: - text: Animal manure [AGRO:00000079] - is_a: Manure [ENVO:00003031] - Pig manure [AGRO:00000080]: - text: Pig manure [AGRO:00000080] - is_a: Animal manure [AGRO:00000079] - Manure digester equipment [ENVO:03501424]: - text: Manure digester equipment [ENVO:03501424] - Nest [ENVO:03501432]: - text: Nest [ENVO:03501432] - Bird's nest [ENVO:00005805]: - text: Bird's nest [ENVO:00005805] - is_a: Nest [ENVO:03501432] - Permafrost [ENVO:00000134]: - text: Permafrost [ENVO:00000134] - Plucking belt [AGRO:00000669]: - text: Plucking belt [AGRO:00000669] - Poultry fluff [UBERON:0008291]: - text: Poultry fluff [UBERON:0008291] - Poultry litter [AGRO:00000080]: - text: Poultry litter [AGRO:00000080] - Sediment [ENVO:00002007]: - text: Sediment [ENVO:00002007] - Soil [ENVO:00001998]: - text: Soil [ENVO:00001998] - Agricultural soil [ENVO:00002259]: - text: Agricultural soil [ENVO:00002259] - is_a: Soil [ENVO:00001998] - Forest soil [ENVO:00002261]: - text: Forest soil [ENVO:00002261] - is_a: Soil [ENVO:00001998] - Straw [ENVO:00003869]: - text: Straw [ENVO:00003869] - Canola straw: - text: Canola straw - is_a: Straw [ENVO:00003869] - Oat straw [FOODON:03309878]: - text: Oat straw [FOODON:03309878] - is_a: Straw [ENVO:00003869] - Water [CHEBI:15377]: - text: Water [CHEBI:15377] - Drinking water [ENVO:00003064]: - text: Drinking water [ENVO:00003064] - is_a: Water [CHEBI:15377] - Groundwater [ENVO:01001004]: - text: Groundwater [ENVO:01001004] - is_a: Water [CHEBI:15377] - Surface water [ENVO:00002042]: - text: Surface water [ENVO:00002042] - is_a: Water [CHEBI:15377] - anatomical_material menu: - name: anatomical_material menu - permissible_values: - Blood [UBERON:0000178]: - text: Blood [UBERON:0000178] - Fluid [UBERON:0006314]: - text: Fluid [UBERON:0006314] - Fluid (cerebrospinal (CSF)) [UBERON:0001359]: - text: Fluid (cerebrospinal (CSF)) [UBERON:0001359] - is_a: Fluid [UBERON:0006314] - Fluid (amniotic) [UBERON:0000173]: - text: Fluid (amniotic) [UBERON:0000173] - is_a: Fluid [UBERON:0006314] - Saliva [UBERON:0001836]: - text: Saliva [UBERON:0001836] - is_a: Fluid [UBERON:0006314] - Tissue [UBERON:0000479]: - text: Tissue [UBERON:0000479] - body_product menu: - name: body_product menu - permissible_values: - Digestive organ content [GENEPIO:0100898]: - text: Digestive organ content [GENEPIO:0100898] - Caecal content [GENEPIO:0100899]: - text: Caecal content [GENEPIO:0100899] - is_a: Digestive organ content [GENEPIO:0100898] - Intestinal content [GENEPIO:0100900]: - text: Intestinal content [GENEPIO:0100900] - is_a: Digestive organ content [GENEPIO:0100898] - Stomach content [GENEPIO:0100901]: - text: Stomach content [GENEPIO:0100901] - is_a: Digestive organ content [GENEPIO:0100898] - Feces [UBERON:0001988]: - text: Feces [UBERON:0001988] - Fecal composite [GENEPIO:0004512]: - text: Fecal composite [GENEPIO:0004512] - is_a: Feces [UBERON:0001988] - Feces (fresh) [GENEPIO:0004512]: - text: Feces (fresh) [GENEPIO:0004512] - is_a: Feces [UBERON:0001988] - Feces (environmental) [GENEPIO:0004514]: - text: Feces (environmental) [GENEPIO:0004514] - is_a: Feces [UBERON:0001988] - Meconium [UBERON:0007109]: - text: Meconium [UBERON:0007109] - is_a: Feces [UBERON:0001988] - Milk [UBERON:0001913]: - text: Milk [UBERON:0001913] - Colostrum [UBERON:0001914]: - text: Colostrum [UBERON:0001914] - is_a: Milk [UBERON:0001913] - Urine [UBERON:0001088]: - text: Urine [UBERON:0001088] - anatomical_part menu: - name: anatomical_part menu - permissible_values: - Carcass [UBERON:0008979]: - text: Carcass [UBERON:0008979] - Swine carcass [FOODON:03311719]: - text: Swine carcass [FOODON:03311719] - is_a: Carcass [UBERON:0008979] - Digestive system [UBERON:0001007]: - text: Digestive system [UBERON:0001007] - Caecum [UBERON:0001153]: - text: Caecum [UBERON:0001153] - is_a: Digestive system [UBERON:0001007] - Colon [UBERON:0001155]: - text: Colon [UBERON:0001155] - is_a: Digestive system [UBERON:0001007] - Digestive gland [UBERON:0006925]: - text: Digestive gland [UBERON:0006925] - is_a: Digestive system [UBERON:0001007] - Foregut [UBERON:0006925]: - text: Foregut [UBERON:0006925] - is_a: Digestive system [UBERON:0001007] - Gall bladder [UBERON:0002110]: - text: Gall bladder [UBERON:0002110] - is_a: Digestive system [UBERON:0001007] - Gastrointestinal system mucosa [UBERON:0004786]: - text: Gastrointestinal system mucosa [UBERON:0004786] - is_a: Digestive system [UBERON:0001007] - Gizzard [UBERON:0005052]: - text: Gizzard [UBERON:0005052] - is_a: Digestive system [UBERON:0001007] - Hindgut [UBERON:0001046]: - text: Hindgut [UBERON:0001046] - is_a: Digestive system [UBERON:0001007] - Intestine [UBERON:0000160]: - text: Intestine [UBERON:0000160] - is_a: Digestive system [UBERON:0001007] - Small intestine [UBERON:0002108]: - text: Small intestine [UBERON:0002108] - is_a: Intestine [UBERON:0000160] - Duodenum [UBERON:0002114]: - text: Duodenum [UBERON:0002114] - is_a: Small intestine [UBERON:0002108] - Ileum [UBERON:0002116]: - text: Ileum [UBERON:0002116] - is_a: Small intestine [UBERON:0002108] - Jejunum [UBERON:0002115]: - text: Jejunum [UBERON:0002115] - is_a: Small intestine [UBERON:0002108] - Stomach [UBERON:0000945]: - text: Stomach [UBERON:0000945] - is_a: Digestive system [UBERON:0001007] - Abomasum [UBERON:0007358]: - text: Abomasum [UBERON:0007358] - is_a: Stomach [UBERON:0000945] - Rumen [UBERON:0007365]: - text: Rumen [UBERON:0007365] - is_a: Stomach [UBERON:0000945] - Excretory system (organizational term): - text: Excretory system (organizational term) - Anus [UBERON:0001245]: - text: Anus [UBERON:0001245] - is_a: Excretory system (organizational term) - Anal gland [UBERON:0011253]: - text: Anal gland [UBERON:0011253] - is_a: Excretory system (organizational term) - Cloaca [UBERON:0000162]: - text: Cloaca [UBERON:0000162] - is_a: Excretory system (organizational term) - Liver [UBERON:0002107]: - text: Liver [UBERON:0002107] - is_a: Excretory system (organizational term) - Kidney [UBERON:0002113]: - text: Kidney [UBERON:0002113] - is_a: Excretory system (organizational term) - Rectum [UBERON:0001052]: - text: Rectum [UBERON:0001052] - is_a: Excretory system (organizational term) - Spleen [UBERON:0002106]: - text: Spleen [UBERON:0002106] - is_a: Excretory system (organizational term) - Urinary bladder [UBERON:0001255]: - text: Urinary bladder [UBERON:0001255] - is_a: Excretory system (organizational term) - Foot [BTO:0000476]: - text: Foot [BTO:0000476] - Head [UBERON:0000033]: - text: Head [UBERON:0000033] - is_a: Foot [BTO:0000476] - Brain [UBERON:0000955]: - text: Brain [UBERON:0000955] - is_a: Foot [BTO:0000476] - Ear [UBERON:0001690]: - text: Ear [UBERON:0001690] - is_a: Foot [BTO:0000476] - Eye [UBERON:0000970]: - text: Eye [UBERON:0000970] - is_a: Foot [BTO:0000476] - Mouth [UBERON:0000165]: - text: Mouth [UBERON:0000165] - is_a: Foot [BTO:0000476] - Nose [UBERON:0000004]: - text: Nose [UBERON:0000004] - is_a: Foot [BTO:0000476] - Nasal turbinal [UBERON:0035612]: - text: Nasal turbinal [UBERON:0035612] - is_a: Nose [UBERON:0000004] - Nasopharynx (NP) [UBERON:0001728]: - text: Nasopharynx (NP) [UBERON:0001728] - is_a: Nose [UBERON:0000004] - Pair of nares [UBERON:0002109]: - text: Pair of nares [UBERON:0002109] - is_a: Nose [UBERON:0000004] - Paranasal sinus [UBERON:0001825]: - text: Paranasal sinus [UBERON:0001825] - is_a: Nose [UBERON:0000004] - Snout [UBERON:0006333]: - text: Snout [UBERON:0006333] - is_a: Nose [UBERON:0000004] - Lymphatic system [UBERON:0006558]: - text: Lymphatic system [UBERON:0006558] - Lymph node [UBERON:0000029]: - text: Lymph node [UBERON:0000029] - is_a: Lymphatic system [UBERON:0006558] - Mesenteric lymph node [UBERON:0002509]: - text: Mesenteric lymph node [UBERON:0002509] - is_a: Lymph node [UBERON:0000029] - Mantle (bird) [GENEPIO:0100927]: - text: Mantle (bird) [GENEPIO:0100927] - Neck [UBERON:0000974]: - text: Neck [UBERON:0000974] - Esophagus [UBERON:0001043]: - text: Esophagus [UBERON:0001043] - is_a: Neck [UBERON:0000974] - Trachea [UBERON:0003126]: - text: Trachea [UBERON:0003126] - is_a: Neck [UBERON:0000974] - Nerve [UBERON:0001021]: - text: Nerve [UBERON:0001021] - Spinal cord [UBERON:0002240]: - text: Spinal cord [UBERON:0002240] - is_a: Nerve [UBERON:0001021] - Organs or organ parts [GENEPIO:0001117]: - text: Organs or organ parts [GENEPIO:0001117] - Organ [UBERON:0000062]: - text: Organ [UBERON:0000062] - is_a: Organs or organ parts [GENEPIO:0001117] - Muscle organ [UBERON:0001630]: - text: Muscle organ [UBERON:0001630] - is_a: Organ [UBERON:0000062] - Skin of body [UBERON:0002097]: - text: Skin of body [UBERON:0002097] - is_a: Organ [UBERON:0000062] - Reproductive system [UBERON:0000990]: - text: Reproductive system [UBERON:0000990] - Embryo [UBERON:0000922]: - text: Embryo [UBERON:0000922] - is_a: Reproductive system [UBERON:0000990] - Fetus [UBERON:0000323]: - text: Fetus [UBERON:0000323] - is_a: Reproductive system [UBERON:0000990] - Ovary [UBERON:0000992]: - text: Ovary [UBERON:0000992] - is_a: Reproductive system [UBERON:0000990] - Oviduct [UBERON:0000993]: - text: Oviduct [UBERON:0000993] - is_a: Reproductive system [UBERON:0000990] - Placenta [UBERON:0001987]: - text: Placenta [UBERON:0001987] - is_a: Reproductive system [UBERON:0000990] - Testis [UBERON:0000473]: - text: Testis [UBERON:0000473] - is_a: Reproductive system [UBERON:0000990] - Uterus [UBERON:0000995]: - text: Uterus [UBERON:0000995] - is_a: Reproductive system [UBERON:0000990] - Vagina [UBERON:0000996]: - text: Vagina [UBERON:0000996] - is_a: Reproductive system [UBERON:0000990] - Yolk sac [UBERON:0001040]: - text: Yolk sac [UBERON:0001040] - is_a: Reproductive system [UBERON:0000990] - Respiratory system [UBERON:0001004]: - text: Respiratory system [UBERON:0001004] - Air sac [UBERON:0009060]: - text: Air sac [UBERON:0009060] - is_a: Respiratory system [UBERON:0001004] - Lung [UBERON:0002048]: - text: Lung [UBERON:0002048] - is_a: Vascular system [UBERON:0007798] - Pleura [UBERON:0000977]: - text: Pleura [UBERON:0000977] - is_a: Respiratory system [UBERON:0001004] - Respiratory system mucosa [UBERON:0004785]: - text: Respiratory system mucosa [UBERON:0004785] - is_a: Respiratory system [UBERON:0001004] - Skeletal system [UBERON:0001434]: - text: Skeletal system [UBERON:0001434] - Skeletal joint [UBERON:0000982]: - text: Skeletal joint [UBERON:0000982] - is_a: Skeletal system [UBERON:0001434] - Bone element [UBERON:0001474]: - text: Bone element [UBERON:0001474] - is_a: Skeletal system [UBERON:0001434] - Thoracic segment of trunk [UBERON:0000915]: - text: Thoracic segment of trunk [UBERON:0000915] - Abdomen [UBERON:0000916]: - text: Abdomen [UBERON:0000916] - is_a: Thoracic segment of trunk [UBERON:0000915] - Muscle of abdomen [UBERON:0002378]: - text: Muscle of abdomen [UBERON:0002378] - is_a: Abdomen [UBERON:0000916] - Peritoneum [UBERON:0002358]: - text: Peritoneum [UBERON:0002358] - is_a: Abdomen [UBERON:0000916] - Vascular system [UBERON:0007798]: - text: Vascular system [UBERON:0007798] - Blood vessel [UBERON:0001981]: - text: Blood vessel [UBERON:0001981] - is_a: Vascular system [UBERON:0007798] - Bursa of Fabricius [UBERON:0003903]: - text: Bursa of Fabricius [UBERON:0003903] - is_a: Vascular system [UBERON:0007798] - Gill [UBERON:0002535]: - text: Gill [UBERON:0002535] - is_a: Vascular system [UBERON:0007798] - Heart [UBERON:0000948]: - text: Heart [UBERON:0000948] - is_a: Vascular system [UBERON:0007798] - Pericardium [UBERON:0002407]: - text: Pericardium [UBERON:0002407] - is_a: Vascular system [UBERON:0007798] - Vent (anatomical) [UBERON:2000298]: - text: Vent (anatomical) [UBERON:2000298] - Bird vent [UBERON:0012464]: - text: Bird vent [UBERON:0012464] - is_a: Vent (anatomical) [UBERON:2000298] - Fish vent [GENEPIO:0100902]: - text: Fish vent [GENEPIO:0100902] - is_a: Vent (anatomical) [UBERON:2000298] - anatomical_region menu: - name: anatomical_region menu - permissible_values: - Dorso-lateral region [BSPO:0000080]: - text: Dorso-lateral region [BSPO:0000080] - Exterior anatomical region [BSPO:0000034]: - text: Exterior anatomical region [BSPO:0000034] - Interior anatomical region [BSPO:0000033]: - text: Interior anatomical region [BSPO:0000033] - food_product menu: - name: food_product menu - permissible_values: - Animal feed [ENVO:02000047]: - text: Animal feed [ENVO:02000047] - Blood meal [FOODON:00001564]: - text: Blood meal [FOODON:00001564] - is_a: Animal feed [ENVO:02000047] - Bone meal [ENVO:02000054]: - text: Bone meal [ENVO:02000054] - is_a: Animal feed [ENVO:02000047] - Brassica carinata meal [FOODON:00004310]: - text: Brassica carinata meal [FOODON:00004310] - is_a: Animal feed [ENVO:02000047] - Canola meal [FOODON:00002694]: - text: Canola meal [FOODON:00002694] - is_a: Animal feed [ENVO:02000047] - Compound feed premix [FOODON:00004323]: - text: Compound feed premix [FOODON:00004323] - is_a: Animal feed [ENVO:02000047] - Compound feed premix (medicated) [FOODON:00004324]: - text: Compound feed premix (medicated) [FOODON:00004324] - is_a: Compound feed premix [FOODON:00004323] - Feather meal [FOODON:00003927]: - text: Feather meal [FOODON:00003927] - is_a: Animal feed [ENVO:02000047] - Fish meal [FOODON:03301620]: - text: Fish meal [FOODON:03301620] - is_a: Animal feed [ENVO:02000047] - Lay ration [FOODON:00004286]: - text: Lay ration [FOODON:00004286] - is_a: Animal feed [ENVO:02000047] - Meat and bone meal [FOODON:00002738]: - text: Meat and bone meal [FOODON:00002738] - is_a: Animal feed [ENVO:02000047] - Meat meal [FOODON:00004282]: - text: Meat meal [FOODON:00004282] - is_a: Animal feed [ENVO:02000047] - Pet food [FOODON:00002682]: - text: Pet food [FOODON:00002682] - is_a: Animal feed [ENVO:02000047] - Soybean meal [FOODON:03302757]: - text: Soybean meal [FOODON:03302757] - is_a: Animal feed [ENVO:02000047] - Animal feed ingredient [FOODON:00004322]: - text: Animal feed ingredient [FOODON:00004322] - Dairy food product [FOODON:00001256]: - text: Dairy food product [FOODON:00001256] - Cheese block (whole or parts) [FOODON:03000287]: - text: Cheese block (whole or parts) [FOODON:03000287] - is_a: Dairy food product [FOODON:00001256] - Cow skim milk (powdered) [FOODON:03310016]: - text: Cow skim milk (powdered) [FOODON:03310016] - is_a: Dairy food product [FOODON:00001256] - Milk [UBERON:0001913]: - text: Milk [UBERON:0001913] - is_a: Dairy food product [FOODON:00001256] - Dietary supplement [FOODON:03401298]: - text: Dietary supplement [FOODON:03401298] - Egg or egg component [FOODON:03420194]: - text: Egg or egg component [FOODON:03420194] - Balut [FOODON:03302184]: - text: Balut [FOODON:03302184] - is_a: Egg or egg component [FOODON:03420194] - Egg yolk [UBERON:0007378]: - text: Egg yolk [UBERON:0007378] - is_a: Egg or egg component [FOODON:03420194] - Poultry egg [FOODON:03000414]: - text: Poultry egg [FOODON:03000414] - is_a: Egg or egg component [FOODON:03420194] - Hen egg (whole) [FOODON:03316061]: - text: Hen egg (whole) [FOODON:03316061] - is_a: Poultry egg [FOODON:03000414] - Poultry egg (whole, shell on) [FOODON:03000415]: - text: Poultry egg (whole, shell on) [FOODON:03000415] - is_a: Poultry egg [FOODON:03000414] - Food mixture [FOODON:00004130]: - text: Food mixture [FOODON:00004130] - Food product analog (food subsitute) [FOODON:00001871]: - text: Food product analog (food subsitute) [FOODON:00001871] - Milk substitute [FOODON:03305408]: - text: Milk substitute [FOODON:03305408] - is_a: Food product analog (food subsitute) [FOODON:00001871] - Meat (whole or parts) [FOODON:03317170]: - text: Meat (whole or parts) [FOODON:03317170] - Cutlet [FOODON:00003001]: - text: Cutlet [FOODON:00003001] - is_a: Meat (whole or parts) [FOODON:03317170] - Filet [FOODON:03530144]: - text: Filet [FOODON:03530144] - is_a: Meat (whole or parts) [FOODON:03317170] - Liver (whole, raw) [FOODON:03309772]: - text: Liver (whole, raw) [FOODON:03309772] - is_a: Meat (whole or parts) [FOODON:03317170] - Meat trim [FOODON:03309475]: - text: Meat trim [FOODON:03309475] - is_a: Meat (whole or parts) [FOODON:03317170] - Rib (meat cut) [FOODON:03530023]: - text: Rib (meat cut) [FOODON:03530023] - is_a: Meat (whole or parts) [FOODON:03317170] - Rib chop [FOODON:00004290]: - text: Rib chop [FOODON:00004290] - is_a: Rib (meat cut) [FOODON:03530023] - Shoulder (meat cut) [FOODON:03530043]: - text: Shoulder (meat cut) [FOODON:03530043] - is_a: Meat (whole or parts) [FOODON:03317170] - Grains, cereals, and bakery product (organizational term): - text: Grains, cereals, and bakery product (organizational term) - Bread loaf (whole or parts) [FOODON:03000288]: - text: Bread loaf (whole or parts) [FOODON:03000288] - is_a: Grains, cereals, and bakery product (organizational term) - Breakfast cereal [FOODON:03311075]: - text: Breakfast cereal [FOODON:03311075] - is_a: Grains, cereals, and bakery product (organizational term) - Bulk grain [FOODON:03309390]: - text: Bulk grain [FOODON:03309390] - is_a: Grains, cereals, and bakery product (organizational term) - Oat grain [FOODON:00003429]: - text: Oat grain [FOODON:00003429] - is_a: Grains, cereals, and bakery product (organizational term) - Legume food product [FOODON:00001264]: - text: Legume food product [FOODON:00001264] - Chickpea (whole) [FOODON:03306811]: - text: Chickpea (whole) [FOODON:03306811] - is_a: Legume food product [FOODON:00001264] - Hummus [FOODON:00003049]: - text: Hummus [FOODON:00003049] - is_a: Legume food product [FOODON:00001264] - Soybean (whole or parts) [FOODON:03000245]: - text: Soybean (whole or parts) [FOODON:03000245] - is_a: Legume food product [FOODON:00001264] - Meat, poultry and fish (organizational term): - text: Meat, poultry and fish (organizational term) - Beef (ground or minced) [FOODON:00001282]: - text: Beef (ground or minced) [FOODON:00001282] - is_a: Meat, poultry and fish (organizational term) - Beef (ground or minced, boneless) [FOODON:03000412]: - text: Beef (ground or minced, boneless) [FOODON:03000412] - is_a: Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, extra lean) [FOODON:03000398]: - text: Beef (ground or minced, extra lean) [FOODON:03000398] - is_a: Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, lean) [FOODON:03000394]: - text: Beef (ground or minced, lean) [FOODON:03000394] - is_a: Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, medium) [FOODON:03000402]: - text: Beef (ground or minced, medium) [FOODON:03000402] - is_a: Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, regular) [FOODON:03000406]: - text: Beef (ground or minced, regular) [FOODON:03000406] - is_a: Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, Sirloin) [FOODON:03000408]: - text: Beef (ground or minced, Sirloin) [FOODON:03000408] - is_a: Beef (ground or minced) [FOODON:00001282] - Beef hamburger (dish) [FOODON:00002737]: - text: Beef hamburger (dish) [FOODON:00002737] - is_a: Meat, poultry and fish (organizational term) - Beef shoulder [FOODON:03000377]: - text: Beef shoulder [FOODON:03000377] - is_a: Meat, poultry and fish (organizational term) - Beef shoulder chop [FOODON:03000387]: - text: Beef shoulder chop [FOODON:03000387] - is_a: Beef shoulder [FOODON:03000377] - Beef sirloin chop [FOODON:03000389]: - text: Beef sirloin chop [FOODON:03000389] - is_a: Meat, poultry and fish (organizational term) - Beef stew chunk [FOODON:00004288]: - text: Beef stew chunk [FOODON:00004288] - is_a: Meat, poultry and fish (organizational term) - Beef tenderloin [FOODON:00003302]: - text: Beef tenderloin [FOODON:00003302] - is_a: Meat, poultry and fish (organizational term) - Beef (whole cut or parts) [FOODON:03000333]: - text: Beef (whole cut or parts) [FOODON:03000333] - is_a: Meat, poultry and fish (organizational term) - Brisket [FOODON:03530020]: - text: Brisket [FOODON:03530020] - is_a: Meat, poultry and fish (organizational term) - Chicken breast [FOODON:00002703]: - text: Chicken breast [FOODON:00002703] - is_a: Meat, poultry and fish (organizational term) - Chicken breast (back off) [FOODON:03000385]: - text: Chicken breast (back off) [FOODON:03000385] - is_a: Chicken breast [FOODON:00002703] - Chicken breast (skinless) [FOODON:00003332]: - text: Chicken breast (skinless) [FOODON:00003332] - is_a: Chicken breast [FOODON:00002703] - Chicken breast (with skin) [FOODON:03000374]: - text: Chicken breast (with skin) [FOODON:03000374] - is_a: Chicken breast [FOODON:00002703] - Chicken breast (skinless, boneless) [FOODON:00003364]: - text: Chicken breast (skinless, boneless) [FOODON:00003364] - is_a: Chicken breast [FOODON:00002703] - Chicken breast cutlet [FOODON:00004308]: - text: Chicken breast cutlet [FOODON:00004308] - is_a: Chicken breast [FOODON:00002703] - Chicken drumstick [FOODON:00002716]: - text: Chicken drumstick [FOODON:00002716] - is_a: Meat, poultry and fish (organizational term) - Chicken drumstick (skinless) [FOODON:03000366]: - text: Chicken drumstick (skinless) [FOODON:03000366] - is_a: Chicken drumstick [FOODON:00002716] - Chicken drumstick (with skin) [FOODON:03000368]: - text: Chicken drumstick (with skin) [FOODON:03000368] - is_a: Chicken drumstick [FOODON:00002716] - Chicken meat [FOODON:00001040]: - text: Chicken meat [FOODON:00001040] - is_a: Meat, poultry and fish (organizational term) - Chicken meat (ground or minced) [FOODON:03311826]: - text: Chicken meat (ground or minced) [FOODON:03311826] - is_a: Chicken meat [FOODON:00001040] - Chicken meat (ground or minced, lean) [FOODON:03000392]: - text: Chicken meat (ground or minced, lean) [FOODON:03000392] - is_a: Chicken meat [FOODON:00001040] - Chicken meat (ground or minced, extra lean) [FOODON:03000396]: - text: Chicken meat (ground or minced, extra lean) [FOODON:03000396] - is_a: Chicken meat [FOODON:00001040] - Chicken meat (ground or minced, medium) [FOODON:03000400]: - text: Chicken meat (ground or minced, medium) [FOODON:03000400] - is_a: Chicken meat [FOODON:00001040] - Chicken meat (ground or minced, regular) [FOODON:03000404]: - text: Chicken meat (ground or minced, regular) [FOODON:03000404] - is_a: Chicken meat [FOODON:00001040] - Chicken meat (ground or minced, boneless) [FOODON:03000410]: - text: Chicken meat (ground or minced, boneless) [FOODON:03000410] - is_a: Chicken meat [FOODON:00001040] - Chicken nugget [FOODON:00002672]: - text: Chicken nugget [FOODON:00002672] - is_a: Meat, poultry and fish (organizational term) - Chicken thigh: - text: Chicken thigh - is_a: Meat, poultry and fish (organizational term) - Chicken thigh (skinless) [FOODON:00003331]: - text: Chicken thigh (skinless) [FOODON:00003331] - is_a: Chicken thigh - Chicken thigh (skinless, with bone): - text: Chicken thigh (skinless, with bone) - is_a: Chicken thigh - Chicken thigh (skinless, boneless) [FOODON:03000417]: - text: Chicken thigh (skinless, boneless) [FOODON:03000417] - is_a: Chicken thigh - Chicken upper thigh [FOODON:03000381]: - text: Chicken upper thigh [FOODON:03000381] - is_a: Chicken thigh (skinless, boneless) [FOODON:03000417] - Chicken upper thigh (with skin) [FOODON:03000383]: - text: Chicken upper thigh (with skin) [FOODON:03000383] - is_a: Chicken upper thigh [FOODON:03000381] - Chicken thigh (with skin) [FOODON:00003330]: - text: Chicken thigh (with skin) [FOODON:00003330] - is_a: Chicken thigh - Chicken thigh (with skin, with bone) [FOODON_00003363]: - text: Chicken thigh (with skin, with bone) [FOODON_00003363] - is_a: Chicken thigh - Chicken wing [FOODON:00002674]: - text: Chicken wing [FOODON:00002674] - is_a: Meat, poultry and fish (organizational term) - Fish food product [FOODON:00001248]: - text: Fish food product [FOODON:00001248] - is_a: Meat, poultry and fish (organizational term) - Fish steak [FOODON:00002986]: - text: Fish steak [FOODON:00002986] - is_a: Fish food product [FOODON:00001248] - Ham food product [FOODON:00002502]: - text: Ham food product [FOODON:00002502] - is_a: Meat, poultry and fish (organizational term) - Head cheese [FOODON:03315658]: - text: Head cheese [FOODON:03315658] - is_a: Meat, poultry and fish (organizational term) - Lamb [FOODON:03411669]: - text: Lamb [FOODON:03411669] - is_a: Meat, poultry and fish (organizational term) - Meat strip [FOODON:00004285]: - text: Meat strip [FOODON:00004285] - is_a: Meat, poultry and fish (organizational term) - Mutton [FOODON:00002912]: - text: Mutton [FOODON:00002912] - is_a: Meat, poultry and fish (organizational term) - Pork chop [FOODON:00001049]: - text: Pork chop [FOODON:00001049] - is_a: Meat, poultry and fish (organizational term) - Pork meat (ground or minced) [FOODON:03309969]: - text: Pork meat (ground or minced) [FOODON:03309969] - is_a: Meat, poultry and fish (organizational term) - Pork meat (ground or minced, boneless) [FOODON:03000413]: - text: Pork meat (ground or minced, boneless) [FOODON:03000413] - is_a: Pork meat (ground or minced) [FOODON:03309969] - Pork meat (ground or minced, extra lean) [FOODON:03000399]: - text: Pork meat (ground or minced, extra lean) [FOODON:03000399] - is_a: Pork meat (ground or minced) [FOODON:03309969] - Pork meat (ground or minced, lean) [FOODON:03000395]: - text: Pork meat (ground or minced, lean) [FOODON:03000395] - is_a: Pork meat (ground or minced) [FOODON:03309969] - Pork meat (ground or minced, medium) [FOODON:03000403]: - text: Pork meat (ground or minced, medium) [FOODON:03000403] - is_a: Pork meat (ground or minced) [FOODON:03309969] - Pork meat (ground or minced, regular) [FOODON:03000407]: - text: Pork meat (ground or minced, regular) [FOODON:03000407] - is_a: Pork meat (ground or minced) [FOODON:03309969] - Pork meat (ground or minced, Sirloin) [FOODON:03000409]: - text: Pork meat (ground or minced, Sirloin) [FOODON:03000409] - is_a: Pork meat (ground or minced) [FOODON:03309969] - Pork shoulder [FOODON:03000376]: - text: Pork shoulder [FOODON:03000376] - is_a: Meat, poultry and fish (organizational term) - Pork shoulder chop [FOODON:03000388]: - text: Pork shoulder chop [FOODON:03000388] - is_a: Pork shoulder [FOODON:03000376] - Pork sirloin chop [FOODON:03000390]: - text: Pork sirloin chop [FOODON:03000390] - is_a: Meat, poultry and fish (organizational term) - Pork steak [FOODON:00003148]: - text: Pork steak [FOODON:00003148] - is_a: Meat, poultry and fish (organizational term) - Pork tenderloin [FOODON:03000416]: - text: Pork tenderloin [FOODON:03000416] - is_a: Meat, poultry and fish (organizational term) - Poultry meat [FOODON:03315883]: - text: Poultry meat [FOODON:03315883] - is_a: Meat, poultry and fish (organizational term) - Leg (poultry meat cut) [FOODON:03530159]: - text: Leg (poultry meat cut) [FOODON:03530159] - is_a: Poultry meat [FOODON:03315883] - Poultry drumstick [FOODON:00003469]: - text: Poultry drumstick [FOODON:00003469] - is_a: Leg (poultry meat cut) [FOODON:03530159] - Neck (poultry meat cut) [FOODON:03530294]: - text: Neck (poultry meat cut) [FOODON:03530294] - is_a: Poultry meat [FOODON:03315883] - Thigh (poultry meat cut) [FOODON:03530160]: - text: Thigh (poultry meat cut) [FOODON:03530160] - is_a: Poultry meat [FOODON:03315883] - Wing (poultry meat cut) [FOODON:03530157]: - text: Wing (poultry meat cut) [FOODON:03530157] - is_a: Poultry meat [FOODON:03315883] - Sausage (whole) [FOODON:03315904]: - text: Sausage (whole) [FOODON:03315904] - is_a: Meat, poultry and fish (organizational term) - Pepperoni [FOODON:03311003]: - text: Pepperoni [FOODON:03311003] - is_a: Sausage (whole) [FOODON:03315904] - Salami [FOODON:03312067]: - text: Salami [FOODON:03312067] - is_a: Sausage (whole) [FOODON:03315904] - Shellfish [FOODON:03411433]: - text: Shellfish [FOODON:03411433] - is_a: Meat, poultry and fish (organizational term) - Shrimp [FOODON:03411237]: - text: Shrimp [FOODON:03411237] - is_a: Meat, poultry and fish (organizational term) - Turkey breast [FOODON:00002690]: - text: Turkey breast [FOODON:00002690] - is_a: Meat, poultry and fish (organizational term) - Turkey breast (back off) [FOODON:03000386]: - text: Turkey breast (back off) [FOODON:03000386] - is_a: Turkey breast [FOODON:00002690] - Turkey breast (skinless) [FOODON:03000372]: - text: Turkey breast (skinless) [FOODON:03000372] - is_a: Turkey breast [FOODON:00002690] - Turkey breast (skinless, boneless) [FOODON:03000373]: - text: Turkey breast (skinless, boneless) [FOODON:03000373] - is_a: Turkey breast [FOODON:00002690] - Turkey breast (with skin) [FOODON:03000375]: - text: Turkey breast (with skin) [FOODON:03000375] - is_a: Turkey breast [FOODON:00002690] - Turkey drumstick [FOODON:03000365]: - text: Turkey drumstick [FOODON:03000365] - is_a: Meat, poultry and fish (organizational term) - Turkey drumstick (skinless) [FOODON:03000367]: - text: Turkey drumstick (skinless) [FOODON:03000367] - is_a: Turkey drumstick [FOODON:03000365] - Turkey drumstick (with skin) [FOODON:03000369]: - text: Turkey drumstick (with skin) [FOODON:03000369] - is_a: Turkey drumstick [FOODON:03000365] - Turkey meat [FOODON:00001286]: - text: Turkey meat [FOODON:00001286] - is_a: Meat, poultry and fish (organizational term) - Turkey meat (ground or minced) [FOODON:00002714]: - text: Turkey meat (ground or minced) [FOODON:00002714] - is_a: Turkey meat [FOODON:00001286] - Turkey meat (ground or minced, lean) [FOODON:03000393]: - text: Turkey meat (ground or minced, lean) [FOODON:03000393] - is_a: Turkey meat [FOODON:00001286] - Turkey meat (ground or minced, extra lean) [FOODON:03000397]: - text: Turkey meat (ground or minced, extra lean) [FOODON:03000397] - is_a: Turkey meat [FOODON:00001286] - Turkey meat (ground or minced, medium) [FOODON:03000401]: - text: Turkey meat (ground or minced, medium) [FOODON:03000401] - is_a: Turkey meat [FOODON:00001286] - Turkey meat (ground or minced, regular) [FOODON:03000405]: - text: Turkey meat (ground or minced, regular) [FOODON:03000405] - is_a: Turkey meat [FOODON:00001286] - Turkey meat (ground or minced, boneless) [FOODON:03000411]: - text: Turkey meat (ground or minced, boneless) [FOODON:03000411] - is_a: Turkey meat [FOODON:00001286] - Turkey thigh [FOODON:00003325]: - text: Turkey thigh [FOODON:00003325] - is_a: Meat, poultry and fish (organizational term) - Turkey thigh (skinless) [FOODON:00003329]: - text: Turkey thigh (skinless) [FOODON:00003329] - is_a: Turkey thigh [FOODON:00003325] - Turkey thigh (skinless, boneless) [FOODON:03000370]: - text: Turkey thigh (skinless, boneless) [FOODON:03000370] - is_a: Turkey thigh [FOODON:00003325] - Turkey thigh (with skin) [FOODON:00003328]: - text: Turkey thigh (with skin) [FOODON:00003328] - is_a: Turkey thigh [FOODON:00003325] - Turkey upper thigh [FOODON:03000382]: - text: Turkey upper thigh [FOODON:03000382] - is_a: Turkey thigh (with skin) [FOODON:00003328] - Turkey upper thigh (with skin) [FOODON:03000384]: - text: Turkey upper thigh (with skin) [FOODON:03000384] - is_a: Turkey thigh (with skin) [FOODON:00003328] - Turkey wing [FOODON:03000371]: - text: Turkey wing [FOODON:03000371] - is_a: Meat, poultry and fish (organizational term) - Veal [FOODON:00003083]: - text: Veal [FOODON:00003083] - is_a: Meat, poultry and fish (organizational term) - Formula fed veal [FOODON:000039111]: - text: Formula fed veal [FOODON:000039111] - is_a: Veal [FOODON:00003083] - Grain-fed veal [FOODON:00004280]: - text: Grain-fed veal [FOODON:00004280] - is_a: Veal [FOODON:00003083] - Microbial food product [FOODON:00001145]: - text: Microbial food product [FOODON:00001145] - Yeast [FOODON:03411345]: - text: Yeast [FOODON:03411345] - is_a: Microbial food product [FOODON:00001145] - Nuts and seed products: - text: Nuts and seed products - Almond (whole or parts) [FOODON:03000218]: - text: Almond (whole or parts) [FOODON:03000218] - is_a: Nuts and seed products - Almond (whole) [FOODON:00003523]: - text: Almond (whole) [FOODON:00003523] - is_a: Almond (whole or parts) [FOODON:03000218] - Chia seed powder [FOODON:00003925]: - text: Chia seed powder [FOODON:00003925] - is_a: Nuts and seed products - Chia seed (whole or parts) [FOODON:03000241]: - text: Chia seed (whole or parts) [FOODON:03000241] - is_a: Nuts and seed products - Flaxseed powder [FOODON:00004276]: - text: Flaxseed powder [FOODON:00004276] - is_a: Nuts and seed products - Hazelnut [FOODON:00002933]: - text: Hazelnut [FOODON:00002933] - is_a: Nuts and seed products - Nut (whole or part) [FOODON:03306632]: - text: Nut (whole or part) [FOODON:03306632] - is_a: Nuts and seed products - Peanut butter [FOODON:03306867]: - text: Peanut butter [FOODON:03306867] - is_a: Nuts and seed products - Sesame seed [FOODON:03310306]: - text: Sesame seed [FOODON:03310306] - is_a: Nuts and seed products - Tahini [FOODON:00003855]: - text: Tahini [FOODON:00003855] - is_a: Nuts and seed products - Walnut (whole or parts) [FOODON:03316466]: - text: Walnut (whole or parts) [FOODON:03316466] - is_a: Nuts and seed products - Prepared food product [FOODON:00001180]: - text: Prepared food product [FOODON:00001180] - Condiment [FOODON:03315708]: - text: Condiment [FOODON:03315708] - is_a: Prepared food product [FOODON:00001180] - Confectionery food product [FOODON:00001149]: - text: Confectionery food product [FOODON:00001149] - is_a: Prepared food product [FOODON:00001180] - Snack food [FOODON:03315013]: - text: Snack food [FOODON:03315013] - is_a: Prepared food product [FOODON:00001180] - Produce [FOODON:03305145]: - text: Produce [FOODON:03305145] - Apple (whole or parts) [FOODON:03310788]: - text: Apple (whole or parts) [FOODON:03310788] - is_a: Produce [FOODON:03305145] - Apple (whole) [FOODON:00002473]: - text: Apple (whole) [FOODON:00002473] - is_a: Apple (whole or parts) [FOODON:03310788] - Arugula greens (raw) [FOODON:00002426]: - text: Arugula greens (raw) [FOODON:00002426] - is_a: Produce [FOODON:03305145] - Avocado [FOODON:00003600]: - text: Avocado [FOODON:00003600] - is_a: Produce [FOODON:03305145] - Cantaloupe (whole or parts) [FOODON:03000243]: - text: Cantaloupe (whole or parts) [FOODON:03000243] - is_a: Produce [FOODON:03305145] - Chili pepper [FOODON:03315873]: - text: Chili pepper [FOODON:03315873] - is_a: Produce [FOODON:03305145] - Coconut (whole or parts) [FOODON:03309861]: - text: Coconut (whole or parts) [FOODON:03309861] - is_a: Produce [FOODON:03305145] - Corn cob (whole or parts) [FOODON:03310791]: - text: Corn cob (whole or parts) [FOODON:03310791] - is_a: Produce [FOODON:03305145] - Cucumber (whole or parts) [FOODON:03000229]: - text: Cucumber (whole or parts) [FOODON:03000229] - is_a: Produce [FOODON:03305145] - Fruit [PO:0009001]: - text: Fruit [PO:0009001] - is_a: Produce [FOODON:03305145] - Goji berry [FOODON:00004360]: - text: Goji berry [FOODON:00004360] - is_a: Produce [FOODON:03305145] - Greens (raw) [FOODON:03310765]: - text: Greens (raw) [FOODON:03310765] - is_a: Produce [FOODON:03305145] - Kale leaf (whole or parts) [FOODON:03000236]: - text: Kale leaf (whole or parts) [FOODON:03000236] - is_a: Produce [FOODON:03305145] - Lettuce head (whole or parts) [FOODON:03000239]: - text: Lettuce head (whole or parts) [FOODON:03000239] - is_a: Produce [FOODON:03305145] - Mango (whole or parts) [FOODON:03000217]: - text: Mango (whole or parts) [FOODON:03000217] - is_a: Produce [FOODON:03305145] - Mushroom (fruitbody) [FOODON:00003528]: - text: Mushroom (fruitbody) [FOODON:00003528] - is_a: Produce [FOODON:03305145] - Papaya (whole or parts) [FOODON:03000228]: - text: Papaya (whole or parts) [FOODON:03000228] - is_a: Produce [FOODON:03305145] - Pattypan squash (whole or parts) [FOODON:03000232]: - text: Pattypan squash (whole or parts) [FOODON:03000232] - is_a: Produce [FOODON:03305145] - Peach [FOODON:00002485]: - text: Peach [FOODON:00002485] - is_a: Produce [FOODON:03305145] - Pepper (whole or parts) [FOODON:03000249]: - text: Pepper (whole or parts) [FOODON:03000249] - is_a: Produce [FOODON:03305145] - Potato [FOODON:03315354]: - text: Potato [FOODON:03315354] - is_a: Produce [FOODON:03305145] - Salad [FOODON:03316042]: - text: Salad [FOODON:03316042] - is_a: Produce [FOODON:03305145] - Scallion (whole or parts) [FOODON:03000250]: - text: Scallion (whole or parts) [FOODON:03000250] - is_a: Produce [FOODON:03305145] - Spinach (whole or parts) [FOODON:03000221]: - text: Spinach (whole or parts) [FOODON:03000221] - is_a: Produce [FOODON:03305145] - Sprout [FOODON:03420183]: - text: Sprout [FOODON:03420183] - is_a: Produce [FOODON:03305145] - Germinated or sprouted seed [FOODON:03420102]: - text: Germinated or sprouted seed [FOODON:03420102] - is_a: Sprout [FOODON:03420183] - Alfalfa sprout [FOODON:00002670]: - text: Alfalfa sprout [FOODON:00002670] - is_a: Germinated or sprouted seed [FOODON:03420102] - Bean sprout [FOODON:00002576]: - text: Bean sprout [FOODON:00002576] - is_a: Germinated or sprouted seed [FOODON:03420102] - Chia sprout [FOODON:00004284]: - text: Chia sprout [FOODON:00004284] - is_a: Germinated or sprouted seed [FOODON:03420102] - Mixed sprouts [FOODON:03000182]: - text: Mixed sprouts [FOODON:03000182] - is_a: Germinated or sprouted seed [FOODON:03420102] - Mung bean sprout [FOODON:03301446]: - text: Mung bean sprout [FOODON:03301446] - is_a: Germinated or sprouted seed [FOODON:03420102] - Tomato (whole or parts) [FOODON:03000227]: - text: Tomato (whole or parts) [FOODON:03000227] - is_a: Produce [FOODON:03305145] - Vegetable (whole or parts) [FOODON:03315308]: - text: Vegetable (whole or parts) [FOODON:03315308] - is_a: Produce [FOODON:03305145] - Spice or herb [FOODON:00001242]: - text: Spice or herb [FOODON:00001242] - Basil (whole or parts) [FOODON:03000233]: - text: Basil (whole or parts) [FOODON:03000233] - is_a: Spice or herb [FOODON:00001242] - Black pepper (whole or parts) [FOODON:03000242]: - text: Black pepper (whole or parts) [FOODON:03000242] - is_a: Spice or herb [FOODON:00001242] - Cardamom (whole or parts) [FOODON:03000246]: - text: Cardamom (whole or parts) [FOODON:03000246] - is_a: Spice or herb [FOODON:00001242] - Chive leaf (whole or parts) [FOODON:03000240]: - text: Chive leaf (whole or parts) [FOODON:03000240] - is_a: Spice or herb [FOODON:00001242] - Coriander powder [FOODON:00004274]: - text: Coriander powder [FOODON:00004274] - is_a: Spice or herb [FOODON:00001242] - Coriander seed (whole or parts) [FOODON:03000224]: - text: Coriander seed (whole or parts) [FOODON:03000224] - is_a: Spice or herb [FOODON:00001242] - Cumin powder [FOODON:00004275]: - text: Cumin powder [FOODON:00004275] - is_a: Spice or herb [FOODON:00001242] - Cumin seed (whole) [FOODON:00003396]: - text: Cumin seed (whole) [FOODON:00003396] - is_a: Spice or herb [FOODON:00001242] - Black cumin seed (whole or parts) [FOODON:03000247]: - text: Black cumin seed (whole or parts) [FOODON:03000247] - is_a: Cumin seed (whole) [FOODON:00003396] - Curry leaf (whole or parts) [FOODON:03000225]: - text: Curry leaf (whole or parts) [FOODON:03000225] - is_a: Spice or herb [FOODON:00001242] - Curry powder [FOODON:03301842]: - text: Curry powder [FOODON:03301842] - is_a: Spice or herb [FOODON:00001242] - Dill spice [FOODON:03310090]: - text: Dill spice [FOODON:03310090] - is_a: Spice or herb [FOODON:00001242] - Fennel (whole or parts) [FOODON:03000244]: - text: Fennel (whole or parts) [FOODON:03000244] - is_a: Spice or herb [FOODON:00001242] - Garlic powder [FOODON:03301844]: - text: Garlic powder [FOODON:03301844] - is_a: Spice or herb [FOODON:00001242] - Ginger root (whole or parts) [FOODON:03000220]: - text: Ginger root (whole or parts) [FOODON:03000220] - is_a: Spice or herb [FOODON:00001242] - Mint leaf (whole or parts) [FOODON:03000238]: - text: Mint leaf (whole or parts) [FOODON:03000238] - is_a: Spice or herb [FOODON:00001242] - Oregano (whole or parts) [FOODON:03000226]: - text: Oregano (whole or parts) [FOODON:03000226] - is_a: Spice or herb [FOODON:00001242] - Paprika [FOODON:03301105]: - text: Paprika [FOODON:03301105] - is_a: Spice or herb [FOODON:00001242] - Parsley leaf (whole or parts) [FOODON:03000231]: - text: Parsley leaf (whole or parts) [FOODON:03000231] - is_a: Spice or herb [FOODON:00001242] - Pepper (ground) [FOODON:03301526]: - text: Pepper (ground) [FOODON:03301526] - is_a: Spice or herb [FOODON:00001242] - Rasam powder [FOODON:00004277]: - text: Rasam powder [FOODON:00004277] - is_a: Spice or herb [FOODON:00001242] - Sage [FOODON:03301560]: - text: Sage [FOODON:03301560] - is_a: Spice or herb [FOODON:00001242] - Turmeric (ground) [FOODON:03310841]: - text: Turmeric (ground) [FOODON:03310841] - is_a: Spice or herb [FOODON:00001242] - Spice [FOODON:03303380]: - text: Spice [FOODON:03303380] - is_a: Spice or herb [FOODON:00001242] - White peppercorn (whole or parts) [FOODON:03000251]: - text: White peppercorn (whole or parts) [FOODON:03000251] - is_a: Spice or herb [FOODON:00001242] - food_product_properties menu: - name: food_product_properties menu - permissible_values: - Food (canned) [FOODON:00002418]: - text: Food (canned) [FOODON:00002418] - Food (cooked) [FOODON:00001181]: - text: Food (cooked) [FOODON:00001181] - Food (cut) [FOODON:00004291]: - text: Food (cut) [FOODON:00004291] - Food (chopped) [FOODON:00002777]: - text: Food (chopped) [FOODON:00002777] - is_a: Food (cut) [FOODON:00004291] - Food (cubed) [FOODON:00004278]: - text: Food (cubed) [FOODON:00004278] - is_a: Food (cut) [FOODON:00004291] - Food (dried) [FOODON:03307539]: - text: Food (dried) [FOODON:03307539] - Food (fresh) [FOODON:00002457]: - text: Food (fresh) [FOODON:00002457] - Food (frozen) [FOODON:03302148]: - text: Food (frozen) [FOODON:03302148] - Food (raw) [FOODON:03311126]: - text: Food (raw) [FOODON:03311126] - Food (unseasoned) [FOODON:00004287]: - text: Food (unseasoned) [FOODON:00004287] - Italian-style food product [FOODON:00004321]: - text: Italian-style food product [FOODON:00004321] - Meat (boneless) [FOODON:00003467]: - text: Meat (boneless) [FOODON:00003467] - Meat (skinless) [FOODON:00003468]: - text: Meat (skinless) [FOODON:00003468] - Meat (with bone) [FOODON:02010116]: - text: Meat (with bone) [FOODON:02010116] - Meat (with skin) [FOODON:02010111]: - text: Meat (with skin) [FOODON:02010111] - Organic food claim or use [FOODON:03510128]: - text: Organic food claim or use [FOODON:03510128] - Ready-to-eat (RTE) [FOODON:03316636]: - text: Ready-to-eat (RTE) [FOODON:03316636] - Soft [PATO:0000387]: - text: Soft [PATO:0000387] - animal_source_of_food menu: - name: animal_source_of_food menu - permissible_values: - Cow [NCBITaxon:9913]: - text: Cow [NCBITaxon:9913] - Fish [FOODON:03411222]: - text: Fish [FOODON:03411222] - Pig [NCBITaxon:9823]: - text: Pig [NCBITaxon:9823] - Poultry [FOODON:03411563]: - text: Poultry [FOODON:03411563] - Chicken [NCBITaxon:9031]: - text: Chicken [NCBITaxon:9031] - is_a: Poultry [FOODON:03411563] - Turkey [NCBITaxon:9103]: - text: Turkey [NCBITaxon:9103] - is_a: Poultry [FOODON:03411563] - Sheep [NCBITaxon:9940]: - text: Sheep [NCBITaxon:9940] - food_product_production_stream menu: - name: food_product_production_stream menu - permissible_values: - Beef cattle production stream [FOODON:03000452]: - text: Beef cattle production stream [FOODON:03000452] - Broiler chicken production stream [FOODON:03000455]: - text: Broiler chicken production stream [FOODON:03000455] - Dairy cattle production stream [FOODON:03000453]: - text: Dairy cattle production stream [FOODON:03000453] - Egg production stream [FOODON:03000458]: - text: Egg production stream [FOODON:03000458] - Layer chicken production stream [FOODON:03000456]: - text: Layer chicken production stream [FOODON:03000456] - Meat production stream [FOODON:03000460]: - text: Meat production stream [FOODON:03000460] - Veal meat production stream [FOODON:03000461]: - text: Veal meat production stream [FOODON:03000461] - is_a: Meat production stream [FOODON:03000460] - Milk production stream [FOODON:03000459]: - text: Milk production stream [FOODON:03000459] - collection_device menu: - name: collection_device menu - permissible_values: - Auger (earth auger) [AGRO:00000405]: - text: Auger (earth auger) [AGRO:00000405] - Box corer [GENEPIO:0100928]: - text: Box corer [GENEPIO:0100928] - Container [OBI:0000967]: - text: Container [OBI:0000967] - Bag [GSSO:008558]: - text: Bag [GSSO:008558] - is_a: Container [OBI:0000967] - Whirlpak sampling bag [GENEPIO:0002122]: - text: Whirlpak sampling bag [GENEPIO:0002122] - is_a: Bag [GSSO:008558] - Bottle [FOODON:03490214]: - text: Bottle [FOODON:03490214] - is_a: Container [OBI:0000967] - Vial [OBI:0000522]: - text: Vial [OBI:0000522] - is_a: Container [OBI:0000967] - Culture plate [GENEPIO:0004318]: - text: Culture plate [GENEPIO:0004318] - Petri dish [NCIT:C96141]: - text: Petri dish [NCIT:C96141] - is_a: Culture plate [GENEPIO:0004318] - Filter [GENEPIO:0100103]: - text: Filter [GENEPIO:0100103] - PONAR grab sampler [GENEPIO:0100929]: - text: PONAR grab sampler [GENEPIO:0100929] - Scoop [GENEPIO:0002125]: - text: Scoop [GENEPIO:0002125] - Soil sample probe [GENEPIO:0100930]: - text: Soil sample probe [GENEPIO:0100930] - Spatula [NCIT:C149941]: - text: Spatula [NCIT:C149941] - Sponge [OBI:0002819]: - text: Sponge [OBI:0002819] - Swab [GENEPIO:0100027]: - text: Swab [GENEPIO:0100027] - is_a: Sponge [OBI:0002819] - Drag swab [OBI:0002822]: - text: Drag swab [OBI:0002822] - is_a: Swab [GENEPIO:0100027] - Surface wipe [OBI:0002824]: - text: Surface wipe [OBI:0002824] - is_a: Swab [GENEPIO:0100027] - Tube [UBERON:0000025]: - text: Tube [UBERON:0000025] - Vacuum device [GENEPIO:0002127]: - text: Vacuum device [GENEPIO:0002127] - Vacutainer [OBIB:0000032]: - text: Vacutainer [OBIB:0000032] - is_a: Vacuum device [GENEPIO:0002127] - collection_method menu: - name: collection_method menu - permissible_values: - Aspiration [HP:0002835]: - text: Aspiration [HP:0002835] - Biopsy [OBI:0002650]: - text: Biopsy [OBI:0002650] - Fecal grab [GENEPIO:0004326]: - text: Fecal grab [GENEPIO:0004326] - Filtration [OBI:0302885]: - text: Filtration [OBI:0302885] - Air filtration [GENEPIO:0100031]: - text: Air filtration [GENEPIO:0100031] - is_a: Filtration [OBI:0302885] - Water filtration [GENEPIO:0100931]: - text: Water filtration [GENEPIO:0100931] - is_a: Filtration [OBI:0302885] - Lavage [OBI:0600044]: - text: Lavage [OBI:0600044] - Bronchoalveolar lavage [GENEPIO:0100032]: - text: Bronchoalveolar lavage [GENEPIO:0100032] - is_a: Lavage [OBI:0600044] - Gastric lavage [GENEPIO:0100033]: - text: Gastric lavage [GENEPIO:0100033] - is_a: Lavage [OBI:0600044] - Necropsy [MMO:0000344]: - text: Necropsy [MMO:0000344] - Phlebotomy [NCIT:C28221]: - text: Phlebotomy [NCIT:C28221] - Rinsing for specimen collection [GENEPIO_0002116]: - text: Rinsing for specimen collection [GENEPIO_0002116] - Scooping [GENEPIO:0100932]: - text: Scooping [GENEPIO:0100932] - Sediment collection [GENEPIO:0100933]: - text: Sediment collection [GENEPIO:0100933] - Soil coring [GENEPIO:0100934]: - text: Soil coring [GENEPIO:0100934] - food_packaging menu: - name: food_packaging menu - permissible_values: - Bag, sack or pouch [FOODON:03490197]: - text: Bag, sack or pouch [FOODON:03490197] - Paper bag, sack or pouch [FOODON:03490120]: - text: Paper bag, sack or pouch [FOODON:03490120] - is_a: Bag, sack or pouch [FOODON:03490197] - Plastic bag, sack or pouch [FOODON:03490166]: - text: Plastic bag, sack or pouch [FOODON:03490166] - is_a: Bag, sack or pouch [FOODON:03490197] - Plastic shrink wrap [FOODON:03490137]: - text: Plastic shrink wrap [FOODON:03490137] - is_a: Plastic bag, sack or pouch [FOODON:03490166] - Plastic wrapper [FOODON:03490128]: - text: Plastic wrapper [FOODON:03490128] - is_a: Plastic bag, sack or pouch [FOODON:03490166] - Bottle or jar [FOODON:03490203]: - text: Bottle or jar [FOODON:03490203] - Can (container) [FOODON:03490204]: - text: Can (container) [FOODON:03490204] - Paper container, treated [FOODON:03490330]: - text: Paper container, treated [FOODON:03490330] - Paper container, untreated [FOODON:03490334]: - text: Paper container, untreated [FOODON:03490334] - Plastic tray or pan [FOODON:03490126]: - text: Plastic tray or pan [FOODON:03490126] - host (common name) menu: - name: host (common name) menu - permissible_values: - Bird [NCBITaxon:8782]: - text: Bird [NCBITaxon:8782] - Chicken [NCBITaxon:9031]: - text: Chicken [NCBITaxon:9031] - is_a: Bird [NCBITaxon:8782] - Seabird [FOODON:00004504]: - text: Seabird [FOODON:00004504] - is_a: Bird [NCBITaxon:8782] - Cormorant [NCBITaxon:9206]: - text: Cormorant [NCBITaxon:9206] - is_a: Seabird [FOODON:00004504] - Double Crested Cormorant [NCBITaxon:56069]: - text: Double Crested Cormorant [NCBITaxon:56069] - is_a: Cormorant [NCBITaxon:9206] - Crane [NCBITaxon:9109]: - text: Crane [NCBITaxon:9109] - is_a: Seabird [FOODON:00004504] - Whooping Crane [NCBITaxon:9117]: - text: Whooping Crane [NCBITaxon:9117] - is_a: Crane [NCBITaxon:9109] - Gull (Seagull) [NCBITaxon:8911]: - text: Gull (Seagull) [NCBITaxon:8911] - is_a: Seabird [FOODON:00004504] - Glaucous-winged Gull [NCBITaxon:119606]: - text: Glaucous-winged Gull [NCBITaxon:119606] - is_a: Gull (Seagull) [NCBITaxon:8911] - Great Black-backed Gull [NCBITaxon:8912]: - text: Great Black-backed Gull [NCBITaxon:8912] - is_a: Gull (Seagull) [NCBITaxon:8911] - Herring Gull [NCBITaxon:35669]: - text: Herring Gull [NCBITaxon:35669] - is_a: Gull (Seagull) [NCBITaxon:8911] - Ring-billed Gull [NCBITaxon:126683]: - text: Ring-billed Gull [NCBITaxon:126683] - is_a: Gull (Seagull) [NCBITaxon:8911] - Eider [NCBITaxon:50366]: - text: Eider [NCBITaxon:50366] - is_a: Seabird [FOODON:00004504] - Common Eider [NCBITaxon:76058]: - text: Common Eider [NCBITaxon:76058] - is_a: Eider [NCBITaxon:50366] - Turkey [NCBITaxon:9103]: - text: Turkey [NCBITaxon:9103] - is_a: Bird [NCBITaxon:8782] - Fish [FOODON:03411222]: - text: Fish [FOODON:03411222] - Rainbow Trout [NCBITaxon:8022]: - text: Rainbow Trout [NCBITaxon:8022] - is_a: Fish [FOODON:03411222] - Salmon [FOODON:00003473]: - text: Salmon [FOODON:00003473] - is_a: Fish [FOODON:03411222] - Atlantic Salmon [NCBITaxon:8030]: - text: Atlantic Salmon [NCBITaxon:8030] - is_a: Salmon [FOODON:00003473] - Chinook salmon [NCBITaxon:74940]: - text: Chinook salmon [NCBITaxon:74940] - is_a: Salmon [FOODON:00003473] - Mammal [FOODON:03411134]: - text: Mammal [FOODON:03411134] - Companion animal [FOODON:03000300]: - text: Companion animal [FOODON:03000300] - is_a: Mammal [FOODON:03411134] - Cow [NCBITaxon:9913]: - text: Cow [NCBITaxon:9913] - is_a: Mammal [FOODON:03411134] - Human [NCBITaxon:9606]: - text: Human [NCBITaxon:9606] - is_a: Mammal [FOODON:03411134] - Pig [NCBITaxon:9823]: - text: Pig [NCBITaxon:9823] - is_a: Mammal [FOODON:03411134] - Sheep [NCBITaxon:9940]: - text: Sheep [NCBITaxon:9940] - is_a: Mammal [FOODON:03411134] - Shellfish [FOODON:03411433]: - text: Shellfish [FOODON:03411433] - Atlantic Lobster [NCBITaxon:6706]: - text: Atlantic Lobster [NCBITaxon:6706] - is_a: Shellfish [FOODON:03411433] - Atlantic Oyster [NCBITaxon:6565]: - text: Atlantic Oyster [NCBITaxon:6565] - is_a: Shellfish [FOODON:03411433] - Blue Mussel [NCBITaxon:6550]: - text: Blue Mussel [NCBITaxon:6550] - is_a: Shellfish [FOODON:03411433] - host (scientific name) menu: - name: host (scientific name) menu - permissible_values: - Bos taurus [NCBITaxon:9913]: - text: Bos taurus [NCBITaxon:9913] - Crassostrea virginica [NCBITaxon:6565]: - text: Crassostrea virginica [NCBITaxon:6565] - Gallus gallus [NCBITaxon:9031]: - text: Gallus gallus [NCBITaxon:9031] - Grus americana [NCBITaxon:9117]: - text: Grus americana [NCBITaxon:9117] - Homarus americanus [NCBITaxon:6706]: - text: Homarus americanus [NCBITaxon:6706] - Homo sapiens [NCBITaxon:9606]: - text: Homo sapiens [NCBITaxon:9606] - Larus argentatus [NCBITaxon:35669]: - text: Larus argentatus [NCBITaxon:35669] - Larus delawarensis [NCBITaxon:126683]: - text: Larus delawarensis [NCBITaxon:126683] - Larus glaucescens [NCBITaxon:119606]: - text: Larus glaucescens [NCBITaxon:119606] - Larus marinus [NCBITaxon:8912]: - text: Larus marinus [NCBITaxon:8912] - Meleagris gallopavo [NCBITaxon:9103]: - text: Meleagris gallopavo [NCBITaxon:9103] - Mytilus edulis [NCBITaxon:6550]: - text: Mytilus edulis [NCBITaxon:6550] - Oncorhynchus mykiss [NCBITaxon:8022]: - text: Oncorhynchus mykiss [NCBITaxon:8022] - Oncorhynchus tshawytscha [NCBITaxon:74940]: - text: Oncorhynchus tshawytscha [NCBITaxon:74940] - Ovis aries [NCBITaxon:9940]: - text: Ovis aries [NCBITaxon:9940] - Phalacrocorax auritus [NCBITaxon:56069]: - text: Phalacrocorax auritus [NCBITaxon:56069] - Salmo salar [NCBITaxon:8030]: - text: Salmo salar [NCBITaxon:8030] - Somateria mollissima [NCBITaxon:76058]: - text: Somateria mollissima [NCBITaxon:76058] - Sus scrofa domesticus [NCBITaxon:9825]: - text: Sus scrofa domesticus [NCBITaxon:9825] - host (food production name) menu: - name: host (food production name) menu - permissible_values: - Cow (by age/production stage) (organizational term): - text: Cow (by age/production stage) (organizational term) - Calf [FOODON:03411349]: - text: Calf [FOODON:03411349] - is_a: Cow (by age/production stage) (organizational term) - Feeder cow [FOODON:00004292]: - text: Feeder cow [FOODON:00004292] - is_a: Cow (by age/production stage) (organizational term) - Finisher cow [FOODON:00004293]: - text: Finisher cow [FOODON:00004293] - is_a: Cow (by age/production stage) (organizational term) - Milker cow [FOODON:03411201]: - text: Milker cow [FOODON:03411201] - is_a: Cow (by age/production stage) (organizational term) - Stocker cow [FOODON:00004294]: - text: Stocker cow [FOODON:00004294] - is_a: Cow (by age/production stage) (organizational term) - Weanling [FOODON:00004295]: - text: Weanling [FOODON:00004295] - is_a: Cow (by age/production stage) (organizational term) - Cow (by sex/reproductive stage) (organizational term): - text: Cow (by sex/reproductive stage) (organizational term) - Bull [FOODON:00000015]: - text: Bull [FOODON:00000015] - is_a: Cow (by sex/reproductive stage) (organizational term) - Cow [NCBITaxon:9913]: - text: Cow [NCBITaxon:9913] - is_a: Cow (by sex/reproductive stage) (organizational term) - Freemartin [FOODON:00004296]: - text: Freemartin [FOODON:00004296] - is_a: Cow (by sex/reproductive stage) (organizational term) - Heifer [FOODON:00002518]: - text: Heifer [FOODON:00002518] - is_a: Cow (by sex/reproductive stage) (organizational term) - Steer [FOODON:00002531]: - text: Steer [FOODON:00002531] - is_a: Cow (by sex/reproductive stage) (organizational term) - Pig (by age/production stage) (organizational term): - text: Pig (by age/production stage) (organizational term) - Finisher pig [FOODON:00003371]: - text: Finisher pig [FOODON:00003371] - is_a: Pig (by age/production stage) (organizational term) - Grower pig [FOODON:00003370]: - text: Grower pig [FOODON:00003370] - is_a: Pig (by age/production stage) (organizational term) - Nursing pig [FOODON:00004297 ]: - text: Nursing pig [FOODON:00004297 ] - is_a: Pig (by age/production stage) (organizational term) - Pig [NCBITaxon:9823]: - text: Pig [NCBITaxon:9823] - is_a: Pig (by age/production stage) (organizational term) - Piglet [FOODON:00003952]: - text: Piglet [FOODON:00003952] - is_a: Pig (by age/production stage) (organizational term) - Weanling (weaner) pig [FOODON:00003373]: - text: Weanling (weaner) pig [FOODON:00003373] - is_a: Pig (by age/production stage) (organizational term) - Pig (by sex/reproductive stage) (organizational term): - text: Pig (by sex/reproductive stage) (organizational term) - Barrow [FOODON:03411280]: - text: Barrow [FOODON:03411280] - is_a: Pig (by sex/reproductive stage) (organizational term) - Boar [FOODON:03412248]: - text: Boar [FOODON:03412248] - is_a: Pig (by sex/reproductive stage) (organizational term) - Gilt [FOODON:00003369]: - text: Gilt [FOODON:00003369] - is_a: Pig (by sex/reproductive stage) (organizational term) - Sow [FOODON:00003333]: - text: Sow [FOODON:00003333] - is_a: Pig (by sex/reproductive stage) (organizational term) - Poultry [FOODON:03411563]: - text: Poultry [FOODON:03411563] - Broiler or fryer chicken [FOODON:03411198]: - text: Broiler or fryer chicken [FOODON:03411198] - is_a: Poultry [FOODON:03411563] - Capon [FOODON:03411711]: - text: Capon [FOODON:03411711] - is_a: Poultry [FOODON:03411563] - Chick [FOODON:00004299]: - text: Chick [FOODON:00004299] - is_a: Poultry [FOODON:03411563] - Chicken [NCBITaxon:9031]: - text: Chicken [NCBITaxon:9031] - is_a: Poultry [FOODON:03411563] - Egg [UBERON:0007379]: - text: Egg [UBERON:0007379] - is_a: Poultry [FOODON:03411563] - Hatchling [FOODON:00004300]: - text: Hatchling [FOODON:00004300] - is_a: Poultry [FOODON:03411563] - Hen [FOODON:00003282]: - text: Hen [FOODON:00003282] - is_a: Poultry [FOODON:03411563] - Layer chicken [FOODON:00004301]: - text: Layer chicken [FOODON:00004301] - is_a: Poultry [FOODON:03411563] - Layer turkey [FOODON:00004302]: - text: Layer turkey [FOODON:00004302] - is_a: Poultry [FOODON:03411563] - Poult [FOODON:00002962]: - text: Poult [FOODON:00002962] - is_a: Poultry [FOODON:03411563] - Pullet [FOODON:00004303]: - text: Pullet [FOODON:00004303] - is_a: Poultry [FOODON:03411563] - Rooster [FOODON:03411714]: - text: Rooster [FOODON:03411714] - is_a: Poultry [FOODON:03411563] - Tom (Gobbler) [FOODON:00004304 ]: - text: Tom (Gobbler) [FOODON:00004304 ] - is_a: Poultry [FOODON:03411563] - Turkey [NCBITaxon:9103]: - text: Turkey [NCBITaxon:9103] - is_a: Poultry [FOODON:03411563] - Sheep [NCBITaxon:9940]: - text: Sheep [NCBITaxon:9940] - Ram [FOODON:00004305]: - text: Ram [FOODON:00004305] - is_a: Sheep [NCBITaxon:9940] - Wether sheep [FOODON:00004306]: - text: Wether sheep [FOODON:00004306] - is_a: Sheep [NCBITaxon:9940] - Ewe [FOODON:03412610]: - text: Ewe [FOODON:03412610] - is_a: Sheep [NCBITaxon:9940] - Lamb [FOODON:03411669]: - text: Lamb [FOODON:03411669] - is_a: Sheep [NCBITaxon:9940] - Fish [FOODON:03411222]: - text: Fish [FOODON:03411222] - Fish egg [FOODON_00004319]: - text: Fish egg [FOODON_00004319] - is_a: Fish [FOODON:03411222] - Fry (fish) [FOODON_00004318]: - text: Fry (fish) [FOODON_00004318] - is_a: Fish [FOODON:03411222] - Juvenile fish [FOODON_00004317]: - text: Juvenile fish [FOODON_00004317] - is_a: Fish [FOODON:03411222] - host_age_bin menu: - name: host_age_bin menu - permissible_values: - First winter [GENEPIO:0100684]: - text: First winter [GENEPIO:0100684] - First summer [GENEPIO:0100685]: - text: First summer [GENEPIO:0100685] - Second winter [GENEPIO:0100686]: - text: Second winter [GENEPIO:0100686] - Second summer [GENEPIO:0100687]: - text: Second summer [GENEPIO:0100687] - Third winter [GENEPIO:0100688]: - text: Third winter [GENEPIO:0100688] - Third summer [GENEPIO:0100689]: - text: Third summer [GENEPIO:0100689] - isolated_by menu: - name: isolated_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] - 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] - organism menu: - name: organism menu - permissible_values: - Acinetobacter [NCBITaxon:469]: - text: Acinetobacter [NCBITaxon:469] - Acinetobacter baumannii [NCBITaxon:470]: - text: Acinetobacter baumannii [NCBITaxon:470] - is_a: Acinetobacter [NCBITaxon:469] - Acinetobacter bereziniae [NCBITaxon:106648]: - text: Acinetobacter bereziniae [NCBITaxon:106648] - is_a: Acinetobacter [NCBITaxon:469] - Acinetobacter ursingii [NCBITaxon:108980]: - text: Acinetobacter ursingii [NCBITaxon:108980] - is_a: Acinetobacter [NCBITaxon:469] - Aeromonas [NCBITaxon:642]: - text: Aeromonas [NCBITaxon:642] - Aeromonas allosaccharophila [NCBITaxon:656]: - text: Aeromonas allosaccharophila [NCBITaxon:656] - is_a: Aeromonas [NCBITaxon:642] - Aeromonas hydrophila [NCBITaxon:644]: - text: Aeromonas hydrophila [NCBITaxon:644] - is_a: Aeromonas [NCBITaxon:642] - Aeromonas rivipollensis [NCBITaxon:948519]: - text: Aeromonas rivipollensis [NCBITaxon:948519] - is_a: Aeromonas [NCBITaxon:642] - Aeromonas salmonicida [NCBITaxon:645]: - text: Aeromonas salmonicida [NCBITaxon:645] - is_a: Aeromonas [NCBITaxon:642] - Campylobacter [NCBITaxon:194]: - text: Campylobacter [NCBITaxon:194] - Campylobacter coli [NCBITaxon:195]: - text: Campylobacter coli [NCBITaxon:195] - is_a: Campylobacter [NCBITaxon:194] - Campylobacter jejuni [NCBITaxon:197]: - text: Campylobacter jejuni [NCBITaxon:197] - is_a: Campylobacter [NCBITaxon:194] - Campylobacter lari [NCBITaxon:201]: - text: Campylobacter lari [NCBITaxon:201] - is_a: Campylobacter [NCBITaxon:194] - Citrobacter [NCBITaxon:544]: - text: Citrobacter [NCBITaxon:544] - Citrobacter braakii [NCBITaxon:57706]: - text: Citrobacter braakii [NCBITaxon:57706] - is_a: Citrobacter [NCBITaxon:544] - Citrobacter freundii [NCBITaxon:546]: - text: Citrobacter freundii [NCBITaxon:546] - is_a: Citrobacter [NCBITaxon:544] - Citrobacter gillenii [NCBITaxon:67828]: - text: Citrobacter gillenii [NCBITaxon:67828] - is_a: Citrobacter [NCBITaxon:544] - Clostridioides [NCBITaxon:1870884]: - text: Clostridioides [NCBITaxon:1870884] - Clostridioides difficile [NCBITaxon:1496]: - text: Clostridioides difficile [NCBITaxon:1496] - is_a: Clostridioides [NCBITaxon:1870884] - Clostridium [NCBITaxon:1485]: - text: Clostridium [NCBITaxon:1485] - Clostridium perfringens [NCBITaxon:1502]: - text: Clostridium perfringens [NCBITaxon:1502] - is_a: Clostridium [NCBITaxon:1485] - Clostridium sporogenes [NCBITaxon:1509]: - text: Clostridium sporogenes [NCBITaxon:1509] - is_a: Clostridium [NCBITaxon:1485] - Comamonas [NCBITaxon:283]: - text: Comamonas [NCBITaxon:283] - Comamonas aquatica [NCBITaxon:225991]: - text: Comamonas aquatica [NCBITaxon:225991] - is_a: Comamonas [NCBITaxon:283] - Enterobacter [NCBITaxon:547]: - text: Enterobacter [NCBITaxon:547] - Enterobacter asburiae [NCBITaxon:61645]: - text: Enterobacter asburiae [NCBITaxon:61645] - is_a: Enterobacter [NCBITaxon:547] - Enterobacter cancerogenus [NCBITaxon:69218]: - text: Enterobacter cancerogenus [NCBITaxon:69218] - is_a: Enterobacter [NCBITaxon:547] - Enterobacter cloacae [NCBITaxon:550]: - text: Enterobacter cloacae [NCBITaxon:550] - is_a: Enterobacter [NCBITaxon:547] - Enterobacter hormaechei [NCBITaxon:158836]: - text: Enterobacter hormaechei [NCBITaxon:158836] - is_a: Enterobacter [NCBITaxon:547] - Enterobacter kobei [NCBITaxon:208224]: - text: Enterobacter kobei [NCBITaxon:208224] - is_a: Enterobacter [NCBITaxon:547] - Enterobacter roggenkampii [NCBITaxon:1812935]: - text: Enterobacter roggenkampii [NCBITaxon:1812935] - is_a: Enterobacter [NCBITaxon:547] - Lelliottia amnigena [NCBITaxon:61646]: - text: Lelliottia amnigena [NCBITaxon:61646] - is_a: Enterobacter [NCBITaxon:547] - Pluralibacter gergoviae [NCBITaxon:61647]: - text: Pluralibacter gergoviae [NCBITaxon:61647] - is_a: Enterobacter [NCBITaxon:547] - Enterococcus [NCBITaxon:1350]: - text: Enterococcus [NCBITaxon:1350] - Enterococcus asini [NCBITaxon:57732]: - text: Enterococcus asini [NCBITaxon:57732] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus avium [NCBITaxon:33945]: - text: Enterococcus avium [NCBITaxon:33945] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus caccae [NCBITaxon:317735]: - text: Enterococcus caccae [NCBITaxon:317735] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus canis [NCBITaxon:214095]: - text: Enterococcus canis [NCBITaxon:214095] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus casseliflavus [NCBITaxon:37734]: - text: Enterococcus casseliflavus [NCBITaxon:37734] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus cecorum [NCBITaxon:44008]: - text: Enterococcus cecorum [NCBITaxon:44008] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus dispar [NCBITaxon:44009]: - text: Enterococcus dispar [NCBITaxon:44009] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus durans [NCBITaxon:53345]: - text: Enterococcus durans [NCBITaxon:53345] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus faecium [NCBITaxon:1352]: - text: Enterococcus faecium [NCBITaxon:1352] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus faecalis [NCBITaxon:1351]: - text: Enterococcus faecalis [NCBITaxon:1351] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus gallinarum [NCBITaxon:1353]: - text: Enterococcus gallinarum [NCBITaxon:1353] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus hirae [NCBITaxon:1354]: - text: Enterococcus hirae [NCBITaxon:1354] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus malodoratus [NCBITaxon:71451]: - text: Enterococcus malodoratus [NCBITaxon:71451] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus mundtii [NCBITaxon:53346]: - text: Enterococcus mundtii [NCBITaxon:53346] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus ratti [NCBITaxon:150033]: - text: Enterococcus ratti [NCBITaxon:150033] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus saccharolyticus [NCBITaxon:41997]: - text: Enterococcus saccharolyticus [NCBITaxon:41997] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus thailandicus [NCBITaxon:417368]: - text: Enterococcus thailandicus [NCBITaxon:417368] - is_a: Enterococcus [NCBITaxon:1350] - Enterococcus villorum [NCBITaxon:112904]: - text: Enterococcus villorum [NCBITaxon:112904] - is_a: Enterococcus [NCBITaxon:1350] - Escherichia [NCBITaxon:561]: - text: Escherichia [NCBITaxon:561] - Escherichia coli [NCBITaxon:562]: - text: Escherichia coli [NCBITaxon:562] - is_a: Escherichia [NCBITaxon:561] - Escherichia fergusonii [NCBITaxon:564]: - text: Escherichia fergusonii [NCBITaxon:564] - is_a: Escherichia [NCBITaxon:561] - Exiguobacterium [NCBITaxon:33986]: - text: Exiguobacterium [NCBITaxon:33986] - Exiguobacterium oxidotolerans [NCBITaxon:223958]: - text: Exiguobacterium oxidotolerans [NCBITaxon:223958] - is_a: Exiguobacterium [NCBITaxon:33986] - Exiguobacterium sp. [NCBITaxon:44751]: - text: Exiguobacterium sp. [NCBITaxon:44751] - is_a: Exiguobacterium [NCBITaxon:33986] - Klebsiella [NCBITaxon:570]: - text: Klebsiella [NCBITaxon:570] - Klebsiella aerogenes [NCBITaxon:548]: - text: Klebsiella aerogenes [NCBITaxon:548] - is_a: Klebsiella [NCBITaxon:570] - Klebsiella michiganensis [NCBITaxon:1134687]: - text: Klebsiella michiganensis [NCBITaxon:1134687] - is_a: Klebsiella [NCBITaxon:570] - Klebsiella oxytoca [NCBITaxon:571]: - text: Klebsiella oxytoca [NCBITaxon:571] - is_a: Klebsiella [NCBITaxon:570] - Klebsiella pneumoniae [NCBITaxon:573]: - text: Klebsiella pneumoniae [NCBITaxon:573] - is_a: Klebsiella [NCBITaxon:570] - Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407]: - text: Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407] - is_a: Klebsiella [NCBITaxon:570] - Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574]: - text: Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574] - is_a: Klebsiella [NCBITaxon:570] - Kluyvera [NCBITaxon:579]: - text: Kluyvera [NCBITaxon:579] - Kluyvera intermedia [NCBITaxon:61648]: - text: Kluyvera intermedia [NCBITaxon:61648] - is_a: Kluyvera [NCBITaxon:579] - Kosakonia [NCBITaxon:1330547]: - text: Kosakonia [NCBITaxon:1330547] - Kosakonia cowanii [NCBITaxon:208223]: - text: Kosakonia cowanii [NCBITaxon:208223] - is_a: Kosakonia [NCBITaxon:1330547] - Leclercia [NCBITaxon:83654]: - text: Leclercia [NCBITaxon:83654] - Leclercia adecarboxylata [NCBITaxon:83655]: - text: Leclercia adecarboxylata [NCBITaxon:83655] - is_a: Leclercia [NCBITaxon:83654] - Listeria [NCBITaxon:1637]: - text: Listeria [NCBITaxon:1637] - Listeria monocytogenes [NCBITaxon:1639]: - text: Listeria monocytogenes [NCBITaxon:1639] - is_a: Listeria [NCBITaxon:1637] - Ochrobactrum [NCBITaxon:528]: - text: Ochrobactrum [NCBITaxon:528] - Pantoea [NCBITaxon:53335]: - text: Pantoea [NCBITaxon:53335] - Pantoea ananatis [NCBITaxon:553]: - text: Pantoea ananatis [NCBITaxon:553] - is_a: Pantoea [NCBITaxon:53335] - Photobacterium [NCBITaxon:657]: - text: Photobacterium [NCBITaxon:657] - Photobacterium sp. [NCBITaxon:660]: - text: Photobacterium sp. [NCBITaxon:660] - is_a: Photobacterium [NCBITaxon:657] - Providencia [NCBITaxon:586]: - text: Providencia [NCBITaxon:586] - Providencia rettgeri [NCBITaxon:587]: - text: Providencia rettgeri [NCBITaxon:587] - is_a: Providencia [NCBITaxon:586] - Pseudoalteromonas [NCBITaxon:53246]: - text: Pseudoalteromonas [NCBITaxon:53246] - Pseudoalteromonas tetraodonis [NCBITaxon:43659]: - text: Pseudoalteromonas tetraodonis [NCBITaxon:43659] - is_a: Pseudoalteromonas [NCBITaxon:53246] - Pseudomonas [NCBITaxon:286]: - text: Pseudomonas [NCBITaxon:286] - Pseudomonas aeruginosa [NCBITaxon:287]: - text: Pseudomonas aeruginosa [NCBITaxon:287] - is_a: Pseudomonas [NCBITaxon:286] - Pseudomonas fluorescens [NCBITaxon:294]: - text: Pseudomonas fluorescens [NCBITaxon:294] - is_a: Pseudomonas [NCBITaxon:286] - Pseudomonas soli [NCBITaxon:1306993]: - text: Pseudomonas soli [NCBITaxon:1306993] - is_a: Pseudomonas [NCBITaxon:286] - Pseudomonas sp. [NCBITaxon:306]: - text: Pseudomonas sp. [NCBITaxon:306] - is_a: Pseudomonas [NCBITaxon:286] - Psychrobacter [NCBITaxon:497]: - text: Psychrobacter [NCBITaxon:497] - Psychrobacter faecalis [NCBITaxon:180588]: - text: Psychrobacter faecalis [NCBITaxon:180588] - is_a: Psychrobacter [NCBITaxon:497] - Psychrobacter sp. [NCBITaxon:56811]: - text: Psychrobacter sp. [NCBITaxon:56811] - is_a: Psychrobacter [NCBITaxon:497] - Rahnella [NCBITaxon:34037]: - text: Rahnella [NCBITaxon:34037] - Rahnella aquatilis [NCBITaxon:34038]: - text: Rahnella aquatilis [NCBITaxon:34038] - is_a: Rahnella [NCBITaxon:34037] - Raoultella [NCBITaxon:160674]: - text: Raoultella [NCBITaxon:160674] - Raoultella ornithinolytica [NCBITaxon:54291]: - text: Raoultella ornithinolytica [NCBITaxon:54291] - is_a: Raoultella [NCBITaxon:160674] - Raoultella planticola [NCBITaxon:575]: - text: Raoultella planticola [NCBITaxon:575] - is_a: Raoultella [NCBITaxon:160674] - Salmonella enterica [NCBITaxon:28901]: - text: Salmonella enterica [NCBITaxon:28901] - Salmonella enterica subsp. enterica [NCBITaxon:59201]: - text: Salmonella enterica subsp. enterica [NCBITaxon:59201] - is_a: Salmonella enterica [NCBITaxon:28901] - Salmonella enterica subsp. arizonae [NCBITaxon:59203]: - text: Salmonella enterica subsp. arizonae [NCBITaxon:59203] - is_a: Salmonella enterica [NCBITaxon:28901] - Serratia [NCBITaxon:613]: - text: Serratia [NCBITaxon:613] - Shewanella [NCBITaxon:22]: - text: Shewanella [NCBITaxon:22] - Shewanella pealeana [NCBITaxon:70864]: - text: Shewanella pealeana [NCBITaxon:70864] - is_a: Shewanella [NCBITaxon:22] - Shewanella putrefaciens [NCBITaxon:24]: - text: Shewanella putrefaciens [NCBITaxon:24] - is_a: Shewanella [NCBITaxon:22] - Shewanella sp. [NCBITaxon:50422]: - text: Shewanella sp. [NCBITaxon:50422] - is_a: Shewanella [NCBITaxon:22] - Staphylococcus [NCBITaxon:1279]: - text: Staphylococcus [NCBITaxon:1279] - Staphylococcus aureus [NCBITaxon:1280]: - text: Staphylococcus aureus [NCBITaxon:1280] - is_a: Staphylococcus [NCBITaxon:1279] - Streptococcus [NCBITaxon:1301]: - text: Streptococcus [NCBITaxon:1301] - Streptococcus alactolyticus [NCBITaxon:29389]: - text: Streptococcus alactolyticus [NCBITaxon:29389] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus bovis [NCBITaxon:1335]: - text: Streptococcus bovis [NCBITaxon:1335] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus equinus [NCBITaxon:1335]: - text: Streptococcus equinus [NCBITaxon:1335] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus gallolyticus [NCBITaxon:315405]: - text: Streptococcus gallolyticus [NCBITaxon:315405] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus infantarius [NCBITaxon:102684]: - text: Streptococcus infantarius [NCBITaxon:102684] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus lutetiensis [NCBITaxon:150055]: - text: Streptococcus lutetiensis [NCBITaxon:150055] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus macedonicus [NCBITaxon:59310]: - text: Streptococcus macedonicus [NCBITaxon:59310] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus pasteurianus [NCBITaxon:197614]: - text: Streptococcus pasteurianus [NCBITaxon:197614] - is_a: Streptococcus [NCBITaxon:1301] - Streptococcus suis [NCBITaxon:1307]: - text: Streptococcus suis [NCBITaxon:1307] - is_a: Streptococcus [NCBITaxon:1301] - Vibrio [NCBITaxon:662]: - text: Vibrio [NCBITaxon:662] - Vibrio cholerae [NCBITaxon:666]: - text: Vibrio cholerae [NCBITaxon:666] - is_a: Vibrio [NCBITaxon:662] - taxonomic_identification_process menu: - name: taxonomic_identification_process menu - permissible_values: - Whole genome sequencing assay [OBI:0002117]: - text: Whole genome sequencing assay [OBI:0002117] - 16S ribosomal gene sequencing assay [OBI:0002763]: - text: 16S ribosomal gene sequencing assay [OBI:0002763] - PCR assay [OBI:0002740]: - text: PCR assay [OBI:0002740] - Comparative phenotypic assessment [OBI:0001546]: - text: Comparative phenotypic assessment [OBI:0001546] - sequenced_by menu: - name: sequenced_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] - 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] - purpose_of_sequencing menu: - name: purpose_of_sequencing menu - permissible_values: - Cluster/Outbreak investigation [GENEPIO:0100001]: - text: Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100001]: - text: Diagnostic testing [GENEPIO:0100001] - Environmental testing [GENEPIO:0100548]: - text: Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003]: - text: Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549]: - text: Clinical trial [GENEPIO:0100549] - is_a: Research [GENEPIO:0100003] - Field experiment [GENEPIO:0100549]: - text: Field experiment [GENEPIO:0100549] - is_a: Research [GENEPIO:0100003] - Surveillance [GENEPIO:0100004]: - text: Surveillance [GENEPIO:0100004] - sequencing_platform menu: - name: sequencing_platform menu - permissible_values: - Illumina [GENEPIO:0001923]: - text: Illumina [GENEPIO:0001923] - Pacific Biosciences [GENEPIO:0001927]: - text: Pacific Biosciences [GENEPIO:0001927] - Ion Torrent [GENEPIO:0002683]: - text: Ion Torrent [GENEPIO:0002683] - Oxford Nanopore Technologies [OBI:0002755]: - text: Oxford Nanopore Technologies [OBI:0002755] - BGI Genomics [GENEPIO:0004324]: - text: BGI Genomics [GENEPIO:0004324] - MGI [GENEPIO:0004325]: - text: MGI [GENEPIO:0004325] - sequencing_instrument menu: - name: sequencing_instrument menu - permissible_values: - Illumina [GENEPIO:0100105]: - text: Illumina [GENEPIO:0100105] - Illumina Genome Analyzer [GENEPIO:0100106]: - text: Illumina Genome Analyzer [GENEPIO:0100106] - is_a: Illumina [GENEPIO:0100105] - Illumina Genome Analyzer II [OBI:0000703]: - text: Illumina Genome Analyzer II [OBI:0000703] - is_a: Illumina [GENEPIO:0100105] - Illumina Genome Analyzer IIx [OBI:0002000]: - text: Illumina Genome Analyzer IIx [OBI:0002000] - is_a: Illumina [GENEPIO:0100105] - Illumina HiScanSQ [GENEPIO:0100109]: - text: Illumina HiScanSQ [GENEPIO:0100109] - is_a: Illumina [GENEPIO:0100105] - Illumina HiSeq [GENEPIO:0100110]: - text: Illumina HiSeq [GENEPIO:0100110] - is_a: Illumina [GENEPIO:0100105] - Illumina HiSeq X [GENEPIO:0100111]: - text: Illumina HiSeq X [GENEPIO:0100111] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq X Five [GENEPIO:0100112]: - text: Illumina HiSeq X Five [GENEPIO:0100112] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq X Ten [GENEPIO:0100113]: - text: Illumina HiSeq X Ten [GENEPIO:0100113] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 1000 [OBI:0002022]: - text: Illumina HiSeq 1000 [OBI:0002022] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 1500 [GENEPIO:0100115]: - text: Illumina HiSeq 1500 [GENEPIO:0100115] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 2000 [OBI:0002001]: - text: Illumina HiSeq 2000 [OBI:0002001] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 2500 [OBI:0002002]: - text: Illumina HiSeq 2500 [OBI:0002002] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 3000 [OBI:0002048]: - text: Illumina HiSeq 3000 [OBI:0002048] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 4000 [OBI:0002049]: - text: Illumina HiSeq 4000 [OBI:0002049] - is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina iSeq [GENEPIO:0100120]: - text: Illumina iSeq [GENEPIO:0100120] - is_a: Illumina [GENEPIO:0100105] - Illumina iSeq 100 [GENEPIO:0100121]: - text: Illumina iSeq 100 [GENEPIO:0100121] - is_a: Illumina iSeq [GENEPIO:0100120] - Illumina NovaSeq [GENEPIO:0100122]: - text: Illumina NovaSeq [GENEPIO:0100122] - is_a: Illumina [GENEPIO:0100105] - Illumina NovaSeq 6000 [GENEPIO:0100123]: - text: Illumina NovaSeq 6000 [GENEPIO:0100123] - is_a: Illumina NovaSeq [GENEPIO:0100122] - Illumina MiniSeq [GENEPIO:0100124]: - text: Illumina MiniSeq [GENEPIO:0100124] - is_a: Illumina [GENEPIO:0100105] - Illumina MiSeq [OBI:0002003]: - text: Illumina MiSeq [OBI:0002003] - is_a: Illumina [GENEPIO:0100105] - Illumina NextSeq [GENEPIO:0100126]: - text: Illumina NextSeq [GENEPIO:0100126] - is_a: Illumina [GENEPIO:0100105] - Illumina NextSeq 500 [OBI:0002021]: - text: Illumina NextSeq 500 [OBI:0002021] - is_a: Illumina NextSeq [GENEPIO:0100126] - Illumina NextSeq 550 [GENEPIO:0100128]: - text: Illumina NextSeq 550 [GENEPIO:0100128] - is_a: Illumina NextSeq [GENEPIO:0100126] - Illumina NextSeq 2000 [GENEPIO:0100129]: - text: Illumina NextSeq 2000 [GENEPIO:0100129] - is_a: Illumina NextSeq [GENEPIO:0100126] - PacBio [GENEPIO:0100130]: - text: PacBio [GENEPIO:0100130] - PacBio RS [GENEPIO:0100131]: - text: PacBio RS [GENEPIO:0100131] - is_a: PacBio [GENEPIO:0100130] - PacBio RS II [OBI:0002012]: - text: PacBio RS II [OBI:0002012] - is_a: PacBio [GENEPIO:0100130] - PacBio Sequel [GENEPIO:0100133]: - text: PacBio Sequel [GENEPIO:0100133] - is_a: PacBio [GENEPIO:0100130] - PacBio Sequel II [GENEPIO:0100134]: - text: PacBio Sequel II [GENEPIO:0100134] - is_a: PacBio [GENEPIO:0100130] - Ion Torrent [GENEPIO:0100135]: - text: Ion Torrent [GENEPIO:0100135] - Ion Torrent PGM [GENEPIO:0100136]: - text: Ion Torrent PGM [GENEPIO:0100136] - is_a: Ion Torrent [GENEPIO:0100135] - Ion Torrent Proton [GENEPIO:0100137]: - text: Ion Torrent Proton [GENEPIO:0100137] - is_a: Ion Torrent [GENEPIO:0100135] - Ion Torrent S5 XL [GENEPIO:0100138]: - text: Ion Torrent S5 XL [GENEPIO:0100138] - is_a: Ion Torrent [GENEPIO:0100135] - Ion Torrent S5 [GENEPIO:0100139]: - text: Ion Torrent S5 [GENEPIO:0100139] - is_a: Ion Torrent [GENEPIO:0100135] - Oxford Nanopore [GENEPIO:0100140]: - text: Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore GridION [GENEPIO:0100141]: - text: Oxford Nanopore GridION [GENEPIO:0100141] - is_a: Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore MinION [GENEPIO:0100142]: - text: Oxford Nanopore MinION [GENEPIO:0100142] - is_a: Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore PromethION [GENEPIO:0100143]: - text: Oxford Nanopore PromethION [GENEPIO:0100143] - is_a: Oxford Nanopore [GENEPIO:0100140] - BGISEQ [GENEPIO:0100144]: - text: BGISEQ [GENEPIO:0100144] - BGISEQ-500 [GENEPIO:0100145]: - text: BGISEQ-500 [GENEPIO:0100145] - is_a: BGISEQ [GENEPIO:0100144] - DNBSEQ [GENEPIO:0100146]: - text: DNBSEQ [GENEPIO:0100146] - DNBSEQ-T7 [GENEPIO:0100147]: - text: DNBSEQ-T7 [GENEPIO:0100147] - is_a: DNBSEQ [GENEPIO:0100146] - DNBSEQ-G400 [GENEPIO:0100148]: - text: DNBSEQ-G400 [GENEPIO:0100148] - is_a: DNBSEQ [GENEPIO:0100146] - DNBSEQ-G400 FAST [GENEPIO:0100149]: - text: DNBSEQ-G400 FAST [GENEPIO:0100149] - is_a: DNBSEQ [GENEPIO:0100146] - DNBSEQ-G50 [GENEPIO:0100150]: - text: DNBSEQ-G50 [GENEPIO:0100150] - is_a: DNBSEQ [GENEPIO:0100146] - sequence_submitted_by menu: - name: sequence_submitted_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] - 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] - attribute_package menu: - name: attribute_package menu - permissible_values: - Pathogen.cl [GENEPIO:0001835]: - text: Pathogen.cl [GENEPIO:0001835] - Pathogen.env [GENEPIO:0100581]: - text: Pathogen.env [GENEPIO:0100581] - experimental_intervention menu: - name: experimental_intervention menu - permissible_values: - Addition of substances to food/water [GENEPIO:0100536]: - text: Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537]: - text: Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538]: - text: Certified animal husbandry practices [GENEPIO:0100538] - Certified organic farming practices [GENEPIO:0100539]: - text: Certified organic farming practices [GENEPIO:0100539] - Change in storage conditions [GENEPIO:0100540]: - text: Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541]: - text: Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542]: - text: Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543]: - text: Fertilizer pre-treatment [GENEPIO:0100543] - Logistic slaughter [GENEPIO:0100545]: - text: Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546]: - text: Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547]: - text: Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346]: - text: Vaccination [NCIT:C15346] - AMR_testing_by menu: - name: AMR_testing_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] - 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] - antimicrobial_phenotype menu: - name: antimicrobial_phenotype menu - permissible_values: - Antibiotic resistance not defined [GENEPIO:0002040]: - text: Antibiotic resistance not defined [GENEPIO:0002040] - Intermediate antimicrobial phenotype [ARO:3004300]: - text: Intermediate antimicrobial phenotype [ARO:3004300] - is_a: Antibiotic resistance not defined [GENEPIO:0002040] - Indeterminate antimicrobial phenotype [GENEPIO:0100585]: - text: Indeterminate antimicrobial phenotype [GENEPIO:0100585] - is_a: Antibiotic resistance not defined [GENEPIO:0002040] - Nonsusceptible antimicrobial phenotype [ARO:3004303]: - text: Nonsusceptible antimicrobial phenotype [ARO:3004303] - Resistant antimicrobial phenotype [ARO:3004301]: - text: Resistant antimicrobial phenotype [ARO:3004301] - Susceptible antimicrobial phenotype [ARO:3004302]: - text: Susceptible antimicrobial phenotype [ARO:3004302] - Susceptible dose dependent antimicrobial phenotype [ARO:3004304]: - text: Susceptible dose dependent antimicrobial phenotype [ARO:3004304] - antimicrobial_measurement_units menu: - name: antimicrobial_measurement_units menu - permissible_values: - milligram per litre (mg/L) [UO:0000273]: - text: milligram per litre (mg/L) [UO:0000273] - millimetre (mm) [UO:0000016]: - text: millimetre (mm) [UO:0000016] - microgram per millilitre (ug/mL) [UO:0000274]: - text: microgram per millilitre (ug/mL) [UO:0000274] - antimicrobial_measurement_sign menu: - name: antimicrobial_measurement_sign menu - permissible_values: - less than (<) [GENEPIO:0001002]: - text: less than (<) [GENEPIO:0001002] - less than or equal to (<=) [GENEPIO:0001003]: - text: less than or equal to (<=) [GENEPIO:0001003] - equal to (==) [GENEPIO:0001004]: - text: equal to (==) [GENEPIO:0001004] - greater than (>) [GENEPIO:0001006]: - text: greater than (>) [GENEPIO:0001006] - greater than or equal to (>=) [GENEPIO:0001005]: - text: greater than or equal to (>=) [GENEPIO:0001005] - antimicrobial_laboratory_typing_method menu: - name: antimicrobial_laboratory_typing_method menu - permissible_values: - Agar diffusion [NCIT:85595]: - text: Agar diffusion [NCIT:85595] - Antimicrobial gradient (E-test) [NCIT:85596]: - text: Antimicrobial gradient (E-test) [NCIT:85596] - is_a: Agar diffusion [NCIT:85595] - Agar dilution [ARO:3004411]: - text: Agar dilution [ARO:3004411] - Broth dilution [ARO:3004397]: - text: Broth dilution [ARO:3004397] - antimicrobial_laboratory_typing_platform menu: - name: antimicrobial_laboratory_typing_platform menu - permissible_values: - BIOMIC Microbiology System: - text: BIOMIC Microbiology System - Microscan [ARO:3004400]: - text: Microscan [ARO:3004400] - Phoenix [ARO:3004401]: - text: Phoenix [ARO:3004401] - Sensititre [ARO:3004402]: - text: Sensititre [ARO:3004402] - Vitek System [ARO:3004403]: - text: Vitek System [ARO:3004403] - antimicrobial_vendor_name: - name: antimicrobial_vendor_name - permissible_values: - Becton Dickinson [ARO:3004405]: - text: Becton Dickinson [ARO:3004405] - "bioM\xE9rieux [ARO:3004406]": - text: "bioM\xE9rieux [ARO:3004406]" - Omron [ARO:3004408]: - text: Omron [ARO:3004408] - Siemens [ARO:3004407]: - text: Siemens [ARO:3004407] - Trek [ARO:3004409]: - text: Trek [ARO:3004409] - antimicrobial_testing_standard menu: - name: antimicrobial_testing_standard menu - permissible_values: - British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]: - text: British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] - Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]: - text: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - "Deutsches Institut f\xFCr Normung (DIN) [ARO:3004367]": - text: "Deutsches Institut f\xFCr Normung (DIN) [ARO:3004367]" - European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]: - text: European Committee on Antimicrobial Susceptibility Testing (EUCAST) - [ARO:3004368] - National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]: - text: National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] - National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]: - text: National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] - "Soci\xE9t\xE9 Fran\xE7aise de Microbiologie (SFM) [ARO:3004369]": - text: "Soci\xE9t\xE9 Fran\xE7aise de Microbiologie (SFM) [ARO:3004369]" - Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]: - text: Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] - Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]: - text: Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] -types: - WhitespaceMinimizedString: - name: WhitespaceMinimizedString - typeof: string - description: 'A string that has all whitespace trimmed off of beginning and end, - and all internal whitespace segments reduced to single spaces. Whitespace includes - #x9 (tab), #xA (linefeed), and #xD (carriage return).' - base: str - uri: xsd:token - Provenance: - name: Provenance - typeof: string - description: A field containing a DataHarmonizer versioning marker. It is issued - by DataHarmonizer when validation is applied to a given row of data. - base: str - uri: xsd:token -settings: - Title_Case: (((?<=\b)[^a-z\W]\w*?|[\W])+) - UPPER_CASE: '[A-Z\W\d_]*' - lower_case: '[a-z\W\d_]*' diff --git a/web/templates/grdi/SOP.pdf b/web/templates/grdi_1m/SOP.pdf similarity index 100% rename from web/templates/grdi/SOP.pdf rename to web/templates/grdi_1m/SOP.pdf diff --git a/web/templates/grdi/exampleInput/GRDI_Test_Data.json b/web/templates/grdi_1m/exampleInput/GRDI_Test_Data.json similarity index 100% rename from web/templates/grdi/exampleInput/GRDI_Test_Data.json rename to web/templates/grdi_1m/exampleInput/GRDI_Test_Data.json diff --git a/web/templates/grdi/exampleInput/GRDI_Test_Data.xlsx b/web/templates/grdi_1m/exampleInput/GRDI_Test_Data.xlsx similarity index 100% rename from web/templates/grdi/exampleInput/GRDI_Test_Data.xlsx rename to web/templates/grdi_1m/exampleInput/GRDI_Test_Data.xlsx diff --git a/web/templates/grdi/exampleInput/GRDI_Test_Data_2.json b/web/templates/grdi_1m/exampleInput/GRDI_Test_Data_2.json similarity index 100% rename from web/templates/grdi/exampleInput/GRDI_Test_Data_2.json rename to web/templates/grdi_1m/exampleInput/GRDI_Test_Data_2.json diff --git a/web/templates/grdi/export.js b/web/templates/grdi_1m/export.js similarity index 100% rename from web/templates/grdi/export.js rename to web/templates/grdi_1m/export.js diff --git a/web/templates/grdi/schema.json b/web/templates/grdi_1m/schema.json similarity index 100% rename from web/templates/grdi/schema.json rename to web/templates/grdi_1m/schema.json diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi_1m/schema.yaml similarity index 100% rename from web/templates/grdi/schema.yaml rename to web/templates/grdi_1m/schema.yaml diff --git a/web/templates/grdi/schema_core.yaml b/web/templates/grdi_1m/schema_core.yaml similarity index 100% rename from web/templates/grdi/schema_core.yaml rename to web/templates/grdi_1m/schema_core.yaml diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi_1m/schema_enums.tsv similarity index 100% rename from web/templates/grdi/schema_enums.tsv rename to web/templates/grdi_1m/schema_enums.tsv diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi_1m/schema_slots.tsv similarity index 100% rename from web/templates/grdi/schema_slots.tsv rename to web/templates/grdi_1m/schema_slots.tsv