diff --git a/dictionary-tables/ODM_countries.csv b/dictionary-tables/ODM_countries.csv index 6202aa0..2d04fc6 100644 --- a/dictionary-tables/ODM_countries.csv +++ b/dictionary-tables/ODM_countries.csv @@ -1,4 +1,4 @@ -Version,2.2.1,,,,,,,,,,,,, +Version,2.2.2,,,,,,,,,,,,, isoCode,isoCodeX,numCode,tld,nameEngl,nameOfficial,sovereignty,countryExonym,capitalExonym,countryEndonym,capitalEndonym,langScript,phone,utc,utcDST AF,AFG,4,.af,Afghanistan,The Islamic Republic of Afghanistan,UN member state,Afghanistan,Kabul,"Afġānistān, افغانستان","Kabul, كابل","Pashto/Dari, (Arabic script)",93,+04:30, AX,ALA,248,.ax,Åland Islands,Åland,Finland,Åland,Mariehamn,"Åland, Ahvenanmaa","Mariehamn, Maarianhamina","Swedish, Finnish",+358 (18),+02:00,+03:00 diff --git a/dictionary-tables/ODM_countries_2.2.1.csv b/dictionary-tables/ODM_countries_2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_countries_2.2.1.csv rename to dictionary-tables/ODM_countries_2.2.2.csv diff --git a/dictionary-tables/ODM_languages.csv b/dictionary-tables/ODM_languages.csv index d0f9abf..45c6bce 100644 --- a/dictionary-tables/ODM_languages.csv +++ b/dictionary-tables/ODM_languages.csv @@ -1,4 +1,4 @@ -Version,2.2.1,,,,,,,, +Version,2.2.2,,,,,,,, lang,langFam,langName,natName,iso6391,iso6392T,firstReleased,lastUpdated,changes,notes eng,Indo-European,English,English,en,eng,2.0.0,2.0.0,, fra,Indo-European,French,Français,fr,fre,2.0.0,2.0.0,, diff --git a/dictionary-tables/ODM_languages_2.2.1.csv b/dictionary-tables/ODM_languages_2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_languages_2.2.1.csv rename to dictionary-tables/ODM_languages_2.2.2.csv diff --git a/dictionary-tables/ODM_lists-HPAIV-H5N1.csv b/dictionary-tables/ODM_lists-HPAIV-H5N1.csv index 3249a80..9041a63 100644 --- a/dictionary-tables/ODM_lists-HPAIV-H5N1.csv +++ b/dictionary-tables/ODM_lists-HPAIV-H5N1.csv @@ -1,105 +1,105 @@ -Version,2.2.1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -sample shed,,,,Site Type Set,,,,Collection Type Set,,,,Boolean Set,,,,Fraction analyzed,,,,Sample material (sample type),,,,PCR Method Set,,,,Target Type Set,,,,Target Set,,,,Genetic Unit Set,,,,Genetic Aggregation Set,,,,,, -partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,,, -airpln,Airplane,Airplane sample shed category type,,bSwrPpl,Branch sewer pipleline,"Specifies a site type that is collection pipe that run lateral to other municpal sewer lines, allowing drainage into the main sewer.",,areaPr,Area proportional sample,An area proportional sample.,,TRUE,TRUE,Boolean data type = TRUE,,liq,Liquid fraction,Liquid fraction of a sample.,,afu,Air filter,Air filter as part of filtration or circulating unit. ,,bioRadDdpcr,Digital droplet emulsification PCR,Describes a PCR analysis done using BioRad's digital droplet emulsification PCR technology.,,sarsCov2,SARS-CoV-2,A group of measures/methods related to the SARS-CoV-2 virus.,,flu,Influenza virus measure,General influenza virus measure,,boc,Breadth of coverage (>=5x depth),Positions with read depth greater or equal to 5.,,pmFloMean,PMMoV- and flow-normalized mean,Mean measure normalized to amount of PMMoV and wastewater flow.,,,, -ccc,Long-term acute care hospital,"Acute care hospitals, or complex contuing care, that provide care for patients with average length of stay longer than 25 days.",,buildCO,Building cleanout,Specifies a site type that is a capped pipe that connects to a building's main sewer line.,,cosca,COSCa ball,COSCa passive sampling device.,,FALSE,FALSE,Boolean data type = FALSE,,mix,Mixed/homogenized sample,Mixed or homogenized sample or fraction analyzed.,,desk,Desk or counter,"Desk, table, countertop or other flat working surface.",,fluiDpcr,Fluidigm digital PCR,Describes a PCR analysis done using FluidIGM's digital PCR technology.,,fluAGrp,Influenza A Virus Group,A group of measures/methods related to Influenza A viruses.,,fluA1,Influenza virus A1,Influenza virus A1 type,,doc,Depth of coverage,The sequencing read depth.,,pmmovNorm,PMMoV-normalized mean,Mean measure normalized to amount of PMMoV.,,,, -cdc,Child day care,Child day care facility.,,estuary,"Estuary, natural water body","Estuary, natural water body",,flowPr,Flow proportional sample,A flow proportional composite sample generally collected by an autosampler.,,,,,,sol,Solid fraction,Solid fraction of a sample.,,faeces,Fecal matter,Fecal matter.,,ltDpcr,Life technologies digital PCR,Describes a PCR analysis done using Life Technologies' digital PCR technology.,,fluBGrp,Influenza B Virus Group,A group of measures/methods related to Influenza B viruses.,,fluA2,influenza virus A2,influenza virus A2 type,,det,Detected,Substance detected or not detected.,,upperCI95,Upper limit of a 95% confidence interval,Specifies the the upper limit of a 95% confidence interval.,,,, -corFcil,Correctional facility,Correctional facility,,lake,"Lake, natural water body","Lake, natural water body",,grb,Grab sample,A single large representative grab sample.,,,,,,NA,Not applicable,The field for which the expected value is not a property of the described object.,,floor,Floor,Floor of a building or room.,,qgDpcr,qiagen digital PCR,Describes a PCR analysis done using Qiagen's digital PCR technology.,,omicronGrp,SARS-CoV-2 Omicron Variant Group,A group of measures/methods related to the SARS-CoV-2 Omicron Variant.,,fluB,Influenza virus B,Influenza virus B type,,gcL,Gene copies per L,Gene or variant copies per litre.,,sdn,Normalized standard deviation,"Standard deviation, normalized.",,,, -dorm,Higher education domitory or residential building,Higher education domitory or residential building,,htSite,Holding tank,Holding tank,,moorSw,Moore swab passive sample,Moore swab passive sample.,,,,,,,,,,htSam,Holding tank wastewater,"Wastewater sampled from a holding tank, such as from an airplane or ship",,qpcr,Quantitative PCR,"Real-time PCR, also called 'quantAggScale' PCR",,deltaGrp,SARS-CoV-2 Delta Variant Group,A group of measures/methods related to the SARS-CoV-2 Delta Variant.,,n,N sars-cov-2 gene target,N sars-cov-2 gene target,,percRec,Percent recovery,Percent of the surrogate recovery for a recovery efficiency control assay.,,menr,Normalized arithmetic mean,"Arithmetic mean, normalized.",,,, -fiNa,First Nation,"Used to categorize a sampleshed that is a First Nation, or on reserve lands.",,lagoon,Lagoon system,Logoon system for extensive wastewater treatment,,surfSw,Surface swab,Surface swab.,,,,,,,,,,nww,Water,"Non-wastewater, coming from any kind of water body",,rainDpcr,Raindance digital PCR,Describes a PCR analysis done using Raindance's digital PCR technology.,,flirtSLipGrp,FLiRT/SLip Variant Group,The group for measures and methods pertaining to the FLiRT and SLip variants of SARS-CoV-2.,,n1n2,Combined N1 and N2 sars-cov-2 gene target,Combined N1 and N2 sars-cov-2 gene target,,prop,Proportion of total,Proportion as a precent of total.,,lowerCI95,Lower limit of a 95% confidence interval,Specifies the the lower limit of a 95% confidence interval.,,,, -hosptl,Hospital,Hospital,,mSwrPpl,Major sewer pipeline,Major sewer pipeline,,timePr,Time proportional sample,A time proportional composite sample generally collected by an autosampler.,,,,,,,,,,pEfflu,Primary clarifier effluent,Effluent obtained after primary clarifiers,,sinProbeOne,"Singleplex, probe-based, one-step RT-qPCR","Describes a PCR method that is singleplex, probe-based, and one-step RT-qPCR.",,,,,,n211i,n211i omicron-variant gene target,n211i omicron-variant gene target,,propV,Proportion of variant in sample,Proportion of a variant as percent of total variants.,,floMean,Flow-normalized mean,Mean measure normalized to wastewater flow.,,,, -ltcf,Long-term care facility,A residential healthcare facility that provides 24-medical care. These are also called skilled nursing facilities.,,ocean,"Ocean, natural water body","Ocean, natural water body",,volPr,Volume proportional sample,A volume proportional sample generally collected by an autosampler.,,,,,,,,,,pSludge,Primary clarifier sludge,Sludge produced by primary clarifiers,,dpcr,Digital PCR (dPCR),Describes a PCR analysis done using digital PCR technology (general).,,,,,,n679k,n679k omicron-variant gene target,n679k omicron-variant gene target,,gcCrA,Gene copies per copy of crAssphage,Gene or variant copies per copy of crAssphage.,,maxVal,Maximum value,Highest value in a range of values for a measure.,,,, -ltcfAl,Long-term care - assisted living or retirement home,A residential facility that provides assistance with daily care but generally does not provide skilled nursing care. ,,pStat,Pumping station,Pumping station,,comp,Composite sample - archival,"A composite sample, usually generated by an autosampler.",,,,,,,,,,pstGrit,Post-grit,Raw wastewater after a treatment plant's headworks (post grit or removal of large solids at a treatment plant but priort to a primary clarifier),,ddpcr,Digital Droplet PCR (ddPCR),Describes a PCR analysis done using digital droplet PCR technology (general).,,,,,,n856k,n856k omicron-variant gene target,n856k omicron-variant gene target,,gcD100,"gene copies per day per 100,000","The unit for measures reflecting the gene copies per day per 100,000 people in the population.",,me,Arithmetic mean,Arithmetic mean.,,,, -ltcfO,Other long-term care,"Other residential facilities that provide daily and/or medical care, but are not defined as nursing home/skilled nursing facilities or assisted living facilities. ",,retPond,Retention pond,Retention pond,,manComp,Manual Composite Sample,Specifies a composite sample where the sub-samples were collected manually.,,,,,,,,,,rawWW,Raw sewage at site,Wastewater without any form of treatment,,,,,,,,,,n969k,n969k omicron-variant gene target,n969k omicron-variant gene target,,gCGS,Gene copies per gram solids,Gene or variant copies per gram solids.,,med,Median,Median.,,,, -municp,Municipality,"A complete municipality, this specifies an entire metropolitan area, either a city, town, etc.",,river,"River, natural water body","River, natural water body",,passiveGen,Passive Sample - General,Used to specify a passive sampling method not otherwise specified was used to collect the sample.,,,,,,,,,,rawWWdown,Raw sewage downstream from a site,Downstream from a site. See partType = rawWWup.,,,,,,,,,,niid19,niid_2019-ncov_n sars-cov-2 gene target,niid_2019-ncov_n sars-cov-2 gene target,,gcMl,Gene copies per mL,Gene or variant copies per millilitre of solution.,,minVal,Minimum value,Lowest value in a range of values for a measure.,,,, -neigh,Neighbourhood,"A municipal neighbourhood, this specifies a sub-section of a larger municipality.",,sea,"Sea, natural water body","Sea, natural water body",,,,,,,,,,,,,,rawWWup,Raw sewage upstream from a site,"Upstream from a site. Used when there is not direct access to a site's wastewater inconjuctiion with downstream sample. For example, if the site is a long-term care home, but ther is not access to the building or property cleanout. Use two sameple, one sample upstream and one sample downstream.",,,,,,,,,,nSarbec,Sarbecovirus-specific N sars-cov-2 gene target,Sarbecovirus-specific N sars-cov-2 gene target,,gcPpmov,Gene copies per PMMoV copy,Gene or variant copies per copy of PMMoV.,,sd,Standard deviation,Standard deviation.,,,, -orb,Other residential building,Individual residential buildings or institutions not captured in other categories,,septTnk,Septic tank,Septic tank,,,,,,,,,,,,,,sEfflu,Secondary clarifier effluent,Effluent obtained after secondary clarifiers,,,,,,,,,,oc43,coronavirus OC43,Measure of the amount of coronavirus OC43.,,gc,Gene copies,Gene or variant copies,,sin,Single,"A value that is not an aggregate measurement (ie. not a mean, median, max or any other) and can be a replicate value.",,,, -school,School,A school serving students in the kindergarten to 12th grade range,,stabPnd,Stabilization pond,Specifies a site type which is a pond designed and built for wastewater treatment to reduce the organic content and remove pathogens from wastewater.,,,,,,,,,,,,,,septage,Septic tank wastewater,Wastewater from within a septic tank,,,,,,,,,,orf1a,ORF1a sars-cov-2 gene target,ORF1a sars-cov-2 gene target,,ct,Cycle threshold or quantification cycle (Ct or Cq),Cycle thresholds in a PCR assay.,,,,,,,, -ship,Ship,A cruise ship or other ship.,,swgTrck,Sewage truck,Sewage truck,,,,,,,,,,,,,,sSludge,Secondary clarifier sludge,Sludge produced by secondary clarifiers,,,,,,,,,,orf1ab,ORF1ab sars-cov-2 gene target,ORF1ab sars-cov-2 gene target,,slope,slope,Slope value of the calibration curve.,,,,,,,, -sss,Social services shelter,Other type of social services shelter,,wwtpInd,Industrial wastewater treatment plant,Industrial wastewater treatment plant,,,,,,,,,,,,,,surface,Other surface,Surface other than floor or desk.,,,,,,,,,,orf1b,ORF1b sars-cov-2 gene target,ORF1b sars-cov-2 gene target,,inter,Intercept,Intercept value of the calibration curve.,,,,,,,, -uCampus,University campus,Universityor college campus - comprising an entire campus or part of a campus.,,wwtpMuC,Municipal wastewater treatment plant for combined sewage,Municipal wastewater treatment plant for combined sewage,,,,,,,,,,,,,,swrSed,Sewer sediment,Sediments obtained in sewer,,,,,,,,,,p100l,p100l delta-variant gene target,p100l delta-variant gene target,,efficient,Efficiency,The efficiency reported for a standard curve.,,,,,,,, -airport,Airport,Airport sample shed category type,,wwtpMuS,Municipal wastewater treatment plant for sanitary sewage only,Municipal wastewater treatment plant for sanitary sewage only,,,,,,,,,,,,,,,,,,,,,,,,,,p2046l,p2046l delta-variant gene target,p2046l delta-variant gene target,,r2,R squared,R-squared value of the calibration curve.,,,,,,,, -terminal,Airport terminal,Airport terminal sample shed category type,,wwtp,Wastewater treatment plant,A general site type for wastewater treatment plants.,,,,,,,,,,,,,,,,,,,,,,,,,,p2287s,p2287s delta-variant gene target,p2287s delta-variant gene target,,,,,,,,,,,, -commFacOth,Commercial facility - not specified,Specifies a site type which is a commercial facility/worksite that is not otherwise captured or described in the geotype set.,,upstream,Upstream sites,A general site type for upstream wastewater sampling sites.,,,,,,,,,,,,,,,,,,,,,,,,,,p3395h,p3395h omicron-variant gene target,p3395h omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a1918v,a1918v delta-variant gene target,a1918v delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a2710t,a2710t omicron-variant gene target,a2710t omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a63t,a63t omicron-variant gene target,a63t omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a67v,a67v omicron-variant gene target,a67v omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d377y,d377y delta-variant gene target,d377y delta-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d3g,d3g omicron-variant gene target,d3g omicron-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d63g,d63g delta-variant gene target,d63g delta-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d796y,d796y omicron-variant gene target,d796y omicron-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d950n,d950n delta-variant gene target,d950n delta-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ddcovE,ddcov_e sars-cov-2 gene target,ddcov_e sars-cov-2 gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ddcovN ,ddcov_n sars-cov-2 gene target,ddcov_n sars-cov-2 gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del143,del143/145,143 or 145 deletion omicron-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del157,del 157/158,157 or 158 deletion delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del2084,del2084/2084,2084 or 2084 deletion omicron-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del212,del212/212,212 or 212 deletion omicron-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del3674,del3674/3676,3674 or 3676 deletion omicron-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del6970,del69/70,69 or 70 deletion omicron-variant gene target.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,e156g,e156g delta-variant gene target,e156g delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,e484a,e484a omicron-variant gene target,e484a omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,eSarbec,Sarbecovirus-specific E sars-cov-2 gene target,Sarbecovirus-specific E sars-cov-2 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,fluA,Influenza A virus,Influenza A virus.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g215c,g215c delta-variant gene target,g215c delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g339d,g339d omicron-variant gene target,g339d omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g496s,g496s omicron-variant gene target,g496s omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g662s,g662s delta-variant gene target,g662s delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,i1566v,i1566v omicron-variant gene target,i1566v omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,i3758v,i3758v omicron-variant gene target,i3758v omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,i82t,i82t delta-variant gene target,i82t delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ip2ip4,Combined ip2 and ip4 sars-cov-2 gene target,Combined ip2 and ip4 sars-cov-2 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,k856r,k856r omicron-variant gene target,k856r omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l452r,l452r delta-variant gene target,l452r delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l981f,l981f omicron-variant gene target,l981f omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q19e,q19e omicron-variant gene target,q19e omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q493r,q493r omicron-variant gene target,q493r omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q498r,q498r omicron-variant gene target,q498r omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q954h,q954h omicron-variant gene target,q954h omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,r203m,r203m delta-variant gene target,r203m delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,rdrpIP2,IP2 rdrp sars-cov-2 gene target,IP2 rdrp sars-cov-2 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,rdrpIP4,IP4 rdrp sars-cov-2 gene target,IP4 rdrp sars-cov-2 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s2083i,s2083i omicron-variant gene target,s2083i omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s371l,s371l omicron-variant gene target,s371l omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s373p,s373p omicron-variant gene target,s373p omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s375f,s375f omicron-variant gene target,s375f omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s477n,s477n omicron-variant gene target,s477n omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,sGene,S sars-cov-2 gene target,S sars-cov-2 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t19r,t19r delta-variant gene target,t19r delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t3646a,t3646a delta-variant gene target,t3646a delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t547k,t547k omicron-variant gene target,t547k omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t9i,t9i omicron-variant gene target,t9i omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,taqpatN,TaqPath N sars-cov-2 gene target,TaqPath N sars-cov-2 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,taqpatS,TaqPath S sars-cov-2 gene target,TaqPath N sars-cov-2 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,v2930l,v2930l delta-variant gene target,v2930l delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,y505h,y505h omicron-variant gene target,y505h omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,covN200,SARS-CoV-2-N200,"SARS-CoV-2 nucleocapsid gene, amino acids 199-202.",,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del142144,Omicron Variant 142-144 Deletion,Omicron Variant 142-144 Deletion,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del156157,Delta Variant 156-157 Deletion,Delta Variant 156-157 Deletion,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del3133,Omicron Variant 142-14431-33 Deletion,Omicron Variant 142-14431-33 Deletion,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ins214epe,Omicron Variant ins214epe Insertion,Omicron Variant ins214epe Insertion,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l24s,Omicron Variant l24s mutation,Omicron Variant l24s mutation,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,lppa24s,Omicron Variant LPPA24S mutation,Omicron Variant LPPA24S mutation,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n211i,n211i omicron-variant gene target,n211i omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n679k,n679k omicron-variant gene target,n679k omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n856k,n856k omicron-variant gene target,n856k omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n969k,n969k omicron-variant gene target,n969k omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p100l,p100l delta-variant gene target,p100l delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p13L,Omicron Variant p13l mutation,Omicron Variant p13l mutation,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p2046l,p2046l delta-variant gene target,p2046l delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p2287s,p2287s delta-variant gene target,p2287s delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p3395h,p3395h omicron-variant gene target,p3395h omicron-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p681r,p681r delta-variant gene target,p681r delta-variant gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,wt214,Delta Variant wt214 gene target,Delta Variant wt214 gene target,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,fluA1A2c,Influenza virus A1 and A2 combined,"Measure of influenza virus A1 and A2 combined, usually due to single fluorescence channel.",,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a67vDel69Del70,Omicron Variant a67v del69 and del70 mutations,"Omicron Variant a67v mutation, and del 69 and del70 mutations co-occuring",,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,h5n1,H5N1 avian influenza A virus (IAV),"General measurement for the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.",,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,h5hema,Influenza A H5 hemagglutinin gene,"Measure of the H5 hemagglutinin gene from the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.",,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n1neur,Influenza A N1 neuraminidase gene,"Measure of the N1 neuraminidase gene from the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.",,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,iavM,Influenza A M gene,"A measure of the M gene found in Influenza A viruses (IAV). The virus has segmented RNA genome and 7th segment, M gene, encodes 2 proteins. M1 is a matrix protein and M2 is a membrane protein. The M gene may be involved in determining host tropism.",,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,r346t,R346T Mutation,The FLiRT/SLip variant mutation R346T.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,f456l,F456L Mutation,The FLiRT/SLip variant mutation F456L.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,v1104l,V1104L Mutation,The FLiRT/SLip variant mutation V1104L,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d339h,D339H Mutation,The FLiRT/SLip variant mutation D339H.,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l455s,L455S Mutation,The FLiRT/SLip variant mutation L455S.,,,,,,,,,,,, \ No newline at end of file +Version,2.2.2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +sample shed,,,,Site Type Set,,,,Collection Type Set,,,,Boolean Set,,,,Fraction analyzed,,,,Sample material (sample type),,,,PCR Method Set,,,,Target Type Set,,,,Target Set,,,,Genetic Unit Set,,,,Genetic Aggregation Set,, +partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc +airpln,Airplane,Airplane sample shed category type,,bSwrPpl,Branch sewer pipleline,"Specifies a site type that is collection pipe that run lateral to other municpal sewer lines, allowing drainage into the main sewer.",,areaPr,Area proportional sample,An area proportional sample.,,TRUE,TRUE,Boolean data type = TRUE,,liq,Liquid fraction,Liquid fraction of a sample.,,afu,Air filter,Air filter as part of filtration or circulating unit. ,,bioRadDdpcr,Digital droplet emulsification PCR,Describes a PCR analysis done using BioRad's digital droplet emulsification PCR technology.,,sarsCov2,SARS-CoV-2,A group of measures/methods related to the SARS-CoV-2 virus.,,flu,Influenza virus measure,General influenza virus measure,,boc,Breadth of coverage (>=5x depth),Positions with read depth greater or equal to 5.,,pmFloMean,PMMoV- and flow-normalized mean,Mean measure normalized to amount of PMMoV and wastewater flow. +ccc,Long-term acute care hospital,"Acute care hospitals, or complex contuing care, that provide care for patients with average length of stay longer than 25 days.",,buildCO,Building cleanout,Specifies a site type that is a capped pipe that connects to a building's main sewer line.,,cosca,COSCa ball,COSCa passive sampling device.,,FALSE,FALSE,Boolean data type = FALSE,,mix,Mixed/homogenized sample,Mixed or homogenized sample or fraction analyzed.,,desk,Desk or counter,"Desk, table, countertop or other flat working surface.",,fluiDpcr,Fluidigm digital PCR,Describes a PCR analysis done using FluidIGM's digital PCR technology.,,fluAGrp,Influenza A Virus Group,A group of measures/methods related to Influenza A viruses.,,fluA1,Influenza virus A1,Influenza virus A1 type,,doc,Depth of coverage,The sequencing read depth.,,pmmovNorm,PMMoV-normalized mean,Mean measure normalized to amount of PMMoV. +cdc,Child day care,Child day care facility.,,estuary,"Estuary, natural water body","Estuary, natural water body",,flowPr,Flow proportional sample,A flow proportional composite sample generally collected by an autosampler.,,,,,,sol,Solid fraction,Solid fraction of a sample.,,faeces,Fecal matter,Fecal matter.,,ltDpcr,Life technologies digital PCR,Describes a PCR analysis done using Life Technologies' digital PCR technology.,,fluBGrp,Influenza B Virus Group,A group of measures/methods related to Influenza B viruses.,,fluA2,influenza virus A2,influenza virus A2 type,,det,Detected,Substance detected or not detected.,,upperCI95,Upper limit of a 95% confidence interval,Specifies the the upper limit of a 95% confidence interval. +corFcil,Correctional facility,Correctional facility,,lake,"Lake, natural water body","Lake, natural water body",,grb,Grab sample,A single large representative grab sample.,,,,,,NA,Not applicable,The field for which the expected value is not a property of the described object.,,floor,Floor,Floor of a building or room.,,qgDpcr,qiagen digital PCR,Describes a PCR analysis done using Qiagen's digital PCR technology.,,omicronGrp,SARS-CoV-2 Omicron Variant Group,A group of measures/methods related to the SARS-CoV-2 Omicron Variant.,,fluB,Influenza virus B,Influenza virus B type,,gcL,Gene copies per L,Gene or variant copies per litre.,,sdn,Normalized standard deviation,"Standard deviation, normalized." +dorm,Higher education domitory or residential building,Higher education domitory or residential building,,htSite,Holding tank,Holding tank,,moorSw,Moore swab passive sample,Moore swab passive sample.,,,,,,,,,,htSam,Holding tank wastewater,"Wastewater sampled from a holding tank, such as from an airplane or ship",,qpcr,Quantitative PCR,"Real-time PCR, also called 'quantAggScale' PCR",,deltaGrp,SARS-CoV-2 Delta Variant Group,A group of measures/methods related to the SARS-CoV-2 Delta Variant.,,n,N sars-cov-2 gene target,N sars-cov-2 gene target,,percRec,Percent recovery,Percent of the surrogate recovery for a recovery efficiency control assay.,,menr,Normalized arithmetic mean,"Arithmetic mean, normalized." +fiNa,First Nation,"Used to categorize a sampleshed that is a First Nation, or on reserve lands.",,lagoon,Lagoon system,Logoon system for extensive wastewater treatment,,surfSw,Surface swab,Surface swab.,,,,,,,,,,nww,Water,"Non-wastewater, coming from any kind of water body",,rainDpcr,Raindance digital PCR,Describes a PCR analysis done using Raindance's digital PCR technology.,,flirtSLipGrp,FLiRT/SLip Variant Group,The group for measures and methods pertaining to the FLiRT and SLip variants of SARS-CoV-2.,,n1n2,Combined N1 and N2 sars-cov-2 gene target,Combined N1 and N2 sars-cov-2 gene target,,prop,Proportion of total,Proportion as a precent of total.,,lowerCI95,Lower limit of a 95% confidence interval,Specifies the the lower limit of a 95% confidence interval. +hosptl,Hospital,Hospital,,mSwrPpl,Major sewer pipeline,Major sewer pipeline,,timePr,Time proportional sample,A time proportional composite sample generally collected by an autosampler.,,,,,,,,,,pEfflu,Primary clarifier effluent,Effluent obtained after primary clarifiers,,sinProbeOne,"Singleplex, probe-based, one-step RT-qPCR","Describes a PCR method that is singleplex, probe-based, and one-step RT-qPCR.",,,,,,n211i,n211i omicron-variant gene target,n211i omicron-variant gene target,,propV,Proportion of variant in sample,Proportion of a variant as percent of total variants.,,floMean,Flow-normalized mean,Mean measure normalized to wastewater flow. +ltcf,Long-term care facility,A residential healthcare facility that provides 24-medical care. These are also called skilled nursing facilities.,,ocean,"Ocean, natural water body","Ocean, natural water body",,volPr,Volume proportional sample,A volume proportional sample generally collected by an autosampler.,,,,,,,,,,pSludge,Primary clarifier sludge,Sludge produced by primary clarifiers,,dpcr,Digital PCR (dPCR),Describes a PCR analysis done using digital PCR technology (general).,,,,,,n679k,n679k omicron-variant gene target,n679k omicron-variant gene target,,gcCrA,Gene copies per copy of crAssphage,Gene or variant copies per copy of crAssphage.,,maxVal,Maximum value,Highest value in a range of values for a measure. +ltcfAl,Long-term care - assisted living or retirement home,A residential facility that provides assistance with daily care but generally does not provide skilled nursing care. ,,pStat,Pumping station,Pumping station,,comp,Composite sample - archival,"A composite sample, usually generated by an autosampler.",,,,,,,,,,pstGrit,Post-grit,Raw wastewater after a treatment plant's headworks (post grit or removal of large solids at a treatment plant but priort to a primary clarifier),,ddpcr,Digital Droplet PCR (ddPCR),Describes a PCR analysis done using digital droplet PCR technology (general).,,,,,,n856k,n856k omicron-variant gene target,n856k omicron-variant gene target,,gcD100,"gene copies per day per 100,000","The unit for measures reflecting the gene copies per day per 100,000 people in the population.",,me,Arithmetic mean,Arithmetic mean. +ltcfO,Other long-term care,"Other residential facilities that provide daily and/or medical care, but are not defined as nursing home/skilled nursing facilities or assisted living facilities. ",,retPond,Retention pond,Retention pond,,manComp,Manual Composite Sample,Specifies a composite sample where the sub-samples were collected manually.,,,,,,,,,,rawWW,Raw sewage at site,Wastewater without any form of treatment,,,,,,,,,,n969k,n969k omicron-variant gene target,n969k omicron-variant gene target,,gCGS,Gene copies per gram solids,Gene or variant copies per gram solids.,,med,Median,Median. +municp,Municipality,"A complete municipality, this specifies an entire metropolitan area, either a city, town, etc.",,river,"River, natural water body","River, natural water body",,passiveGen,Passive Sample - General,Used to specify a passive sampling method not otherwise specified was used to collect the sample.,,,,,,,,,,rawWWdown,Raw sewage downstream from a site,Downstream from a site. See partType = rawWWup.,,,,,,,,,,niid19,niid_2019-ncov_n sars-cov-2 gene target,niid_2019-ncov_n sars-cov-2 gene target,,gcMl,Gene copies per mL,Gene or variant copies per millilitre of solution.,,minVal,Minimum value,Lowest value in a range of values for a measure. +neigh,Neighbourhood,"A municipal neighbourhood, this specifies a sub-section of a larger municipality.",,sea,"Sea, natural water body","Sea, natural water body",,,,,,,,,,,,,,rawWWup,Raw sewage upstream from a site,"Upstream from a site. Used when there is not direct access to a site's wastewater inconjuctiion with downstream sample. For example, if the site is a long-term care home, but ther is not access to the building or property cleanout. Use two sameple, one sample upstream and one sample downstream.",,,,,,,,,,nSarbec,Sarbecovirus-specific N sars-cov-2 gene target,Sarbecovirus-specific N sars-cov-2 gene target,,gcPpmov,Gene copies per PMMoV copy,Gene or variant copies per copy of PMMoV.,,sd,Standard deviation,Standard deviation. +orb,Other residential building,Individual residential buildings or institutions not captured in other categories,,septTnk,Septic tank,Septic tank,,,,,,,,,,,,,,sEfflu,Secondary clarifier effluent,Effluent obtained after secondary clarifiers,,,,,,,,,,oc43,coronavirus OC43,Measure of the amount of coronavirus OC43.,,gc,Gene copies,Gene or variant copies,,sin,Single,"A value that is not an aggregate measurement (ie. not a mean, median, max or any other) and can be a replicate value." +school,School,A school serving students in the kindergarten to 12th grade range,,stabPnd,Stabilization pond,Specifies a site type which is a pond designed and built for wastewater treatment to reduce the organic content and remove pathogens from wastewater.,,,,,,,,,,,,,,septage,Septic tank wastewater,Wastewater from within a septic tank,,,,,,,,,,orf1a,ORF1a sars-cov-2 gene target,ORF1a sars-cov-2 gene target,,ct,Cycle threshold or quantification cycle (Ct or Cq),Cycle thresholds in a PCR assay.,,,, +ship,Ship,A cruise ship or other ship.,,swgTrck,Sewage truck,Sewage truck,,,,,,,,,,,,,,sSludge,Secondary clarifier sludge,Sludge produced by secondary clarifiers,,,,,,,,,,orf1ab,ORF1ab sars-cov-2 gene target,ORF1ab sars-cov-2 gene target,,slope,slope,Slope value of the calibration curve.,,,, +sss,Social services shelter,Other type of social services shelter,,wwtpInd,Industrial wastewater treatment plant,Industrial wastewater treatment plant,,,,,,,,,,,,,,surface,Other surface,Surface other than floor or desk.,,,,,,,,,,orf1b,ORF1b sars-cov-2 gene target,ORF1b sars-cov-2 gene target,,inter,Intercept,Intercept value of the calibration curve.,,,, +uCampus,University campus,Universityor college campus - comprising an entire campus or part of a campus.,,wwtpMuC,Municipal wastewater treatment plant for combined sewage,Municipal wastewater treatment plant for combined sewage,,,,,,,,,,,,,,swrSed,Sewer sediment,Sediments obtained in sewer,,,,,,,,,,p100l,p100l delta-variant gene target,p100l delta-variant gene target,,efficient,Efficiency,The efficiency reported for a standard curve.,,,, +airport,Airport,Airport sample shed category type,,wwtpMuS,Municipal wastewater treatment plant for sanitary sewage only,Municipal wastewater treatment plant for sanitary sewage only,,,,,,,,,,,,,,,,,,,,,,,,,,p2046l,p2046l delta-variant gene target,p2046l delta-variant gene target,,r2,R squared,R-squared value of the calibration curve.,,,, +terminal,Airport terminal,Airport terminal sample shed category type,,wwtp,Wastewater treatment plant,A general site type for wastewater treatment plants.,,,,,,,,,,,,,,,,,,,,,,,,,,p2287s,p2287s delta-variant gene target,p2287s delta-variant gene target,,,,,,,, +commFacOth,Commercial facility - not specified,Specifies a site type which is a commercial facility/worksite that is not otherwise captured or described in the geotype set.,,upstream,Upstream sites,A general site type for upstream wastewater sampling sites.,,,,,,,,,,,,,,,,,,,,,,,,,,p3395h,p3395h omicron-variant gene target,p3395h omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a1918v,a1918v delta-variant gene target,a1918v delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a2710t,a2710t omicron-variant gene target,a2710t omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a63t,a63t omicron-variant gene target,a63t omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a67v,a67v omicron-variant gene target,a67v omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d377y,d377y delta-variant gene target,d377y delta-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d3g,d3g omicron-variant gene target,d3g omicron-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d63g,d63g delta-variant gene target,d63g delta-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d796y,d796y omicron-variant gene target,d796y omicron-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d950n,d950n delta-variant gene target,d950n delta-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ddcovE,ddcov_e sars-cov-2 gene target,ddcov_e sars-cov-2 gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ddcovN ,ddcov_n sars-cov-2 gene target,ddcov_n sars-cov-2 gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del143,del143/145,143 or 145 deletion omicron-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del157,del 157/158,157 or 158 deletion delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del2084,del2084/2084,2084 or 2084 deletion omicron-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del212,del212/212,212 or 212 deletion omicron-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del3674,del3674/3676,3674 or 3676 deletion omicron-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del6970,del69/70,69 or 70 deletion omicron-variant gene target.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,e156g,e156g delta-variant gene target,e156g delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,e484a,e484a omicron-variant gene target,e484a omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,eSarbec,Sarbecovirus-specific E sars-cov-2 gene target,Sarbecovirus-specific E sars-cov-2 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,fluA,Influenza A virus,Influenza A virus.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g215c,g215c delta-variant gene target,g215c delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g339d,g339d omicron-variant gene target,g339d omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g496s,g496s omicron-variant gene target,g496s omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,g662s,g662s delta-variant gene target,g662s delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,i1566v,i1566v omicron-variant gene target,i1566v omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,i3758v,i3758v omicron-variant gene target,i3758v omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,i82t,i82t delta-variant gene target,i82t delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ip2ip4,Combined ip2 and ip4 sars-cov-2 gene target,Combined ip2 and ip4 sars-cov-2 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,k856r,k856r omicron-variant gene target,k856r omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l452r,l452r delta-variant gene target,l452r delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l981f,l981f omicron-variant gene target,l981f omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q19e,q19e omicron-variant gene target,q19e omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q493r,q493r omicron-variant gene target,q493r omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q498r,q498r omicron-variant gene target,q498r omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,q954h,q954h omicron-variant gene target,q954h omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,r203m,r203m delta-variant gene target,r203m delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,rdrpIP2,IP2 rdrp sars-cov-2 gene target,IP2 rdrp sars-cov-2 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,rdrpIP4,IP4 rdrp sars-cov-2 gene target,IP4 rdrp sars-cov-2 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s2083i,s2083i omicron-variant gene target,s2083i omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s371l,s371l omicron-variant gene target,s371l omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s373p,s373p omicron-variant gene target,s373p omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s375f,s375f omicron-variant gene target,s375f omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,s477n,s477n omicron-variant gene target,s477n omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,sGene,S sars-cov-2 gene target,S sars-cov-2 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t19r,t19r delta-variant gene target,t19r delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t3646a,t3646a delta-variant gene target,t3646a delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t547k,t547k omicron-variant gene target,t547k omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,t9i,t9i omicron-variant gene target,t9i omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,taqpatN,TaqPath N sars-cov-2 gene target,TaqPath N sars-cov-2 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,taqpatS,TaqPath S sars-cov-2 gene target,TaqPath N sars-cov-2 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,v2930l,v2930l delta-variant gene target,v2930l delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,y505h,y505h omicron-variant gene target,y505h omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,covN200,SARS-CoV-2-N200,"SARS-CoV-2 nucleocapsid gene, amino acids 199-202.",,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del142144,Omicron Variant 142-144 Deletion,Omicron Variant 142-144 Deletion,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del156157,Delta Variant 156-157 Deletion,Delta Variant 156-157 Deletion,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,del3133,Omicron Variant 142-14431-33 Deletion,Omicron Variant 142-14431-33 Deletion,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,ins214epe,Omicron Variant ins214epe Insertion,Omicron Variant ins214epe Insertion,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l24s,Omicron Variant l24s mutation,Omicron Variant l24s mutation,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,lppa24s,Omicron Variant LPPA24S mutation,Omicron Variant LPPA24S mutation,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n211i,n211i omicron-variant gene target,n211i omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n679k,n679k omicron-variant gene target,n679k omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n856k,n856k omicron-variant gene target,n856k omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n969k,n969k omicron-variant gene target,n969k omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p100l,p100l delta-variant gene target,p100l delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p13L,Omicron Variant p13l mutation,Omicron Variant p13l mutation,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p2046l,p2046l delta-variant gene target,p2046l delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p2287s,p2287s delta-variant gene target,p2287s delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p3395h,p3395h omicron-variant gene target,p3395h omicron-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,p681r,p681r delta-variant gene target,p681r delta-variant gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,wt214,Delta Variant wt214 gene target,Delta Variant wt214 gene target,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,fluA1A2c,Influenza virus A1 and A2 combined,"Measure of influenza virus A1 and A2 combined, usually due to single fluorescence channel.",,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,a67vDel69Del70,Omicron Variant a67v del69 and del70 mutations,"Omicron Variant a67v mutation, and del 69 and del70 mutations co-occuring",,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,h5n1,H5N1 avian influenza A virus (IAV),"General measurement for the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.",,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,h5hema,Influenza A H5 hemagglutinin gene,"Measure of the H5 hemagglutinin gene from the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.",,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,n1neur,Influenza A N1 neuraminidase gene,"Measure of the N1 neuraminidase gene from the Highly Pathogenic Avian Influenza Virus (HPAIV), the H5N1 Influenza A Virus (IAV) subtype.",,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,iavM,Influenza A M gene,"A measure of the M gene found in Influenza A viruses (IAV). The virus has segmented RNA genome and 7th segment, M gene, encodes 2 proteins. M1 is a matrix protein and M2 is a membrane protein. The M gene may be involved in determining host tropism.",,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,r346t,R346T Mutation,The FLiRT/SLip variant mutation R346T.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,f456l,F456L Mutation,The FLiRT/SLip variant mutation F456L.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,v1104l,V1104L Mutation,The FLiRT/SLip variant mutation V1104L,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,d339h,D339H Mutation,The FLiRT/SLip variant mutation D339H.,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,l455s,L455S Mutation,The FLiRT/SLip variant mutation L455S.,,,,,,,, \ No newline at end of file diff --git a/dictionary-tables/ODM_lists-HPAIV-H5N1_v2.2.1.csv b/dictionary-tables/ODM_lists-HPAIV-H5N1_v2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_lists-HPAIV-H5N1_v2.2.1.csv rename to dictionary-tables/ODM_lists-HPAIV-H5N1_v2.2.2.csv diff --git a/dictionary-tables/ODM_lists-planes.csv b/dictionary-tables/ODM_lists-planes.csv index e7353b6..971764b 100644 --- a/dictionary-tables/ODM_lists-planes.csv +++ b/dictionary-tables/ODM_lists-planes.csv @@ -1,4 +1,4 @@ -Version,2.2.1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Version,2.2.2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Target,Mutation,,,,Target,Allele,,,,Target,Variant,,,,Genetic Unit Set,,,,saMaterial,"(sample material, 'sample type')",,,Sample Collection,,,,Fraction analyzed,,,,methodID,(PCR//Sequencing),,,,pcrSet,"(for partID = pcrmeth, label = PCR method)",,,scriptSet,"(for partID = scriptVersion, label = Script version)",,,seqStratSet,"(for partID = seqStrat, label = Sequencing strategy)",,,seqSelSet,"(for partID = seqSel, label = Sequencing selection)",,,seqLaySet,"(for partID = seqLay, label = Sequencing layout)",,,Aggregation,,,,target type,,,,sample shed,,,,Airport,,,methodID,(PCR//Sequencing),,,Target,,, partID,label,partDesc,unitSetID,,partID,label,partDesc,unitSetID,,partID,label,partDesc,unitSetID,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,catSet,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,partID,label,partDesc,,IATA code,Airport,Country,partID,label,partDesc,,partID,label,partDesc,unitSetID n1n2,Combined N1 and N2 sars-cov-2 gene target,Combined N1 and N2 sars-cov-2 gene target,geneticUnitSet,,cov2Me,SARS-CoV-2 measure,Measure the amount of SARS-CoV-2 virus.,geneticUnitSet,,mu,Mu,B.1.621,geneticUnitSet,,boc,Breadth of coverage (>=5x depth),Positions with read depth greater or equal to 5.,,afu,Air filter,Air filter as part of filtration or circulating unit. ,,areaPr,Area proportional sample,An area proportional sample.,,liq,Liquid fraction,Liquid fraction of a sample.,,primer,Genetic primer,Method ID used for indicating the primer used for a PCR or sequencing assay.,primerSet,,bioRadDdpcr,Digital droplet emulsification PCR,Describes a PCR analysis done using BioRad's digital droplet emulsification PCR technology.,,gromstole,Gromstole 1.0 Script,Gromstole 1.0 Script for sequencing.,,amp,Amplicon sequencing,Specifies the amplicon strategy for genetic sequencing,,ranSeq,Random sequencing selection method,Specifies the random selection method for sequencing,,sinLay,Single Layout,Specifies the single layout for a sequencing method,,floMean,Flow-normalized mean,Mean measure normalized to wastewater flow.,,allele,Alleles class,Measures and methods related to alleles.,,airpln,Airplane,Airplane sample shed category type,,AAR,Aarhus,Denmark,,*** PCR method ***,,,,*** Mutation ***,, diff --git a/dictionary-tables/ODM_lists-planes_v2.2.1.csv b/dictionary-tables/ODM_lists-planes_v2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_lists-planes_v2.2.1.csv rename to dictionary-tables/ODM_lists-planes_v2.2.2.csv diff --git a/dictionary-tables/ODM_parts_2.2.1.csv b/dictionary-tables/ODM_parts_2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_parts_2.2.1.csv rename to dictionary-tables/ODM_parts_2.2.2.csv diff --git a/dictionary-tables/ODM_sets_2.2.1.csv b/dictionary-tables/ODM_sets_2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_sets_2.2.1.csv rename to dictionary-tables/ODM_sets_2.2.2.csv diff --git a/dictionary-tables/ODM_translations_2.2.1.csv b/dictionary-tables/ODM_translations_2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_translations_2.2.1.csv rename to dictionary-tables/ODM_translations_2.2.2.csv diff --git a/dictionary-tables/ODM_zones.csv b/dictionary-tables/ODM_zones.csv index 2858484..0c11f05 100644 --- a/dictionary-tables/ODM_zones.csv +++ b/dictionary-tables/ODM_zones.csv @@ -1,4 +1,4 @@ -Version,2.2.1, +Version,2.2.2, isoCode,isoZone,zoneName AD,AD-02,Canillo AD,AD-03,Encamp diff --git a/dictionary-tables/ODM_zones_2.2.1.csv b/dictionary-tables/ODM_zones_2.2.2.csv similarity index 100% rename from dictionary-tables/ODM_zones_2.2.1.csv rename to dictionary-tables/ODM_zones_2.2.2.csv diff --git a/templates/Airports_Report_Template-0.4.1.xlsx b/templates/Airports_Report_Template-0.4.1.xlsx new file mode 100644 index 0000000..a34e28a Binary files /dev/null and b/templates/Airports_Report_Template-0.4.1.xlsx differ diff --git a/templates/H5N1_Report_Template-0.1.1.xlsx b/templates/H5N1_Report_Template-0.1.1.xlsx new file mode 100644 index 0000000..1839e45 Binary files /dev/null and b/templates/H5N1_Report_Template-0.1.1.xlsx differ diff --git a/templates/ODM_templates_2.2.0.xlsx b/templates/ODM_templates_2.2.0.xlsx deleted file mode 100644 index a95b70a..0000000 Binary files a/templates/ODM_templates_2.2.0.xlsx and /dev/null differ diff --git a/templates/ODM_templates_2.2.2.xlsx b/templates/ODM_templates_2.2.2.xlsx new file mode 100644 index 0000000..75d5702 Binary 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