An instance of the "database identifiers field category" that contains the "bioproject accession field". A data field category which refers to database identifier fields. database identifiers https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z database identifiers slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 database identifiers field category prov_rona_99 An identifier data field which describes the user-defined name for the sample. sample collector sample identifier sample_collector_sample_ID specimen collector sample ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector sample identifier field sample collector sample identifier slot specimen collector sample ID slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Every Sample 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. specimen collector sample ID field SR20-12345 A data field which describes the primary identifer of a related specimen previously submitted to the repository. related specimen primary ID related specimen primary identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z related specimen primary ID slot related specimen primary identifier field related specimen primary identifier slot Monkeypox CanCOGeN SARS-CoV-2 Example Guidance: Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. related specimen primary ID field prov_rona_99 A data field which describes the identifer assigned to a sequenced isolate in Integrated Rapid Infectious Disease Analysis (IRIDA) bioinformatics platform. IRIDA sample identifier IRIDA sample name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA sample ID slot IRIDA sample identifier slot IRIDA sample name slot Integrated Rapid Infectious Disease Analysis sample ID field Integrated Rapid Infectious Disease Analysis sample ID slot Integrated Rapid Infectious Disease Analysis sample identifier field Integrated Rapid Infectious Disease Analysis sample identifier slot Integrated Rapid Infectious Disease Analysis sample name field Integrated Rapid Infectious Disease Analysis sample name slot CanCOGeN SARS-CoV-2 Example Guidance: Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). IRIDA sample name field PRJNA623807 An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) umbrella accession number of the BioProject to which the BioSample belongs. umbrella bioproject accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z umbrella bioproject accession slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects. umbrella bioproject accession field PRJNA12345 An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) accession number of the BioProject(s) to which the BioSample belongs. bioproject accession bioproject_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioproject accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: 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. bioproject accession field SAMN14180202 A data field which describes the identifier assigned to a BioSample in International Nucleotide Sequence Database Collaboration (INSDC) archives. biosample accession biosample_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z biosample accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. biosample accession field SRR11177792 A data field which describes 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 International Nucleotide Sequence Database Collaboration (INSDC). SRA accession SRA_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z SRA accession slot Sequence Read Archive accession field Sequence Read Archive accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 DDBJ = DNA DataBank of Japan Example Guidance: 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. SRA accession field MN908947.3 A data field which describes the GenBank/ENA/DDBJ identifier assigned to the sequence in the International Nucleotide Sequence Database Collaboration (INSDC) archives. GenBank accession GenBank/ENA/DDBJ accession GenBank_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GenBank accession slot GenBank/ENA/DDBJ accession field GenBank/ENA/DDBJ accession slot National Genetic Sequence Data Base accession field National Genetic Sequence Data Base accession slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 GenBank = National Genetic Sequence Data Base; ENA = European Nucleotide Archive; DDBJ = DNA DataBank of Japan Example Guidance: Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly). GenBank accession field EPI_ISL_123456 An identifier data field which describes the Global Initiative on Sharing Avian Influenza Data (GISAID) accession number assigned to the sequence. GISAID accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GISAID accession slot Global Initiative on Sharing Avian Influenza Data accession field Global Initiative on Sharing Avian Influenza Data accession slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Store the accession returned from the GISAID submission. GISAID accession field SHK123456 A data field which describes the identifier assigned to a sample by a third party service provider. third party lab sample ID third party lab sample identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z third party lab sample ID slot third party lab sample identifier field third party lab sample identifier slot CanCOGeN SARS-CoV-2 Example Guidance: Store the sample identifier supplied by the third party services provider. third party lab sample ID field An instance of the "sample collection and processing field category" that contains the "sample collection date field". A data field category which refers to sample collection and processing information fields. sample collection and processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection and processing slot category GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 sample collection and processing field category Public Health Agency of Canada A data field which describes the name of the organization with which the sample collector is affiliated. sample collected by sample_collected_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected by slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. sample collected by field johnnyblogs@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the sample. sample collector contact email sample_collector_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact email slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The email address can represent a specific individual or laboratory. sample collector contact email field 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada A data field which describes the mailing address of the agency submitting the sample. sample collector contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact address slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code sample collector contact address field Centers for Disease Control and Prevention A data field which describes the name of the agency that generated the sequence. sequence submitted by sequence_submitted_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitted by slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. sequence submitted by field RespLab@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the sequence. sequence submitter contact email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitter contact email slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The email address can represent a specific individual or laboratory. sequence submitter contact email field 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada A data field which describes the mailing address of the agency submitting the sequence. sequence submitter contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitter contact address slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code sequence submitter contact address field 2020-03-19 A data field which describes the date on which the sample was collected. sample collection date sample_collection_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection date slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add .jitter. to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. sample collection date field year A data field which describes the precision to which the "sample collection date" was provided. sample collection date precision https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection date precision slot Monkeypox CanCOGeN SARS-CoV-2 Used to further describe the .sample collection date field. [GENEPIO:0001174]. Example Guidance: 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.. sample collection date precision field 2020-03-20 A data field which describes the date on which the sample was received. sample received date sample_received_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample received date slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The date the sample was received by a lab that was not the point of collection. ISO 8601 standard .YYYY-MM-DD.. sample received date field South Africa [GAZ:00001094] A data field which describes the country of origin of the sample. geo_loc name (country) geographical location country name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (country) slot geographical location country name field geographical location country name slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the country name from the pick list in the template geo_loc name (country) field Western Cape A data field which describes the state, province, or territory of origin of the sample. geo_loc name (state/province/territory) geographical location state or province or territory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (state/province/territory) slot geographical location state or province or territory name field geographical location state or province or territory name slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (state/province/territory) field Vancouver A data field which describes the city of origin of the sample. geo_loc name (city) geographical location city name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (city) slot geographical location city name field geographical location city name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (city) field Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] A data field which describes the taxonomic name of the organism. organism https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z organism slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: 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. organism field Diagnostic testing [GENEPIO:0100002] A data field which describes the reason that the sample was collected. purpose of sampling purpose_of_sampling https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sampling slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select a value from the pick list in the template. purpose of sampling field Screening of bat specimens in museum collections. A data field which describes additional information pertaining to the reason the sample was collected. purpose of sampling details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sampling details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a free text description of the sampling strategy or samples collected. purpose of sampling details field Switch Health A data field which describes the name of the third party company or laboratory that provided services. third party lab service provider name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z third party lab service provider name slot CanCOGeN SARS-CoV-2 Example Guidance: Provide the full, unabbreviated name of the company or laboratory. third party lab service provider name field swab A data field which describes the type of specimen submitted to the National Microbiology Laboratory (NML) for testing. NML submitted specimen type National Microbiology Laboratory submitted specimen type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z NML submitted specimen type slot National Microbiology Laboratory submitted specimen type field National Microbiology Laboratory submitted specimen type slot Monkeypox CanCOGeN SARS-CoV-2 Example Guidance: This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. NML submitted specimen type field Specimen sampling methods testing A data field which describes the relationship of the current specimen to the specimen/sample previously submitted to the repository. Related specimen relationship type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z Related specimen relationship type slot Monkeypox CanCOGeN SARS-CoV-2 Example Guidance: Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Related specimen relationship type field Blood [UBERON:0000178] A data field which describes the substance obtained from an anatomical part of an organism. anatomical material anatomical_material https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z anatomical material slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. anatomical material field Nasopharynx (NP) [UBERON:0001728] A data field which describes the anatomical part of an organism. anatomical part anatomical_part https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z anatomical part slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. anatomical part field Feces [UBERON:0001988] A data field which describes the substance excreted/secreted from an organism. body product body_product https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z body product slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. body product field Soil, water, sewage, door handle, bed handrail, face mask, etc. Example input: Face mask [OBI:0002787] A data field which describes the substance obtained from the natural or man-made environment. environmental material environmental_material https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z environmental material slot GRDI Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. environmental material field Hospital, wet market, bat cave, etc. Example input: Hospital [ENVO:00002173] A data field which describes an environmental location as a site in the natural or built environment. environmental site environmental_site https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z environmental site slot GRDI PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. environmental site field Swab [GENEPIO:0100027] A data field which describes the instrument or container used to collect the sample. collection device collection_device https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection device slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. collection device field Bronchoalveolar lavage (BAL) [GENEPIO:0100032] A data field which describes the process used to collect the sample. collection method collection_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection method slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. collection method field SC2SamplingProtocol 1.2 A data field which describes the name and version of a particular protocol used for sampling. collection protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection protocol slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version of the protocol used to collect the samples. collection protocol field Virus passage [GENEPIO:0100039] A data field which describes any processing applied to the sample during or after receiving the sample. specimen processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in .lab host., .passage number., and .passage method. fields. If none of the processes in the pick list apply, put .not applicable.. specimen processing field Vero E6 cell line [BTO:0004755] A data field which describes the name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. lab host https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lab host slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Type of cell line used for propagation. Select a value form the pick list. If not passaged, put .not applicable.. lab host field 3 A data field which describes the number of passages. passage number https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z passage number slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide number of known passages. If not passaged, put .not applicable. passage number field AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain. A data field which describes how the organism was passaged. passage method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z passage method slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Free text. Provide a short description. If not passaged, put .not applicable.. passage method field RNA (Total) [OBI:0000895] A data field which describes the biomaterial extracted from samples for the purpose of sequencing. biomaterial extracted https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z biomaterial extracted slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the biomaterial extracted from the pick list in the template. biomaterial extracted field An instance of the "host information field category" that contains the "host (scientific name) field". A data field category which refers to host information fields. host information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host information slot category GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host information field category Human [NCBITaxon:9606] A host field which describes the commonly used name of the host. host (common name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (common name) slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put .not applicable.. host (common name) field Homo sapiens [NCBITaxon:9606] A host field which describes the taxonomic or scientific name of the host. host (scientific name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (scientific name) slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put .not applicable.. host (scientific name) field Asymptomatic [NCIT:C3833] A host field which describes the health status of the host at the time of sample collection. host health state https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health state slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host health state field Hospitalized (ICU) [GENEPIO:0100046] A host data field which describes additional information pertaining to the health or disease status of the host at time of collection. host health status details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health status details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host health status details field Recovered [NCIT:C49498] A host data field which describes the disease outcome in the host. host health outcome https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health outcome slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host health outcome field COVID-19 [MONDO:0100096] A host data field which describes the name of the disease experienced by the host. host disease host_disease https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host disease slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under “host health state details”. .COVID-19. should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put “not applicable”. host disease field 79 A host data field which describes the age of the host at the time of sampling. host age https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide age. Age-binning is also acceptable. host age field year [UO:0000036] A host data field which describes the units used to measure the host's age. host age unit https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age unit slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide the age units used to measure the host's age from the pick list. host age unit field 50 - 59 [GENEPIO:0100054] A host data field which describes the age category of the host at the time of sampling. host age bin https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age bin slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. host age bin field Male [NCIT:C46109] A host data field which describes the gender of the host at the time of sample collection. host gender https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host gender slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host gender field South Africa [GAZ:00001094] A host geographical location field which describes the country where the host resides. host residence geo_loc name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host residence geo_loc name (country) slot host residence geographical location country name field host residence geographical location country name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select a value from the pick list. host residence geo_loc name (country) field Quebec A host geographical location field which describes the state or province or territory of residence of the host. host residence geo_loc name (state/province/territory) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host residence geo_loc name (state/province/territory) slot host residence geographical location state or province or territory name field host residence geographical location state or province or territory name slot Monkeypox Monkeypox-International CanCOGeN SARS-CoV-2 Example Guidance: Select the province/territory name from pick list provided in the template. host residence geo_loc name (state/province/territory) field BCxy123 A host data field which describes the unique identifier by which each host can be referred to. host subject ID host subject identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host subject ID slot host subject identifier field host subject identifier slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. host subject ID field 2020-03-16 A data field which describes the date on which the symptoms began or were first noted. symptom onset date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z symptom onset date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide the symptom onset date in ISO 8601 standard format .YYYY-MM-DD.. symptom onset date field Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] A data field which describes the perceived change in function or sensation (loss, disturbance or appearance) indicative of a disease, reported by a patient. Generally, "symptoms" are subjective and reported by the patient, while "signs" are observed and reported by a clinician. However, data collected using case report forms are usually relayed by the patient and thus both are deamed "reported by a patient" in this definition. signs and symptoms https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z signs and symptoms slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select all of the symptoms experienced by the host from the pick list. signs and symptoms field Asthma [HP:0002099] A data field which describes a medical condition that existed prior to the current infection (pre-existing condition) or a variable associated with an increased risk of disease or infection (risk factor). pre-existing conditions and risk factors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z pre-existing conditions and risk factors slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors field Acute respiratory failure [MONDO:0001208] A data field which describes medical complications that are believed to have occurred as a result of host disease. complications https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z complications slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select all of the complications experienced by the host from the pick list. complications field An instance of the "host vaccination information field category" that contains the "host vaccination status field". A data field category which refers to host vaccination information fields. host vaccination information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host vaccination information slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host vaccination information field category Fully Vaccinated [GENEPIO:0100100] A data field which describes the vaccination status of the host. host vaccination status https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host vaccination status slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Statuses associated with this field: fully vaccinated, partially vaccinated, or not vaccinated. Example Guidance: Select the vaccination status of the host from the pick list. host vaccination status field 2 A data field which describes the number of doses of the vaccine received by the host. number of vaccine doses received https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z number of vaccine doses received slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Record how many doses of the vaccine the host has received. number of vaccine doses received field An instance of the "host exposure information field category" that contains the "exposure event field". A data field category which refers to host exposure information fields. host exposure information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host exposure information slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host exposure information field category South Africa [GAZ:00001094] A geographical data field which describes the country where the host was likely exposed to the causative agent of the illness. location of exposure geo_loc name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z location of exposure geo_loc name (country) slot location of exposure geographical location country name field location of exposure geographical location country name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list. location of exposure geo_loc name (country) field New York City A geographical data field which describes the name of the city that was the destination of most recent travel. destination of most recent travel (city) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination city of most recent travel field destination city of most recent travel slot destination of most recent travel (city) slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (city) field California A geographical data field which describes the name of the province that was the destination of most recent travel. destination of most recent travel (state/province/territory) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination of most recent travel (state/province/territory) slot destination state or province or territory of most recent travel field destination state or province or territory of most recent travel slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (state/province/territory) field United Kingdom [GAZ:00002637] A geographical data field which describes the name of the country that was the destination of most recent travel. destination of most recent travel (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination of most recent travel (country) slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (country) field 2020-03-16 A date field which describes the date of an individual's most recent departure from their primary residence (at time of data collection) on a journey to one or more other locations. most recent travel departure date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z most recent travel departure date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the travel departure date in ISO 8601 standard format .YYYY-MM-DD.. most recent travel departure date field 2020-04-26 A date field which describes the date of an individual's most recent return to some residence from a journey originating at that residence. most recent travel return date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z most recent travel return date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the travel return date in ISO 8601 standard format .YYYY-MM-DD.. most recent travel return date field Canada, Vancouver; USA, Seattle; Italy, Milan A data field which describes an individuals travel history in last six months. travel history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z travel history slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text. travel history field Mass Gathering [GENEPIO:0100237] A data field which describes an event leading to exposure. exposure event https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure event slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, select the exposure event from the pick list. exposure event field Direct (human-to-human contact) [TRANS:0000001] A data field which describes the exposure transmission contact type. exposure contact level https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure contact level slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select direct or indirect exposure from the pick list. exposure contact level field Patient [OMRSE:00000030] A data field which describes the role of the host in relation to the exposure setting. host role https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host role slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. host role field Healthcare Setting [GENEPIO:0100201] A data field which describes the setting leading to exposure. exposure setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure setting slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. exposure setting field Host role - Other: Bus Driver A data field which describes additional host exposure information. exposure details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Free text description of the exposure. exposure details field An instance of the "host reinfection information field category" that contains the "prior infection isolate field". A data field category which refers to host reinfection information fields. host reinfection information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host reinfection information slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 host reinfection information field category Prior infection [GENEPIO:0100234] A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. prior SARS-CoV-2 infection field SARS-CoV-2/human/USA/CA-CDPH-001/2020 A data field which describes the identifier of the isolate found in the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection isolate https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection isolate ID slot prior SARS-CoV-2 infection isolate identifier field prior SARS-CoV-2 infection isolate identifier slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the isolate name of the most recent prior infection. Structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date.. prior SARS-CoV-2 infection isolate ID field 2021-01-23 A data field which describes the date of diagnosis of the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format .YYYY-MM-DD.. prior SARS-CoV-2 infection date field Prior antiviral treatment [GENEPIO:0100037] A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) treatment with an antiviral agent. prior SARS-CoV-2 antiviral treatment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. prior SARS-CoV-2 antiviral treatment field Remdesivir A data field which describes the name of the antiviral treatment agent administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 antiviral treatment agent https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment agent slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put .No treatment.. If multiple antiviral agents were administered, list them all separated by commas. prior SARS-CoV-2 antiviral treatment agent field 2021-01-28 A data field which describeds the date treatment was first administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 antiviral treatment date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format .YYYY-MM-DD.. prior SARS-CoV-2 antiviral treatment date field An instance of the "sequencing field category" that contains the "sequencing date field". A data field category which refers to sequencing information fields. sequencing, sequencing information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing information slot category sequencing slot category GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 sequencing field category Baseline surveillance (random sampling) [GENEPIO:0100005] A data field which describes the reason that the sample was sequenced. purpose of sequencing purpose_of_sequencing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sequencing slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the .purpose of sampling. field. purpose of sequencing field Screened for S gene target failure (S dropout) A data field which describes the description of why the sample was sequenced providing specific details. purpose of sequencing details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sequencing details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. purpose of sequencing details field 2021-04-26 A date field which describes the date the sample was sequenced. sequencing date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the sequencing date in ISO 8601 standard format .YYYY-MM-DD.. sequencing date field XYZ_123345 A data field which describes user-specified identifier for the library prepared for sequencing. library ID library identifier library_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z library ID slot library identifier field library identifier slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. library ID field 300bp A data field which describes the length of the amplicon generated by polymerase chain reaction (PCR) amplification. amplicon size https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z amplicon size slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the amplicon size, including the units. amplicon size field Nextera XT A data field which describes the name of the library preparation kit used to generate the library being sequenced. Some specification definitions may be more specific on the type of library preparation kit used (e.g. DNA). library preparation kit library_preparation_kit https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z library preparation kit slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the library preparation kit used. library preparation kit field FAB06069 A data field which describes the barcode of the flow cell used for sequencing. flow cell barcode https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z flow cell barcode slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the barcode of the flow cell used for sequencing the sample. flow cell barcode field Oxford Nanopore MinION [GENEPIO:0100142] A data field which describes the model of the sequencing instrument used. sequencing instrument sequencing_instrument https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing instrument slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select the sequencing instrument from the pick list. sequencing instrument field 1D_DNA_MinION, ARTIC Network Protocol V3 A data field which describes the name and version number of the sequencing protocol used. sequencing protocol name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing protocol name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version of the sequencing protocol. sequencing protocol name field Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. A data field which describes the protocol used to generate the sequence. sequencing protocol sequencing_protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing protocol slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: .Viral sequencing was performed following a tiling amplicon strategy using the <fill in> primer scheme. Sequencing was performed using a <fill in> sequencing instrument. Libraries were prepared using <fill in> library kit. . sequencing protocol field AB456XYZ789 A data field which describes the manufacturer's kit number. sequencing kit number https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing kit number slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Alphanumeric value. sequencing kit number field https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv A data field which describes the specifications of the primers (primer sequences, binding positions, fragment size generated, etc.) used to generate the amplicons to be sequenced. amplicon pcr primer scheme https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z amplicon pcr primer scheme slot amplicon polymerase chain reaction primer scheme field amplicon polymerase chain reaction primer scheme slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version of the primer scheme used to generate the amplicons for sequencing. amplicon pcr primer scheme field An instance of the "bioinformatics and QC metrics field category" that contains the "dehosting method field". A data field category which refers to bioinformatics and quality control (QC) metrics fields. bioinformatics and QC metrics https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioinformatics and QC metrics slot category bioinformatics and Quality Control metrics field category bioinformatics and Quality Control metrics slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 PHA4GE QC Tag bioinformatics and QC metrics field category Porechop 0.2.3 A data field which describes the method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. raw sequence data processing method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z raw sequence data processing method slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version numbers of the software used to process the raw data. raw sequence data processing method field Nanostripper 1.2.3 A data field which describes the method used to remove host reads from the pathogen sequence. dehosting method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z dehosting method slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version number of the software used to remove host reads. dehosting method field ncov123assembly3 A data field which describes the name of the consensus sequence. consensus sequence name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version number of the consensus sequence. consensus sequence name field pathogenassembly123.fasta A data field which describes the user-defined filename of the FASTA file. assembly filename consensus sequence filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and version number of the consensus sequence FASTA file. consensus sequence filename field /User/Documents/RespLab/Data/ncov123assembly.fasta A data field which describes the filepath of the consensus sequence file. consensus sequence filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the consensus sequence FASTA file. consensus sequence filepath field Ivar A data field which describes the name of the software used to generate the consensus sequence. consensus sequence software name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence software name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the software used to generate the consensus sequence. consensus sequence software name field 1.3 A data field which describes the version of the software used to generate the consensus sequence. consensus sequence software version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence software version slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the version of the software used to generate the consensus sequence. consensus sequence software version field 95% A data field which describes the percentage of the reference genome covered by the sequenced data, to a prescribed depth. breadth of coverage value https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z breadth of coverage value slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide value as a percent. breadth of coverage value field 400x A data field which describes the average number of reads representing a given nucleotide in the reconstructed sequence. depth of coverage value https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z depth of coverage value slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide value as a fold of coverage. depth of coverage value field 100x A data field which describes the threshold used as a cut-off for the depth of coverage. depth of coverage threshold https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z depth of coverage threshold slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the threshold fold coverage. depth of coverage threshold field ABC123_S1_L001_R1_001.fastq.gz A data field which describes the user-specified filename of the read 1 (r1) FASTQ file. r1 fastq filename r1_fastq_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r1 fastq filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the r1 FASTQ filename. r1 fastq filename field ABC123_S1_L001_R2_001.fastq.gz A data field which describes the user-specified filename of the read 2 (r2) FASTQ file. r2 fastq filename r2_fastq_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r2 fastq filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the r2 FASTQ filename. r2 fastq filename field /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz A data field which describes the filepath of the read 1 (r1) FASTQ file. r1 fastq filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r1 fastq filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the r1 FASTQ file. r1 fastq filepath field /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz A data field which describes the filepath of the read 2 (r2) FASTQ file. r2 fastq filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r2 fastq filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the r2 FASTQ file. r2 fastq filepath field batch1a_sequences.fast5 A data field which describes the user-specified filename of the FAST5 file. fast5 filename fast5_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z fast5 filename slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the FAST5 filename. fast5 filename field /User/Documents/RespLab/Data/batch1a_sequences.fast5 A data field which describes the filepath of the FAST5 file. fast5 filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z fast5 filepath slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the filepath of the FAST5 file. fast5 filepath field 387566 A data field which describes the number of total base pairs generated by the sequencing process. number of base pairs sequenced https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z number of base pairs sequenced slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a numerical value (no need to include units). number of base pairs sequenced field 38677 A data field which describes the file size of the assembled genome described as the number of base pairs. consensus genome length https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus genome length slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a numerical value (no need to include units). consensus genome length field 300 A data field which describes the number of N (unidentified nucleotide) symbols present in the consensus fasta sequence, per 100kbp of sequence. Ns per 100 kbp Ns per 100 kilobase pairs https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z Ns per 100 kbp slot Ns per 100 kilobase pairs field Ns per 100 kilobase pairs slot unidentified nucleotides per 100 kbp field unidentified nucleotides per 100 kbp slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a numerical value (no need to include units). Ns per 100 kbp field NC_045512.2 A data field which describes the persistent, unique identifier of a genome database entry. reference genome accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z reference genome accession slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the accession number of the reference genome. reference genome accession field https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members A data field which describes the name and version number of the bioinformatics protocol used. bioinformatics protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioinformatics protocol slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol, or a link if deposited in a protocol repository. bioinformatics protocol field An instance of the "lineage and variant information field category" that contains the "lineage/clade name field". A data field category which refers to lineage and variant information fields. lineage and variant information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage and variant information slot category PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 lineage and variant information field category B.1.1.7 A data field which describes the name of the lineage or clade. lineage/clade name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade name field lineage or clade name slot lineage/clade name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the Pangolin or Nextstrain lineage/clade name. lineage/clade name field Pangolin A data field which describe the name of the software used to determine the lineage/clade. lineage/clade analysis software name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade analysis software name field lineage or clade analysis software name slot lineage/clade analysis software name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name of the software used to determine the lineage/clade. lineage/clade analysis software name field 2.1.10 A data field which describes the version of the software used to determine the lineage/clade. lineage/clade analysis software version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade analysis software version field lineage or clade analysis software version slot lineage/clade analysis software version slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the version of the software used ot determine the lineage/clade. lineage/clade analysis software version field Variant of Concern (VOC) [GENEPIO:0100083] A data field which describes the variant classification of the lineage/clade. variant designation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z variant designation slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. variant designation field RT-qPCR RT-qPCR TaqPath assay: S gene target failure A data field which describes the evidence used to make the variant determination. variant evidence variant evidence details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z variant evidence details slot variant evidence slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Example Guidance: Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. variant evidence details field variant evidence field An instance of the "pathogen diagnostic testing field category" that contains the "diagnostic pcr protocol field". A data field category which refers to pathogen diagnostic testing information fields. pathogen diagnostic testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z pathogen diagnostic testing slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 pathogen diagnostic testing field category An instance of the "contributor acknowledgement field category" that contains the "authors field". A data field category which refers to contributor acknowledgement information fields. contributor acknowledgement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z contributor acknowledgement slot category Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 contributor acknowledgement field category Tejinder Singh, Fei Hu, Johnny Blogs A data field which describes the names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. authors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z data authors slot data contributors fields data contributors slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Include the first and last names of all individuals that should be attributed, separated by a comma. data authors field DataHarmonizer v1.4.3, PHA4GE v1.0.0 A data field which describes the DataHarmonizer software and template version provenance. DataHarmonizer provenance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z DataHarmonizer provenance slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The current software and template version information will be automatically generated in this field after the user utilizes the .validate. function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer provenance field Yes [NCIT:C49488] A data field which describes whether the sample was collected from an individual in quarantine. sample collected in quarantine https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected in quarantine slot PHA4GE SARS-CoV-2 Example Guidance: Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. sample collected in quarantine field Jitter added to publicly shared collection dates to prevent re-identifiability. A data field which describes how any data elements were altered to preserve patient privacy. data abstraction details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z data abstraction details slot PHA4GE SARS-CoV-2 Example Guidance: If applicable, provide a description of how each data element was abstracted. data abstraction details field Derbyshire A data field which describes the county or region of origin of the sample. geo_loc name (county/region) geographical location county or region name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (county/region) slot geographical location county or region name field geographical location county or region name slot PHA4GE SARS-CoV-2 Example Guidance: Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (county/region) field ABCD1234 A data field which describes the identifier used to specify an epidemiologically detected case of disease. case ID case identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z case ID slot case identifier field case identifier slot Monkeypox Monkeypox-International CanCOGeN SARS-CoV-2 Example Guidance: Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. epidemiology case ID field hCoV-19/Canada/prov_rona_99/2020 An identifier data field which describes the user-defined Global Initiative on Sharing Avian Influenza Data (GISAID) virus name assigned to the sequence. GISAID virus name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GISAID virus name slot Global Initiative on Sharing Avian Influenza Data virus name field Global Initiative on Sharing Avian Influenza Data virus name slot Monkeypox PHA4GE SARS-CoV-2 Example Guidance: GISAID virus names should be in the format .hCoV-19/Country/Identifier/year.. GISAID virus name field URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179 A data field which describes the identifier for the physical specimen. host specimen voucher https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host specimen voucher ID slot host specimen voucher identifier field host specimen voucher identifier slothost specimen voucher ID field host specimen voucher slot PHA4GE SARS-CoV-2 Example Guidance: Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher=.[<institution-code>:[<collection-code>:]]<specimen_id>.): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier host specimen voucher field /culture_collection="ATCC:26370 A data field which describes the name of the source collection and unique culture identifier. culture collection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z culture collection slot PHA4GE SARS-CoV-2 Example Guidance: Format: .<institution-code>:[<collection-code>:]<culture_id>.. For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. culture collection ID field CanCOGeN Sampling Strategy 1.0 A data field which describes the name of the sample plan implemented for sample collection. sample plan name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan name slot PHA4GE SARS-CoV-2 Example Guidance: Provide the name and version of the sample plan outlining the sample strategy. sample plan name field 38.98 N A data field which describes the latitude coordinates of the geographical location of sample collection. geo_loc latitude geographical location latitude https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc latitude slot geographical location latitude field geographical location latitude slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 Example Guidance: Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format .d[d.dddd] N|S.. geo_loc latitude field 77.11 W A data field which describes the longitude coordinates of the geographical location of sample collection. geo_loc longitude geographical location longitude https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc longitude slot geographical location longitude field geographical location longitude slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 Example Guidance: Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format .d[dd.dddd] W|E.. geo_loc longitude field 25 swabs were pooled and further prepared as a single sample during library prep. A data field which describes detailed information regarding the processing applied to a sample during or after receiving the sample. specimen processing details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing details slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide a free text description of any processing details applied to a sample. specimen processing details field Indigenous, European A host data field which describes the self-identified ethnicity(ies) of the host. host ethnicity https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host ethnicity slot PHA4GE SARS-CoV-2 Example Guidance: If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. host ethnicity field Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the first dose of a vaccine regimen. vaccination dose 1 vaccine name vaccination dose one vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 1 vaccine name slot vaccination dose one vaccine name field vaccination dose one vaccine name slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list vaccination dose 1 vaccine name field 2021-03-01 A host data field which describes the date the first dose of a vaccine was administered. vaccination dose 1 vaccination date vaccination dose one vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 1 vaccination date slot vaccination dose one vaccination date field vaccination dose one vaccination date slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 1 vaccination date field Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the second dose of a vaccine regimen. vaccination dose 2 vaccine name vaccination dose two vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 2 vaccine name slot vaccination dose two vaccine name field vaccination dose two vaccine name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list vaccination dose 2 vaccine name field 2021-09-01 A host data field which describes the date the second dose of a vaccine was administered. vaccination dose 2 vaccination date vaccination dose two vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 2 vaccination date slot vaccination dose two vaccination date field vaccination dose two vaccination date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 2 vaccination date field Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the third dose of a vaccine regimen. vaccination dose 3 vaccine name vaccination dose three vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 3 vaccine name slot vaccination dose three vaccine name field vaccination dose three vaccine name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list vaccination dose 3 vaccine name field 2021-12-30 A host data field which describes the date the third dose of a vaccine was administered. vaccination dose 3 vaccination date vaccination dose three vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 3 vaccination date slot vaccination dose three vaccination date field vaccination dose three vaccination date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 3 vaccination date field Pfizer-BioNTech (Comirnaty) A data field which describes the name of the vaccine administered as the fourth dose of a vaccine regimen. vaccination dose 4 vaccine name vaccination dose four vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 4 vaccine name slot vaccination dose four vaccine name field vaccination dose four vaccine name slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list vaccination dose 4 vaccine name field 2022-01-15 A host data field which describes the date the fourth dose of a vaccine was administered. vaccination dose 4 vaccination date vaccination dose four vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 4 vaccination date slot vaccination dose four vaccination date field vaccination dose four vaccination date slot PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 4 vaccination date field Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 A host data field which describes the description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. vaccination history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination history slot Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. vaccination history field Air A data field which describes the type of entry point a traveler arrives through. travel point of entry type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z travel point of entry type slot CanCOGeN SARS-CoV-2 Example Guidance: Select the point of entry type. travel point of entry type field day 1 A data field which describes the day a traveller was tested on or after arrival at their point of entry. border testing test day type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z border testing test day type slot CanCOGeN SARS-CoV-2 Example Guidance: Select the test day. border testing test day type field Public Health Ontario (PHO) A data field which describes the name of the agency that generated the sequence. sequenced by sequenced_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by slot GRDI Monkeypox-International Monkeypox Example Guidance: 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).. sequenced by field RespLab@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the sequence. sequenced by contact email sequenced_by_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact email slot GRDI Monkeypox-International Monkeypox Example Guidance: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca sequenced by contact email field 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada A data field which describes the mailing address of the agency submitting the sequence. sequenced by contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact address slot Monkeypox-International Monkeypox Example Guidance: The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country sequenced by contact address field bvn5567, RA1-HH789 A data field which describes an alternative sample identifier assigned to the sample by another organization. alternative sample ID alternative sample identifier alternative_sample_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z alternative sample ID slot alternative sample identifier field alternative sample identifier slot GRDI Example Guidance: Provide any alternative identifiers for the sample here, separated by commas. Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. If the information is unknown or cannot be provided, leave blank or provide a null value. alternative sample ID field Topp Lab A data field which describes the specific laboratory affiliation of the sample collector. sample collected by laboratory name sample_collected_by_laboratory_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected by laboratory name slot GRDI Example Guidance: 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. sample collected by laboratory name field Watershed Project (HA-120) A data field which describes the project/initiative/program for which the sample was collected. sample collection project name sample_collection_project_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection project name slot GRDI Example Guidance: 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. sample collection project name field National Microbiological Baseline Study in Broiler Chicken A data field which describes the name of the study design for a surveillance project. sample plan name sample_plan_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan name slot GRDI Example Guidance: 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. sample plan name field 2001_M205 A data field which describes the identifier of the study design for a surveillance project. sample plan ID sample plan identifier sample_plan_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan ID slot sample plan identifier field sample plan identifier slot GRDI Example Guidance: 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. sample plan ID field Enterics Lab Manager A data field which describes the name or job title of the contact responsible for follow-up regarding the sample. sample collector contact name sample_collector_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact name slot GRDI Example Guidance: 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. sample collector contact name field Antimicrobial pre-treatment [GENEPIO:0100537] A data field which describes the activities or variables introduced upstream of sample collection that may affect the sample collected. presampling activity presampling_activity https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z presampling activity slot GRDI Example Guidance: If there was presampling activity that would affect the sample prior to collection (this is different than sample processing which happens after the sample is collected), 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. presampling activity field Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. A data field which describes the details of the activities or variables introduced upstream of sample collection that may affect the sample collected. presampling activity details presampling_activity_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z presampling activity details slot GRDI Example Guidance: Briefly describe the presampling activity details using free text. presampling activity details field Samples pooled [OBI:0600016] A data field which describes the processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. specimen processing specimen_processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing slot GRDI Example Guidance: 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. specimen processing field Credit River" as opposed to "river A data field which describes the name of a specific geographical location (i.e. toponym). geo_loc name (site) geographical location site name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (site) slot geographical location site name field geographical location site name slot GRDI Example Guidance: Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). geo_loc name (site) field United States of America [GAZ:00002459] A data field which describes the country of origin of a food product. food product origin geo loc name (country) food product origin geographical location country name food_product_origin geo_loc_name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product origin geo loc name (country) slot food product origin geographical location country name field food product origin geographical location country name slot GRDI Example Guidance: 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. food product origin geo loc name (country) field South Africa [GAZ:00001094] A host geographical location field which describes the country of origin of the host. host origin geo loc name (country) host origin geographical location name host_origin geo_loc_name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host origin geo loc name (country) slot host origin geographical location name field host origin geographical location name slot GRDI Example Guidance: 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. host origin geo loc name (country) field RTE Prosciutto from deli A data field which describes the original sample description provided by the sample collector. original sample description original_sample_description https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z original sample description slot GRDI Example Guidance: 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. original sample description field 5 m A data field which describes the depth of some water. water depth water_depth https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z water depth slot GRDI Example Guidance: Provide the depth of water with a value and unit. water depth field 25C A data field which describes the temperature of some air. air temperature air_temperature https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z air temperature slot GRDI Example Guidance: Provide the temperature of the air with a value and unit. Do not provide a symbol for degree e.g. oC air temperature field Rain [ENVO:01001564] A data field which describes the state of the atmosphere at a place and time. Regarding heat, dryness, sunshine, wind, rain, etc. weather type weather_type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z weather type slot GRDI Example Guidance: Provide the weather conditions at the time of sample collection. weather type field Turkey [NCBITaxon:9103] A data field which describes the type of animal or plant population inhabiting an area. animal or plant population animal_or_plant_population https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z animal or plant population slot GRDI Example Guidance: 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. animal or plant population field Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] A data field which describes material consumed and digested for nutritional value or enjoyment. food product food_product https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product slot GRDI Example Guidance: This field includes animal feed. If applicable, provide the standardized term and ontology ID for the anatomical material. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/foodon. If not applicable, leave blank. food product field Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] A data field which describes any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. food product properties food_product_properties https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product properties slot GRDI Example Guidance: Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). food product properties field Chicken [NCBITaxon:9031] A data field which describes the animal from which the food product was derived. animal source of food animal_source_of_food https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z animal source of food slot GRDI Example Guidance: Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. animal source of food field Plastic tray or pan [FOODON:03490126] A data field which describes the type of packaging used to contain a food product. food packaging food_packaging https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food packaging slot GRDI Example Guidance: If known, provide information regarding how the food product was packaged. food packaging field Frozen at -20C A data field which describes the way that a specimen is or was stored. sample storage method sample_storage_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample storage method slot GRDI Example Guidance: Provide a description of how the same was stored. sample storage method field PBS + 20% glycerol A data field which describes the material or matrix in which a sample is stored. sample storage medium sample_storage_medium https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample storage medium slot GRDI Example Guidance: Provide a description of the material or matrix used to store the sample. sample storage medium field Sea ecotype A host field which describes the biotype resulting from selection in a particular habitat. host (ecotype) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (ecotype) slot GRDI Example Guidance: Provide the name of the ecotype of the host organism. host (ecotype) field Holstein A host field which describes 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. host (breed) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (breed) slot GRDI Example Guidance: Provide the name of the breed of the host organism. host (breed) field Calf [FOODON:03411349] A host field which describes the name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. host (food production name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (food production name) slot GRDI Example Guidance: Select the host's food production name from the pick list. host (food production name) field An instance of the "strain and isolation information field category" that contains the "isolate received date field". An instance of the "strain and isolation information field category" that contains the "microbiological method field". A data field category which refers to strain and isolation information fields. strain and isolation information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z 2022-06-25T03:32:51.876Z strain and isolation information slot category GRDI strain and isolation information field category MFHPB-30 A data field which describes the laboratory method used to grow, prepare, and/or isolate the microbial isolate. microbiological method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z microbiological method slot GRDI Example Guidance: 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. microbiological method field K12 A data field which describes the strain identifier. strain https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z strain slot GRDI Example Guidance: A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. strain field SARS-CoV-2/human/USA/CA-CDPH-001/2020 A data field which describes the identifier of the specific isolate. isolate isolate ID isolate identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolate ID slot isolate field isolate identifier field isolate identifier slot isolate slot GRDI Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the .isolate. name is propagated throughtout different databases. As such, structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date.. isolate ID field PHAC_45678 A data field which describes an isolate identifier assigned to the isolate by another organization. alternative isolate ID alternative isolate identifier alternative_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z alternative isolate ID slot alternative isolate identifier field alternative isolate identifier slot GRDI Example Guidance: If one or more alternative isolate_IDs are available, record them all here, separated by a comma. alternative isolate ID field SUB_ON_1526 A data field which describes the identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. progeny isolate ID progeny isolate identifier progeny_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z progeny isolate ID slot progeny isolate identifier field progeny isolate identifier slot GRDI Example Guidance: If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. progeny isolate ID field GRDI_LL_12345 A data field which describes the identifier of the isolate in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. IRIDA isolate ID IRIDA isolate identifier IRIDA_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA isolate ID slot IRIDA isolate identifier field IRIDA isolate identifier slot Integrated Rapid Infectious Disease Analysis isolate ID field Integrated Rapid Infectious Disease Analysis isolate ID slot Integrated Rapid Infectious Disease Analysis isolate identifier field Integrated Rapid Infectious Disease Analysis isolate identifier slot GRDI Example Guidance: 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. IRIDA isolate ID field 666 A data field which describes the identifier of the project in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. IRIDA project ID IRIDA project identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA project ID slot IRIDA project identifier field IRIDA project identifier slot Integrated Rapid Infectious Disease Analysis project ID field Integrated Rapid Infectious Disease Analysis project ID slot Integrated Rapid Infectious Disease Analysis project identifier field Integrated Rapid Infectious Disease Analysis project identifier slot GRDI Example Guidance: Provide the IRIDA .project ID.. IRIDA project ID field Public Health Agency of Canada (PHAC) [GENEPIO:0100551] A data field which describes the name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. isolated by isolated_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by slot GRDI Example Guidance: 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. isolated by field Topp Lab A data field which describes the specific laboratory affiliation of the individual who performed the isolation procedure. isolated by laboratory name isolated_by_laboratory_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by laboratory name slot GRDI Example Guidance: 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. isolated by laboratory name field Enterics Lab Manager A data field which describes the name or title of the contact responsible for follow-up regarding the isolate. isolated by contact name isolated_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by contact name slot GRDI Example Guidance: 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. isolated by contact name field enterics@lab.ca A data field which describes the email address of the contact responsible for follow-up regarding the isolate. isolated by contact email isolated_by_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by contact email slot GRDI Example Guidance: 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. isolated by contact email field 2020-10-30 A date field which describes the date on which the isolate was isolated from a sample. isolation date isolation_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolation date slot GRDI Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. isolation date field 2020-11-15 A date field which describes the date on which the isolate was received by the laboratory. isolate received date isolate_received_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolate received date slot GRDI Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. isolate received date field Heidelberg A data field which describes the serovar of the organism. serovar https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z serotype field serotype slot serovar slot GRDI Example Guidance: Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. serovar field SISTR 1.0.1 A data field which describes the method used to determine the serovar. serotyping method serotyping_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z serotyping method slot GRDI Example Guidance: 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. serotyping method field 47 A data field which describes the phagetype of the organism. phagetype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z phagetype slot GRDI Example Guidance: Provide if known. If unknown, put “missing”. phagetype field Topp Lab A data field which describes the specific laboratory affiliation of those responsible for sequencing the isolate's genome. sequenced by laboratory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by laboratory name slot GRDI Example Guidance: 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. sequenced by laboratory name field Enterics Lab Manager A data field which describes the name or title of the contact responsible for follow-up regarding the sequence. sequenced by contact name sequenced_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact name slot GRDI Example Guidance: 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. sequenced by contact name field AMR-GRDI (PA-1356) A data field which describes the name of the project/initiative/program for which sequencing was performed. sequencing project name sequencing_project_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing project name slot GRDI Example Guidance: 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. sequencing project name field Illumina [GENEPIO:0001923] A data field which describes the platform technology used to perform the sequencing. sequencing platform sequencing_platform https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing platform slot GRDI Example Guidance: 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. sequencing platform field Enterics Lab Manager A data field which describes the name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. sequence submitted by contact name sequence_submitted_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z sequence submitted by contact name slot GRDI Example Guidance: 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. sequence submitted by contact name field PMID: 33205991 A data field which describes the identifier for a publication. publication ID publication identifier publication_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z publication ID slot publication identifier field publication identifier slot GRDI Example Guidance: 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. publication ID field Pathogen.env A data field which describes the attribute package used to structure metadata in an International Nucleotide Sequence Database Collaboration (INSDC) BioSample. attribute package attribute_package https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z attribute package slot GRDI Example Guidance: 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”. attribute package field An instance of the "public repository information field category" that contains the "publication ID field". A data field category which refers to public repository information fields. public repository information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z public repository information slot category GRDI public repository information field category An instance of the "risk assessment information field category" that contains the "prevalence metrics field". A data field category which refers to risk assessment information fields. risk assessment information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z risk assessment information slot category GRDI risk assessment information field category An instance of the "antimicrobial resistance field category" that contains the "AMR* laboratory typing method field". *AMR = antimicrobial resistance A data field category which refers to antimicrobial resistance fields. antimicrobial resistance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z antimicrobial resistance slot category GRDI antimicrobial resistance field category Number of total samples collected, Number of positive samples A data field which describes metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. prevalence metrics prevalence_metrics https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z prevalence metrics slot GRDI Example Guidance: 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. prevalence metrics field Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. A data field which describes the details pertaining to the prevalence metrics from a surveillance project. prevalence metrics details prevalence_metrics_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z prevalence metrics details slot GRDI Example Guidance: If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. prevalence metrics details field Abattoir [ENVO:01000925] A data field which describes the stage of food production. stage of production stage_of_production https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z stage of production slot GRDI Example Guidance: Provide the stage of food production from which the sample was taken. Select a value form the pick list provided. stage of production field Vaccination [NCIT:C15346] A data field which describes the category of the experimental intervention applied in the food production system. experimental intervention experimental_intervention https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z experimental intervention slot GRDI Example Guidance: 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. experimental intervention field 2% cranberry solution mixed in feed a data field which describes the details of the experimental intervention applied in the food production system. experiment intervention details experiment_intervention_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z experiment intervention details slot GRDI Example Guidance: If an experimental intervention was applied in the survey, provide details in this field as free text. experiment intervention details field Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] A data field which describes the name of the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by AMR_testing_by antimicrobial resistance testing by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by slot antimicrobial resistance testing by field antimicrobial resistance testing by slot GRDI Example Guidance: 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. AMR testing by field Topp Lab A data field which describes the name of the lab within the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by laboratory name AMR_testing_by_laboratory_name antimicrobial resistance testing by laboratory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by laboratory name slot antimicrobial resistance testing by laboratory name field antimicrobial resistance testing by laboratory name slot GRDI Example Guidance: 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. AMR testing by laboratory name field Enterics Lab Manager A data field which describes the name of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by contact name AMR_testing_by_contact_name antimicrobial resistance testing by contact name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by contact name slot antimicrobial resistance testing by contact name field antimicrobial resistance testing by contact name slot GRDI Example Guidance: 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. AMR testing by contact name field johnnyblogs@lab.ca A data field which describes the email of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by contact email AMR_testing_by_contact_email antimicrobial resistance testing by contact email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by contact email slot antimicrobial resistance testing by contact email field antimicrobial resistance testing by contact email slot GRDI Example Guidance: 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. AMR testing by contact email field 2022-04-03 A data field which describes the date the antimicrobial resistance (AMR) testing was performed. AMR testing date AMR_testing_date antimicrobial resistance testing date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing date slot antimicrobial resistance testing date field antimicrobial resistance testing date slot GRDI Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. AMR testing date field 8 An antimicrobial resistance (AMR) field which describes the maximum measurement for a sample to be considered “sensitive” to this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing susceptible breakpoint AMR_testing_susceptible_breakpoint antimicrobial resistance testing susceptible breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing susceptible breakpoint slot antimicrobial resistance testing susceptible breakpoint field antimicrobial resistance testing susceptible breakpoint slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. AMR testing susceptible breakpoint field 16 An antimicrobial resistance (AMR) field which describes intermediate measurement(s) where a sample would be considered to have an “intermediate” phenotype for this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing intermediate breakpoint AMR_testing_intermediate_breakpoint antimicrobial resistance testing intermediate breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing intermediate breakpoint slot antimicrobial resistance testing intermediate breakpoint field antimicrobial resistance testing intermediate breakpoint slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the qualifier is implied. AMR testing intermediate breakpoint field 32 An antimicrobial resistance (AMR) field which describes minimum measurement for a sample to be considered “resistant” to this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing resistant breakpoint AMR_testing_resistant_breakpoint antimicrobial resistance testing resistant breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing resistant breakpoint slot antimicrobial resistance testing resistant breakpoint field antimicrobial resistance testing resistant breakpoint slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. AMR testing resistant breakpoint field 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. An antimicrobial resistance (AMR) field which describes additional details associated with the testing standard used for determination of resistance phenotype. AMR testing standard details AMR_testing_standard_details antimicrobial resistance testing standard details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard details slot antimicrobial resistance testing standard details field antimicrobial resistance testing standard details slot GRDI Example Guidance: This information may include the year or location where the testing standard was published. If not applicable, leave blank. AMR testing standard details field Amoxicillin-clavulanic [ARO:3003997] A data field which describes the name of the agent that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent name antimicrobial_agent_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z antimicrobial agent name slot GRDI Example Guidance: The names of the drug have already been matched with measurement, breakpoint, and phenotype fields in the template. No need to add these unless the drug of interest is not present. Use the Term Request System to request the addition of other agents. antimicrobial agent name field 4 A data field which describes the measured value of antimicrobial resistance (AMR). Dependent on the value specified in the 'antimicrobial agent name field' [GENEPIO:0100521] AMR measurement AMR_measurement antimicrobial resistance measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement slot antimicrobial resistance measurement field antimicrobial resistance measurement slot GRDI Example Guidance: This field should only contain a number (either an integer or a number with decimals). AMR measurement field mg/L A data field which describes the units of the antimicrobial resistance (AMR) measurement. Dependent on the numerical value specified in the 'AMR measurement field' [GENEPIO:0100522] AMR measurement units AMR_measurement_units antimicrobial resistance measurement units https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement units slot antimicrobial resistance measurement units field antimicrobial resistance measurement units slot GRDI Example Guidance: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. AMR measurement units field == A data field which describes the qualifier associated with the antibiotic resistance (AMR) measurement. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR measurement sign AMR_measurement_sign antimicrobial resistance measurement sign https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement sign slot antimicrobial resistance measurement sign field antimicrobial resistance measurement sign slot GRDI Example Guidance: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. AMR measurement sign field Susceptible antimicrobial phenotype [ARO:3004302] A data field which describes an antimicrobial resistance (AMR) phenotype, as determined by the antibiotic susceptibility measurement and testing standard for the antibiotic specified. Dependent on the value specified in the 'antimicrobial agent name field' [GENEPIO:0100521] AMR phenotype AMR_phenotype antimicrobial resistance phenotype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR phenotype slot antimicrobial resistance phenotype field antimicrobial resistance phenotype slot GRDI Example Guidance: Select a phenotype from the pick list provided. AMR phenotype field Broth dilution [ARO:3004397] An antimicrobial resistance (AMR) field which describes the general method used for antibiotic susceptibility testing. AMR laboratory typing method AMR_laboratory_typing_method antimicrobial resistance laboratory typing method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing method slot antimicrobial resistance laboratory typing method field antimicrobial resistance laboratory typing method slot GRDI Example Guidance: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. AMR laboratory typing method field Sensitire [ARO:3004402] An antimicrobial resistance (AMR) field which describes the brand/platform used for antibiotic susceptibility testing. AMR laboratory typing platform AMR_laboratory_typing_platform antimicrobial resistance laboratory typing platform https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing platform slot antimicrobial resistance laboratory typing platform field antimicrobial resistance laboratory typing platform slot GRDI Example Guidance: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. AMR laboratory typing platform field CMV3AGNF An antimicrobial resistance (AMR) field which describes the specific name and version of the plate, panel, or other platform used for antibiotic susceptibility testing. AMR laboratory typing platform version AMR_laboratory_typing_platform_version antimicrobial resistance laboratory typing platform version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing platform version slot antimicrobial resistance laboratory typing platform version field antimicrobial resistance laboratory typing platform version slot GRDI Example Guidance: Include any additional information about the antimicrobial susceptibility test such as the drug panel details. AMR laboratory typing platform version field Sensititre An antimicrobial resistance (AMR) field which describes the name of the vendor of the testing platform used. AMR vendor name AMR_vendor_name antimicrobial resistance vendor name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR vendor name slot antimicrobial resistance vendor name field antimicrobial resistance vendor name slot GRDI Example Guidance: Provide the full name of the company (avoid abbreviations). AMR vendor name field Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] An antimicrobial resistance (AMR) field which describes testing standard used for determination of resistance phenotype. AMR testing standard AMR_testing_standard antimicrobial resistance testing standard https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard slot antimicrobial resistance testing standard antimicrobial resistance testing standard field antimicrobial resistance testing standard slot GRDI Example Guidance: Select a testing standard from the pick list provided. AMR testing standard field M100 An antimicrobial resistance (AMR) field which describes version number associated with the testing standard used for determination of resistance phenotype. If applicable, include a version number for the testing standard used. AMR testing standard version AMR_testing_standard_version antimicrobial resistance testing standard version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard version slot antimicrobial resistance testing standard version field antimicrobial resistance testing standard version slot GRDI Example Guidance: If applicable, include a version number for the testing standard used. AMR testing standard version field Prior infection A data field which describes the absence or presence of a prior Monkeypox infection. prior Monkeypox infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox infection slot Monkeypox-International Monkeypox Example Guidance: If known, provide information about whether the individual had a previous Monkeypox infection. Select a value from the pick list. prior Monkeypox infection field 2022-06-20 A data field which describes the date of diagnosis of the prior Monkeypox infection. prior Monkeypox infection date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox infection date slot Monkeypox-International Monkeypox Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior Monkeypox infection date in ISO 8601 standard format .YYYY-MM-DD.. prior Monkeypox infection date field Prior antiviral treatment A data field which describes the absence or presence of antiviral treatment for a prior Monkeypox infection. prior Monkeypox antiviral treatment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox antiviral treatment slot Monkeypox-International Monkeypox Example Guidance: If known, provide information about whether the individual had a previous Monkeypox antiviral treatment. Select a value from the pick list. prior Monkeypox antiviral treatment field AZT was administered for HIV infection during the prior Monkeypox infection. A data field which describes the antiviral treatment for any infection during the prior Moneypox infection period. prior antiviral treatment during prior Monkeypox infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior antiviral treatment during prior Monkeypox infection slot Monkeypox-International Monkeypox Example Guidance: Provide a description of any antiviral treatment administered for viral infections (not including Monkeypox treatment) during the prior Monkeypox infection period. This field is meant to capture concurrent treatment information. prior antiviral treatment during prior Monkeypox infection field ncov-tools A data field which describes the name of the method used to assess whether a sequence passed a predetermined quality control threshold. quality control method name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc method name field qc method name slot quality control method name field quality control method name slot PHA4GE QC Tag quality control method name field 1.2.3 A data field which describes the version number of the method used to assess whether a sequence passed a predetermined quality control threshold. quality control method version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc method version field qc method version slot quality control method version field quality control method version slot PHA4GE QC Tag quality control method version field sequence failed quality control [GENEPIO:0100564] A data field which describes the determination of a quality control assessment. quality control determination https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc determination field qc determination slot quality control determination field quality control determination slot PHA4GE QC Tag quality control determination field low average genome coverage [GENEPIO:0100570] A data field which describes the reason contributing to, or causing, a low quality determination in a quality control assessment. quality control issues https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc issues field qc issues slot quality control issues field quality control issues slot PHA4GE QC Tag quality control issues field CT value of 39. Low viral load. Low DNA concentration after amplification. A data field which describes the details surrounding a low quality determination in a quality control assessment. quality control details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc details field qc details slot quality control details field quality control details slot PHA4GE QC Tag quality control details field Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection A data field which describes treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. antiviral therapy https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z antiviral therapy slot Monkeypox-International Monkeypox Example Guidance: Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. antiviral therapy field PCR assay [OBI:0002740] A data field which describes the type of planned process by which an organismal entity is associated with a taxon or taxa. taxonomic identification process taxonomic_identification_process https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z taxonomic identification process slot GRDI Example Guidance: 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. taxonomic identification process field Biolog instrument A data field which describes the details of the process used to determine the taxonomic identification of an organism. taxonomic identification process details taxonomic_identification_process_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z taxonomic identification process details slot GRDI Example Guidance: Briefly describe the taxonomic identififcation method details using free text. taxonomic identification process details field 2020-05-25 A data field which describes the 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. food quality date food_quality_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food quality date slot GRDI Example Guidance: 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. food quality date field 2020-05-25 A data field which descibes the food product's packaging date as marked by a food manufacturer or retailer. food packaging date food_packaging_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food packaging date slot GRDI Example Guidance: 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. food packaging date field A data item which describes an organism bearing a host role. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host column host slot; host organism field; host organism slot host field A data field which describes a geographical location. geo_loc field geo_loc slot https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z geographical location column geographical location slot geographical location field A field that describes the host country of reisdence. A data field which describes the geographical location of a host organism. host geo_loc https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host geographical location column host geographical location slot host geographical location field third party lab sample ID field A data field which describes a symbol that is part of a centrally registered identifier database (CRID) and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/IAO_0000577 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z ID column identifier column ID field ID slot identifier slot identifier field A data field which describes the particular day, month and/or year an event has happened or will happen. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z date column date slot date field A data field which describes the vaccination information of a host organism. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host vaccination column host vaccination slot host vaccination field A data field which describes antimicrobial information. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z antimicrobial column antimicrobial slot antimicrobial field A data field which describes antimicrobial resistance information. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR column antimicrobial resistance column AMR field AMR slot antimicrobial resistance slot antibiotic field antimicrobial resistance field A data field which describes the exposure information of a host organism. https://orcid.org/0000-0002-9578-0788 2023-01-01T03:32:48.197Z exposure column exposure slot exposure field A data field which describes prior infection information of a host organism. https://orcid.org/0000-0002-9578-0788 2023-01-01T03:32:48.197Z prior infection column prior infection slot prior infection field E gene (orf4) [GENEPIO:0100151] A data field which describes the name of the gene used in the diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name slot gene name field PCREGene 2.0 A data field which describes the name and version number of the reverse transcription polymerase chain reaction (RT-PCR) protocol used for diagnostic marker amplification. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol slot diagnostic polymerase chain reaction protocol field diagnostic polymerase chain reaction protocol slot diagnostic pcr protocol field 21 A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value slot diagnostic polymerase chain reaction cycle threshold field diagnostic polymerase chain reaction cycle threshold slot diagnostic pcr Ct value field A data field which describes quality control information. https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc column quality control column qc field qc slot quality control slot quality control field E gene (orf4) [GENEPIO:0100151] A data field which describes the name and version number of the protocol used for diagnostic marker amplification. gene name 1 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 1 field gene name 1 slot gene name one Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gene name 1 field EGenePCRTest 2 A data field which describes the name and version number of the protocol used for diagnostic marker amplification. diagnostic pcr protocol 1 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol 1 field diagnostic pcr protocol 1 slot diagnostic pcr protocol one Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. diagnostic pcr protocol 1 field 21 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 1 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value 1 field diagnostic pcr Ct value 1 slot diagnostic pcr Ct value one Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the cycle threshold (Ct) value of the sample from the diagnostic RT-PCR test. diagnostic pcr Ct value 1 field RdRp gene (nsp12) [GENEPIO:0100168] A data field which describes the name and version number of the protocol used for diagnostic marker amplification. gene name 2 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 2 field gene name 2 slot gene name two Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gene name 2 field RdRpGenePCRTest 3 A data field which describes the name and version number of the protocol used for diagnostic marker amplification. diagnostic pcr protocol 2 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol 2 field diagnostic pcr protocol 2 slot diagnostic pcr protocol two Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. diagnostic pcr protocol 2 field 36 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 2 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value 2 field diagnostic pcr Ct value 2 slot diagnostic pcr Ct value two Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the cycle threshold (Ct) value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 2 field RdRp gene (nsp12) [GENEPIO:0100168] A data field which describes the name of the gene used in the diagnostic RT-PCR test. gene name 3 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 3 field gene name 3 slot gene name three Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gene name 3 field RdRpGenePCRTest 3 A data field which describes the name and version number of the protocol used for diagnostic marker amplification. diagnostic pcr protocol 3 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol 3 field diagnostic pcr protocol 3 slot diagnostic pcr protocol three Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. diagnostic pcr protocol 3 field 30 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 3 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value 3 field diagnostic pcr Ct value 3 slot diagnostic pcr Ct value three Monkeypox Monkeypox-International PHA4GE SARS-CoV-2 CanCOGeN SARS-CoV-2 Example Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 3 field G2R_G (TNFR) [GENEPIO:0100510] A data field which describes the name of the gene used in the diagnostic RT-PCR test. gene name 4 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 4 field gene name 4 slot gene name four Monkeypox Example Guidance: Select the name of the gene used for the diagnostic PCR from the standardized pick list. gene name 4 field 27 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 4 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z Monkeypox Example Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 4 field RNAse P [GENEPIO:0100508] A data field which describes the name of the gene used in the diagnostic RT-PCR test. gene name 5 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name 5 slot gene name five gene name5 field Monkeypox Example Guidance: Select the name of the gene used for the diagnostic PCR from the standardized pick list. gene name 5 field 30 A data field which describes the Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. diagnostic pcr Ct value 5 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z Monkeypox Example Guidance: Provide the CT value of the sample from the second diagnostic RT-PCR test. diagnostic pcr Ct value 5 field