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