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GSCID/BRC Project and Sample Application Standard: Core Project

v1.3
Finalized by the GSCID/BRC Metadata Working Group


How to interpret the document:
BOLD: Field name
ITALICS: Attributes of the field

1. Project Title
Core Project Field ID: CP1
Description: Descriptive title of the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: Sequencing of isolates from 2023 outbreak of pseudopneumovirus in Antarctica
Data Source: Sample Provider
Comments:
OBO Foundry Synonym:
investigation title
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001622
OBO Definition: A textual entity that denotes an investigation.
Other Synonym: BioProject:Title*;MIxS: project name;

2. Project ID
Core Project Field ID: CP2
Description: Unique identifier of the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: RRI-112233445
Data Source: GSCID
Comments:
OBO Foundry Synonym:
investigation identifier
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001628
OBO Definition: A CRID symbol used to identify an investigation.
Other Synonym:

3. Project Description
Core Project Field ID: CP3
Description: Textual description of the project including hypothesis, rationale, goals, etc.
Data Categories: Investigation
Allowed Values: textual abstract or hyperlink to project description document; for GSCID projects this could simply be the white paper proposal
Syntax: free text
Example Values: Nasal swabs were collected from 45 patients experiencing respiratory distress during emergency room visit from May - August of 2023 in Antarctica to determine the genome sequences of this new outbreak virus for comparison with previously circulating strains
Data Source: Sample Provider
Comments:
OBO Foundry Synonym:
investigation description
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001615
OBO Definition: A textual entity that describes an investigation.
Other Synonyms: BioProject:Description*;

4. Project Relevance
Core Project Field ID: CP4
Description: Indicates how the knowledge derived from the project can be applied, and to what field(s).
Data Categories: Investigation
Allowed Values: Agricultural, Medical, Industrial, Evolution, Environmental, Model organism, Other
Syntax: pick list
Example Values: Medical
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: study design
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0500000
OBO Definition: A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Other Synonyms: BioProject:Relevance*;

5. Sample Scope
Core Project Field ID: CP5
Description: Indicates the scope and purity of the biological sample used for the project.
Data Categories: Investigation Allowed Values: Monoisolate, Multiisolate, Multispecies, Environment, Synthetic, Single cell, Other
Syntax: pick list
Example Values: Monoisolate
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: specimen-based scope of investigation specification
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001884
OBO Definition: specimen-based scope of investigation specification
Other Synonyms: BioProject:Sample Scope*;

6. Target Material
Core Project Field ID: CP6
Description: Indicates the type of material that is isolated from the sample for use in the project.
Data Categories: Investigation
Allowed Values: Genome, Transcriptome, Proteome, Purified chromosome, Reagent, Phenotype, Other
Syntax: pick list
Example Values: Genome
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: target material in specimen specification
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001882
OBO Definition: target material in specimen specification
Other Synonyms: BioProject:Material*;

7. Target Capture
Core Project Field ID: CP7
Description: Indicates the scale, or type, of information that the project is designed to generate from the sample material.
Data Categories: Investigation
Allowed Values: Whole, Targeted locus/loci, Clone ends, Exome, Random survey, Other
Syntax: pick list
Example Values: Whole
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: target capture specification
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001899
OBO Definition: target capture specification
Other Synonyms: BioProject:Capture*;

8. Project Method
Core Project Field ID: CP8
Description: Indicates the general approach used to obtain data.
Data Categories: Investigation
Allowed Values: Sequencing, Array, Mass Spectrometry, Other
Syntax: pick list
Example Values: Sequencing
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: investigation assay specification
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001896
OBO Definition: investigation assay specification
Other Synonyms: BioProject:Methodology*;

9. Project Objectives
Core Project Field ID: CP9
Description: Indicates the project goals with respect to the type of data that will be generated and submitted to an INSDC database.
Data Categories: Investigation
Allowed Values: Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, Expression, Maps, Phenotype, Other
Syntax: pick list
Example Values: Assembly; Annotation
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: specification of data to be generated in an investigation
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001892
OBO Definition: specification of data to be generated in an investigation
Other Synonyms: BioProject:Objective*;

10. Grant Agency
Core Project Field ID: CP10
Description: The name of the agency providing funding support for the specimen collection and sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: U.S. National Institutes of Health; Bill and Melinda Gates Foundation
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: grant agency
OBO Foundry Purl: submitted to OBI
OBO Definition: An organization that provides funding support for projects such as investigations.
Other Synonyms:

11. Supporting Grants/Contract ID
Core Project Field ID: CP11
Description: Unique identifier of the grant(s) and/or contract(s) that supports the specimen collection and sequencing project
Data Categories: Investigation
Allowed Values: free text; not applicable allowed
Syntax: free text
Example Values: N01AI40041; HHSN266200400041C
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: grant ID
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001629
OBO Definition: A CRID symbol used to identify a grant.
Other Synonyms: BioProject:Grant ID;

12. Publication Citation
Core Project Field ID: CP12
Description: Citation for scientific publication(s) related to the specimens included in the project and/or the sequence derived from the project and/or its interpretation
Data Categories: Investigation
Allowed Values: PubMed ID; Digital Object Identifier (DOI); not applicable allowed
Syntax: free text
Example Values: PMID:22260278; DOI:10.1126/science.323.5915.713a
Data Source: Sample Provider
Comments: Separate multiple entries with a semicolon (;).
OBO Foundry Synonym: PubMed ID
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001617
OBO Definition: A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information.
Other Synonyms: BioProject:PubMed ID, DOI;MixS: ref_biomaterial;

13. Sample Provider Principal Investigator (PI) Name
Core Project Field ID: CP13
Description: Name of the responsible investigator providing the sample set and metadata for the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: Jane Z. Doe
Data Source: Sample Provider
Comments: BioProject:will be included as custom attribute and concatenated together with "Sample Provider PI's Institution" and "Sample Provider PI's email" fields.
OBO Foundry Synonym: specimen provider principal investigator
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001889
OBO Definition: A person who is a principal investigator and provides the specimen
Other Synonyms:

14. Sample Provider PI's Institution
Core Project Field ID: CP14
Description: Institutional affiliation of the responsible investigator providing the sample set and metadata for the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: Random Research Institute (RRI)
Data Source: Sample Provider
Comments: BioProject: will be included as custom attribute and concatenated together with "Sample Provider PI's Institution" and "Sample Provider PI's email" fields.
OBO Foundry Synonym: organization of specimen provider principal investigator
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001880
OBO Definition: An organization that is the affiliation of the principal investigator providing the specimens for the investigation
Other Synonyms:

15. Sample Provider PI's email
Core Project Field ID: CP15
Description: Preferred email address of the responsible investigator providing the sample set and metadata for the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: jane_doe@aol.com
Data Source: Sample Provider
Comments: BioProject: will be included as custom attribute and concatenated together with "Sample Provider Principal Investigator (PI) Name" and "Sample Provider PI's Institution" fields.
OBO Foundry Synonym: email address of specimen provider principal investigator
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001903
OBO Definition: An email address of the principal investigator providing the specimens for the investigation
Other Synonyms:

16. Sequencing Facility
Core Project Field ID: CP16
Description: Name of the facility resposible for sequence determination; in many cases this will be one of the DMID-supported Genome Sequence Centers for Infectious Diseases (GSCIDs)
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: Awesome Sequencing Center (ASC)
Data Source: GSCID
Comments:
OBO Foundry Synonym: sequencing facility organization
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001891
OBO Definition: An organization that provides sequence determination service
Other Synonyms:

17. Sequencing Facility Contact Name
Core Project Field ID: CP17
Description: Name of the responsible investigator leading the sequencing project at the sequencing facility
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: John Q. Smith
Data Source: GSCID
Comments:
OBO Foundry Synonym:
sequencing facility contact person
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001888
OBO Definition: A person who is the contact representative at the sequencing facility
Other Synonyms:

18. Sequencing Facility Contact's Institution
Core Project Field ID: CP18
Description: Institutional affiliation of the responsible investigator leading the sequencing project at the sequencing facility
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: University of Excellence (UOE)
Data Source: GSCID
Comments:
OBO Foundry Synonym:
organization of sequencing facility contact person
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001897
OBO Definition: An organization that is the affiliation of the contact representative at the sequencing facility
Other Synonyms:

19. Sequencing Facility Contact's email
Core Project Field ID: CP19
Description: Preferred email address of the responsible investigator leading the sequencing project at the sequencing facility
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: john_smith@gmail.com
Data Source: GSCID
Comments:
OBO Foundry Synonym:
email address of sequencing facility contact person
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001894
OBO Definition: An email address of the contact representative at the sequencing facility
Other Synonyms:

20. Bioinformatics Resource Center
Core Project Field ID: CP20
Description: Name of the DMID-sponsored Bioinformatics Resource Center (BRC) that contains the metadata linked to the organism sequence
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: New Pathogen Resource (NewPR)
Data Source: BRC
Comments:
OBO Foundry Synonym
: Bioinformatics Resource Center
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001626
OBO Definition: An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them.
Other Synonyms:

21. Bioinformatics Resource Center Contact Name
Core Project Field ID: CP21
Description: Name of the investigator at the BRC responsible for managing the data derived from the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: Joe Bioinfo
Data Source: BRC
Comments:
OBO Foundry Synonym:
Bioinformatics Resource Center contact person
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001883
OBO Definition: A person who is the contact representative of a Bioinformatics Resource Center
Other Synonyms:

22. Bioinformatics Resource Center Contact's Institution
Core Project Field ID: CP22
Description: Institutional affiliation of the investigator at the BRC responsible for managing the data derived from the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: Advanced Bioinformatics Consortium (ABC)
Data Source: BRC
Comments:
OBO Foundry Synonym: organization of Bioinformatics Resource Center contact person
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001881
OBO Definition: An organization that is the affiliation of the person who is contact representative of a Bioinformatics
Resource Center
Other Synonyms:

23. Bioinformatics Resource Center Contact's email
Core Project Field ID: CP23
Description: Preferred email address of the investigator at the BRC responsible for managing the data derived from the sequencing project
Data Categories: Investigation
Allowed Values: free text
Syntax: free text
Example Values: joe_bioinfo@abc.org
Data Source: BRC
Comments:
OBO Foundry Synonym:
email address of Bioinformatics Resource Center contact person
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001887
OBO Definition: An email address of the person who is contact representative of a Bioinformatics Resource Center
Other Synonyms:

Last Updated January 07, 2014