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GSCID/BRC Project and Sample Application Standard: Project Specific

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

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

1. Isolate
Project-Specific Field ID: PS1
Field Name: Isolate
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: isolate
NCBI Component Definition:
OBO Foundry Synonym:
OBO Foundry Purl:
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2. Host Disease Stage
Project-Specific Field ID: PS2
Field Name: Host Disease Stage
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: host-disease-stage
NCBI Component Definition: Stage of disease at the time of sampling
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3. Host Disease Outcome
Project-Specific Field ID: PS3
Field Name: Host Disease Outcome
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: host-disease-outcome
NCBI Component Definition: Final outcome of disease, e.g., death, chronic disease, recovery
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4. Host Description
Project-Specific Field ID: PS4
Field Name: Host Description
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: host-description
NCBI Component Definition: Additional information not included in other defined vocabulary fields
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5. Specimen Voucher
Project-Specific Field ID: PS5
Field Name: Specimen Voucher
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: specimen-voucher
NCBI Component Definition: Formal identifier of the Type Specimen of the source organism, usually stored in an institute collection. Name of the Institution and their internal Collection and/or sample codes.
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6. Genotype
Project-Specific Field ID: PS6
Field Name: Genotype
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: genotype
NCBI Component Definition: observed genotype
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7. Serotype
Project-Specific Field ID: PS7
Field Name: Serotype
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: serotype
NCBI Component Definition: Taxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Same as serovar and serogroup. e.g. serotype="H1N1" in Influenza A virus CY098518.
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8. Serovar
Project-Specific Field ID: PS8
Field Name: Serovar
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: serovar
NCBI Component Definition: Taxonomy below subspecies; a variety (in bacteria, fungi or virus) usually based on its antigenic properties. Same as serovar and serotype. Sometimes used as species identifier in bacteria with shaky taxonomy, e.g. Leptospira, serovar saopaolo S76607 (65357 in Entrez).
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9. Pathotype
Project-Specific Field ID: PS9
Field Name: Pathotype
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: pathotype
NCBI Component Definition: Some bacterial specific pathotypes (example Eschericia coli - STEC, UPEC)
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10. Passage History
Project-Specific Field ID: PS10
Field Name: Passage History
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: passage-history
NCBI Component Definition: Number of passages and passage method
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11. Lab Host
Project-Specific Field ID: PS11
Field Name: Lab Host
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: lab-host
NCBI Component Definition: Originally meaning host on which a parasite is maintained in the lab, which may not be the same as the natural host (example hamster cells used to support a parasite normally found in mouse in the wild). Also seen used (in dbEST and dbGSS) to list the bacterial strain in which a plasmid construct library is maintained in the lab (e.g. ID:167152 lab-host DH10B T1-resistant).
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12. Subgroup
Project-Specific Field ID: PS12
Field Name: Subgroup
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: subgroup
NCBI Component Definition: Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate.
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13. Subtype
Project-Specific Field ID: PS13
Field Name: Subtype
Description:
NCBI Component Name: BioSample
NCBI Component Synonym: subtype
NCBI Component Definition: Used as classifier in viruses (e.g. HIV type 1, Group M, Subtype A).
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Last Updated January 07, 2014