DMID Metadata Standards Project Specific

v1.4
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: 
OBO Foundry Definition: 
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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 
OBO Foundry Synonym: 
OBO Foundry Purl: 
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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 
OBO Foundry Synonym: 
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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. 
OBO Foundry Synonym: 
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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. 
OBO Foundry Synonym: 
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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). 
OBO Foundry Synonym: 
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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). 
OBO Foundry Synonym: 
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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. 
OBO Foundry Synonym: 
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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). 
OBO Foundry Synonym: 
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