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GSCID/BRC Project and Sample Application Standard: Bacteria Specific

v1.3

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

1. Bacteria Antibiotic Sensitivity
Project-Specific Field ID: BAC1
Field Name: Bacteria Antibiotic Sensitivity
Description: Results of tests for antibiotic resistance, usually measured in minimum inhibitory concentration (MIC). Format: name of an antibiotic followed by 'MIC' other name of other metric and a measure of the quantity of antibiotic in ug/ml.
NCBI Component Name: BioSample
NCBI Component Synonym:
NCBI Component Definition:
OBO Foundry Synonym: drug susceptibility of infectious agent
OBO Foundry Purl: http://purl.obolibrary.org/obo/IDO_0000470
OBO Foundry Definition: A drug susceptibility that inheres in an infectious agent and is the degree to which the infectious agent can be harmed or inhibited from surviving by a drug.
Other Synonym: encoded traits (MIxS)
Data Categories: Pathogen Characteristics
Allowed Values: text
Alternate Allowed Values:
Unknown/Not Applicable/Censored Allowed: All allowed
Syntax:
Example Values: “kanamycin MIC 100 μg/ml; streptomycin MIC 20 μg/ml.”
Data Source:
Comments:

2. Bacteria Biovar
Project-Specific Field ID: BAC2
Field Name: Bacteria Biovar
Description: Commonly used descriptor of distinguishing physical or biochemical characteristics of a bacteria.
NCBI Component Name: BioSample
NCBI Component Synonym:
NCBI Component Definition:
OBO Foundry Synonym: bio-variety
OBO Foundry Purl: http://purl.obolibrary.org/obo/TAXRANK_0000032 (NOTE: Purl for this term is specified in http://purl.obolibrary.org/obo/taxrank.owl but produces Term Not Found page in Ontobee.)
OBO Foundry Definition:
Other Synonym: subspecific genetic lineage (MIxS)
Data Categories: Pathogen Characteristics
Allowed Values: text
Alternate Allowed Values:
Unknown/Not Applicable/Censored Allowed: All allowed
Syntax:
Example Values: “biovar 4” as in “B suis 2579 (biovar 4)”
Data Source:
Comments:

3. Bacteria Chromosome Content
Project-Specific Field ID: BAC3
Field Name: Bacteria Chromosome Content
Description: Number of chromosomes in bacteria.
NCBI Component Name: BioSample
NCBI Component Synonym:
NCBI Component Definition:
OBO Foundry Synonym:
OBO Foundry Purl: http://purl.obolibrary.org/obo/GO_0005694
OBO Foundry Definition:
Other Synonym: number of replicons (MIxS)
Data Categories: Pathogen Characteristics
Allowed Values: integer
Alternate Allowed Values:
Unknown/Not Applicable/Censored Allowed: Unknown/Censored
Syntax:
Example Values: 1
Data Source:
Comments:

4. Bacteria Extra Chromosomal Elements
Project-Specific Field ID: BAC4
Field Name: Bacteria Extrachromosomal Content
Description: Number of extrachromosomal elements in bacteria.
NCBI Component Name: BioSample
NCBI Component Synonym:
NCBI Component Definition:
OBO Foundry Synonym:
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0000430
OBO Foundry Definition:
Other Synonym: extrachromosomal elements (MIxS)
Data Categories: Pathogen Characteristics
Allowed Values: integer
Alternate Allowed Values:
Unknown/Not Applicable/Censored Allowed: Unknown/Censored
Syntax:
Example Values: 2
Data Source:
Comments:

5. Bacteria Pathovar
Project-Specific Field ID: BAC5
Field Name: Bacteria Pathovar
Description: Commonly used descriptor of distinguishing physical or biochemical characteristics of a bacteria.
NCBI Component Name: BioSample
NCBI Component Synonym: pathovar
NCBI Component Definition:
OBO Foundry Synonym: patho-variety
OBO Foundry Purl: http://purl.obolibrary.org/obo/TAXRANK_0000048 (NOTE: Purl for this term is specified in http://purl.obolibrary.org/obo/taxrank.owl but produces Term Not Found page in Ontobee.)
OBO Foundry Definition:
Other Synonym: subspecific genetic lineage (MIxS)
Data Categories: Pathogen Characteristics
Allowed Values: text
Alternate Allowed Values:
Unknown/Not Applicable/Censored Allowed: All allowed.
Syntax:
Example Values: “BCG” as in “M. bovis-BCG”
Data Source:
Comments:

6. Bacteria Serotype
Project-Specific Field ID: BAC6
Field Name: Bacteria Serotype
Description: Serotype of the bacteria identified in the isolate sample. This is an identity determined by the data generated by the sequencing center.
NCBI Component Name: BioSample
NCBI Component Synonym: serovar
NCBI Component Definition:
OBO Foundry Synonym:
OBO Foundry Purl: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Serotype
OBO Foundry Definition:
Other Synonym: subspecific genetic lineage (MIxS)
Data Categories: Pathogen Characteristics
Allowed Values: text
Alternate Allowed Values:
Unknown/Not Applicable/Censored Allowed: All allowed.
Syntax:
Example Values: “Typhi” as in “S. enterica subsp. enterica ser. Typhi”
Data Source:
Comments:

7. Bacteria Serotyping Method
Project-Specific Field ID: BAC7
Field Name: Bacteria Serotyping Method
Description: Experimental technique used to determine the serotype of the pathogen species in the isolate sample
NCBI Component Name: BioSample
NCBI Component Synonym:
NCBI Component Definition:
OBO Foundry Synonym:
OBO Foundry Purl: http://purl.bioontology.org/ontology/SNOMEDCT/258075003
OBO Foundry Definition:
Other Synonym: subspecific genetic lineage (MIxS)
Data Categories: Pathogen Characteristics
Allowed Values: text
Alternate Allowed Values:
Unknown/Not Applicable/Censored Allowed: All allowed.
Syntax:
Example Values: “Kauffmann-White method”
Data Source:
Comments:

Last Updated January 07, 2014