Notice

Because of a lapse in government funding, the information on this website may not be up to date, transactions submitted via the website may not be processed, and the agency may not be able to respond to inquiries until appropriations are enacted.

Updates regarding government operating status and resumption of normal operations can be found at USA.gov.

DMID Metadata Standards Bacteria Specific

v1.4

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:

Content last reviewed on January 7, 2014