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:​