Ontology Download README

Ontologies at the Comprehensive Antibiotic Resistance Database are freely available under
the Creative Commons CC-BY license version 4.0, https://creativecommons.org/licenses/by/4.0/

CITATION:

Alcock et al. 2023. "CARD 2023: expanded curation, support for machine learning, and resistome 
prediction at the Comprehensive Antibiotic Resistance Database" Nucleic Acids Research, 
51, D690-D699. https://pubmed.ncbi.nlm.nih.gov/36263822/


ONTOLOGIES:

Data on the four core ontologies underlying the CARD are provided in three formats: OBO, 
TSV, and JSON. The Antibiotic Resistance Ontology is additional available in OWL format.
The ontologies are:

ARO - The Antibiotic Resistance Ontology that serves as the primary organizing principle 
of the CARD.

MO - CARD's Model Ontology which describes the different antimicrobial resistance gene 
detection models encoded in the CARD and used by the Resistance Gene Identifier.

NCBITaxon - A slim version of the NCBI Taxonomy used by the CARD to track source pathogen
of molecular sequences.

RO - CARD's Relationship Ontology which describes the different relationship types between 
ontology terms.

VIRO - CARD's draft Virulence Ontology describing bacterial virulence. Currently not under
development.

CARD SHORT NAMES:

A CARD-specific abbreviation for AMR gene names associated with Antibiotic Resistance
Ontology terms, often not based on the literature. This is used for programmatic and 
compatibility purposes and is not ontologically relevant. Each ontology term with an 
associated AMR detection model has a CARD Short Name that appears in CARD data files 
and output generated by RGI. If the original gene name is less than 15 characters, the 
CARD short name is identical; if the gene name is greater than 15 characters, the CARD 
Short Name has been abbreviated by CARD curators specifically to identify the proper 
gene or protein name. All CARD Short Names are unique and have whitespace characters 
replaced by underscore characters. The convention for pathogen names is capitalized 
first letter of the genus followed by the lowercase first three letters of the species 
name. The antibiotic abbreviations are from https://journals.asm.org/journal/aac/abbreviations
plus some custom abbreviations by the CARD curators. Simple CARD Short Names often do not
involve either, e.g. CTX-M-15, but where applicable the CARD Short Names follow pathogen_gene
or pathogen_gene_drug. The full lists of abbreviations can be found at:
https://card.mcmaster.ca/latest/data