ARO

The Antibiotic Resistance Ontology describes antibiotic resistance genes and mutations, their products, mechanisms, and associated phenotypes, as well as antibiotics and their molecular targets. It is integrated with the Comprehensive Antibiotic Resistance Database (https://card.mcmaster.ca), a curated resource containing high-quality reference data on the molecular basis of antimicrobial resistance.

License

Ontologies at the Comprehensive Antibiotic Resistance Database are freely available under the Creative Commons CC-BY license version 4.0.

Contributing

The Antibiotic Resistance Ontology (ARO) is continuously improved by the Comprehensive Antibiotic Resistance Database (CARD) curation team, with updates released every 1-3 months here and at the CARD website. This repo (https://github.com/arpcard/aro) does not accept pull requests, but instead only reflects the latest release at card.mcmaster.ca. Please request additions or modifications to the ARO either here via https://github.com/arpcard/aro/issues or at https://github.com/arpcard/amr_curation. The curation team will work with you to incorporate your suggestions into the next release of the ARO.

ARO Next

Ontologies, also known as controlled vocabularies, provide a conceptual framework to organize knowledge, best exemplified in CARD by the ARO’s confersresistanceto_antibiotic relationship; for example, CTX-M-15 confersresistanceto_antibiotic cefalotin. In this example, two concepts (CTX-M-15 and cefalotin) are associated via an ontological relationship, of which the ARO uses many. These relationships allow ARO to act as a knowledge graph relating molecules, genes, mutations, resistance mechanisms, and drug targets. Yet, the ARO reflects several shortcuts in its development, as our initial goal was the rapid development of tools for ARG annotation. A lack of interoperable architecture with other ontologies hampers its utility for the broader data science community, e.g., data harmonization efforts, ontological interoperability, and well-structured data for artificial intelligence. While registered in the OBO Foundry of interoperable ontologies, ARO violates two key aspects of formal ontologies: (1) proper upper ontology structures (e.g., "object", "property", "relation") required for semantic interoperability among ontologies and (2) resolution of orthogonality, i.e., the re-use of terms from existing ontologies. For example, beta-lactamases are described in ARO:3000001 beta-lactamase, but ARO lacks linkages to the Gene Ontology (GO:0008800 beta-lactamase activity) and Chemical Entities of Biological Interest ontology (CHEBI:35627 β-lactam). As AMR research relies on an accurate and well-designed ARO, we are undertaking the development of the next generation of ARO at ARO Next as a core activity to resolve design and orthogonality flaws. At this stage, ARO Next is a stand-alone effort separate from card.mcmaster.ca like our Mobilome Ontology efforts, but will replace the version in card.mcmaster.ca once ready. Community input into ARO Next is very welcome.

Stable Release Versions

The latest version of the ontology can always be found at:

http://purl.obolibrary.org/obo/aro.owl

(note this will not show up until the request has been approved by obofoundry.org)

Contact

Please contact us at card@mcmaster.ca.