In biomedical sciences, ontologies are used to annotate and organize data stored in knowledge databases and facilitate their exploitation. Following the pioneering work of the Gene Ontology at the turn of the century, the Open Biomedical and Biological Ontologies (OBO) Foundry was created to coordinate the development of a family of interoperable ontologies sharing a core set of principles. The Foundry now includes more than 150 ontologies. The Ontology Development Kit (ODK) [1] was developed to facilitate the implementation of standardized ontology development practices across the Foundry. It takes the form of a Docker image that provides ontology editors with all the command-line tools they need to manage, edit, build, and test their ontologies, as well as standardized and carefully crafted Makefile rules to pilot all steps of the ontology life cycle. In recent years, many ontologies such as the Uberon multi-species anatomy ontology, the Cell Ontology (CL), or the Unified Phenotype Ontology (uPheno) have been converted to use the ODK. By moving most of the management, building, and testing logic from the individual ontologies to the ODK, the kit aims to make the life of ontology editors easier, by allowing them to focus solely on actual ontology editing, all the while contributing to the standardisation of the various ontologies.
[1] Nicolas Matentzoglu, Chris Mungall, and Damien Goutte-Gattat (2021). Ontology Development Kit. doi:10.5281/zenodo.5762512
Speakers: Damien Goutte-Gattat