Ontologies are becoming increasingly relevant for integration, reuse and interoperability of complex biomedical data. However, to stay relevant, ontologies require constant evolution, especially in dynamic domains such as life-sciences research data. To satisfy the needs of domain experts, there must be a mechanism to request ontology updates and new terms. The current options typically involve emailing the ontology maintainer and waiting for the next release, or extending the ontology with private terms, both of which are quite unsatisfactory. This lack of a more efficient user-driven ontology update mechanism was pointed out by domain experts who are using CDD’s new tool BioAssay Express (BAE). BAE allows users to annotate their bioassays in a semi-automated and standardized fashion using highly-accessed ontologies (BioAssay Ontology (BAO), Gene Ontology (GO), Disease Ontology (DOID), and Drug Target Ontology (DTO) among others) in the background. Our goal in the OntoloBridge project is to help various users of BAE (researchers performing curation, dedicated curators, IT specialists, ontology owners, and librarians/repositories) request and update the existing vocabulary provided by BAO in a semi-automated way, with a user-friendly interface. Furthermore, APIs and tools including templates from the Center for Expanded Data Annotation Retrieval (CEDAR) will be created to allow users to request new ontology terms or changes to existing terms easily during the annotation process. Part of this integration involves the ability to request new terms as placeholders that will get filled in with the official URI once the request has been approved, in order to not disrupt the annotation workflow. In this way, we’re aiming to increase the Findability, Interoperability, Accessibility, and Reproducibility (FAIR) of ontologies by bringing the ontology maintainers and ontology users closer together.

OntoloBridge: A semi-automated ontology update request system

256th National Meeting (2018)

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