OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

TLDR

Biological ontologies organize experimental data, but integrating multiple independently developed ontologies often leads to incompatibilities. The OBO Foundry was established to promote ontology development, harmonization, and sharing by formalizing guiding principles. The authors encoded these principles as operational rules, built automated validation checks and a dashboard, and curated metadata across all ontologies with stakeholder coordination. Applying the checks to the full OBO suite uncovered compliance gaps and showed that objective evaluation can improve ontology quality and interoperability, supporting FAIR data goals. Database URL http://obofoundry.org.

Abstract

Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology's compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR). Database URL http://obofoundry.org/.