The use of Foundational Ontologies in Bioinformatics

Ontologies have been used in biomedicine for several pur- poses, such as knowledge representation, data analysis and integration. The FAIR principles recommend the use of controlled vocabularies, such as ontologies, to define data terms precisely. However, ontologies are currently modelled following different approaches, sometimes defining overlapping concepts with conflicting definitions, which can harm data FAIRness. Foundational ontologies are defined as domain-independent ontologies that describe the most basic concepts of our world, and thus used to lessen the interoperability problem. With the aim to investigate how foundational ontologies can improve the benefits of FAIR data for life sciences research, we observed a need to assess how they are used in the area. To support our investigation, we conducted a systematic literature analysis, in which we selected appropriate works according to predefined criteria. From the selected works, we identified that, besides being used for several purposes, there is almost no empirical evidence testing the claims for or against the use of foundational ontologies. This indicates a need for evaluating the use of such artefacts in bioinformatics. Similarly, we observed a low adherence to formal ontology construction and evaluation methods during ontologies development, which can im- pact the quality and sustainability of ontologies, and thus the FAIRness of ontologized data.