The use of Foundational Ontologies in Bioinformatics

César Henrique Bernabé*, Núria Queralt Rosinach, Vítor Estevão Silva Souza, Luiz Olavo Bonino da Silva Santos, Annika Jacobsen, Barend Mons, Marco Roos

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

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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.
Original languageEnglish
Title of host publicationSWAT4HCLS 2022
Publication statusPublished - Jan 2022
Event13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022 - Online, Leiden, Netherlands
Duration: 10 Jan 202214 Jan 2022
Conference number: 13

Publication series

NameCEUR workshop proceedings


Conference13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022
Abbreviated titleSWAT4HCLS 2022
Internet address


  • Systematic Literature Review
  • Foundational Ontologies
  • FAIR
  • Biomedical ontologies
  • Ontology Engineering
  • Ontology Evaluation
  • Ontology Application


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