OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem.

Journal: Bioinformatics (Oxford, England)
Published Date: May 6, 2025

Abstract

SUMMARY: The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently, there has been a significant increase in the size and complexity of ontologies due to new scales of biological knowledge, such as spatial transcriptomics, new ontology development methodologies, and curation on an increased scale. Existing Web-based tools for ontology browsing such as BioPortal and OntoBee do not support the full range of definitions used by today's ontologies. In order to support the community going forward, we have developed OLS4, implementing the complete OWL2 specification, internationalization support for multiple languages, and a new user interface with UX enhancements such as links out to external databases. OLS4 has replaced OLS3 in production at EMBL-EBI and has a backward compatible API supporting users of OLS3 to transition.

Authors

  • James McLaughlin
    Nanotechnology and Integrated Bioengineering Centre, Ulster University, Jordanstown, Northern Ireland, United Kingdom.
  • Josh Lagrimas
    Samples, Phenotypes and Ontologies Team (SPOT), EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
  • Haider Iqbal
    EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
  • Helen Parkinson
    European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • Henriette Harmse
    Samples, Phenotypes and Ontologies Team (SPOT), EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.

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