BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies.

Journal: Nucleic acids research
Published Date: Jul 7, 2025

Abstract

BioPortal (https://bioportal.bioontology.org) is the world's most comprehensive repository of biomedical ontologies. It provides infrastructure for finding, sharing, searching, and utilizing biomedical ontologies. Launched in 2005, BioPortal now includes 1549 ontologies (1182 of them public). Its open, freely accessible website enables anyone (i) to browse the ontology library, (ii) to search for terms across ontologies, (iii) to browse mappings between terms, (iv) to see popularity ratings and recommendations on which ontologies are most relevant to their use cases, (v) to annotate text with ontology terms, (vi) to submit an ontology, and (vii) to request ontology changes. The library of ontologies can be accessed programmatically via a REST application programming interface (API). Recent enhancements include a BioPortal knowledge graph that integrates knowledge from multiple ontologies; a unified data model for interoperability with other knowledge sources; ontology popularity ratings and recommendations for relevant ontologies; and the ability to request ontology changes via a simple user interface that automatically converts user change requests to GitHub Pull Requests that specify the edits that will be made to the ontology upon approval.

Authors

  • Jennifer Vendetti
    Center for Biomedical Informatics Research, Stanford University, 3180 Porter Dr., Palo Alto, CA 94304, United States.
  • Nomi L Harris
    Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
  • Michael V Dorf
    Center for Biomedical Informatics Research, Stanford University, Palo Alto, CA 94304, United States.
  • Alex Skrenchuk
    Center for Biomedical Informatics Research, Stanford University, Palo Alto, CA 94304, United States.
  • J Harry Caufield
    Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
  • Rafael S Gonçalves
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA. rafael.goncalves@stanford.edu.
  • John B Graybeal
    Center for Biomedical Informatics Research, Stanford University, 3180 Porter Dr., Palo Alto, CA 94304, United States.
  • Harshad Hegde
  • Timothy Redmond
    Center for Biomedical Informatics Research, Stanford University, Palo Alto, CA 94304, United States.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Mark A Musen
    Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305-5479, United States. Electronic address: musen@stanford.edu.

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