OAEI Bio-ML 2026

Ontologies

The biomedical source ontologies behind the three pairs. NCIT, DOID and FMA now ship with the Hugging Face download; only SNOMED CT is obtained separately — under an Affiliate Licence or by contacting us for a research-only copy.

OAEI Bio-ML matches whole biomedical ontologies. Most of them now ship with the dataset: the Hugging Face download bundles the NCIT, DOID, and FMA ontology files alongside the task data, so for most pairs there is nothing extra to obtain. The one exception is SNOMED CT, which its licence does not permit us to redistribute — you obtain it yourself, either under a SNOMED CT Affiliate Licence or by contacting us for a copy strictly for research purposes. This page lists each source, its licence, and which pair needs which. The public-facing references are distributed with the task data.

Which ontologies each pair needs

PairProvided in the downloadYou obtain yourself
NCIT–DOIDNCIT, DOID—
SNOMED–FMAFMASNOMED CT
SNOMED–NCITNCITSNOMED CT

NCIT, DOID, SNOMED CT and FMA are the four ontologies matched across the three pairs; three of them (NCIT, DOID, FMA) travel with the download and only SNOMED CT is obtained separately. MONDO and the UMLS Metathesaurus underlie the organiser-side reference construction (the gold references are grounded in UMLS/Mondo) — participants do not need them to run the tasks.

Sources and licences

Provided in the Hugging Face download

These three ship with the OAEI-ML/bio-ml dataset (edition tag 2026), so you do not need to fetch them separately. The publisher links are kept for provenance and version reference.

  • NCIT — NCI Thesaurus (cancer / clinical; licence: CC BY 4.0) A reference terminology covering cancer and general clinical concepts, published by the U.S. National Cancer Institute. Provenance: the NCI Thesaurus or the OBO PURL purl.obolibrary.org/obo/ncit.owl; also on BioPortal.

  • DOID — Human Disease Ontology (disease; licence: CC0 1.0) A standardised ontology of human diseases. Provenance: disease-ontology.org or the OBO PURL purl.obolibrary.org/obo/doid.owl.

  • FMA — Foundational Model of Anatomy (anatomy; per its own licence) A reference ontology of human anatomy from the Structural Informatics Group, University of Washington. Provenance: the FMA project page or BioPortal.

Obtain yourself: SNOMED CT

  • SNOMED CT (clinical terminology; licence: SNOMED CT Affiliate Licence) A comprehensive clinical healthcare terminology from SNOMED International, used in the SNOMED-FMA and SNOMED-NCIT pairs. Its licence does not permit us to redistribute it, so you obtain a copy yourself by either route:
    1. Under a SNOMED CT Affiliate Licence — free of charge in UMLS-member territories via the UMLS Terminology Services (UTS), or otherwise through SNOMED International; or
    2. Contact us to obtain a copy strictly for research purposes.

Reference-construction resources (organiser-side)

These underlie how the gold references were built. Participants do not need them to produce or score submissions; they are documented here for transparency.

  • MONDO — Mondo Disease Ontology (disease; licence: CC BY 4.0) A harmonised disease ontology from the Monarch Initiative. Source: mondo.monarchinitiative.org or the OBO PURL purl.obolibrary.org/obo/mondo.owl.

  • UMLS Metathesaurus (metathesaurus; licence: UMLS Metathesaurus Licence via UTS) The Unified Medical Language System integrates many biomedical vocabularies; it underlies the reference construction for every pair. Source (free UTS account): uts.nlm.nih.gov — see the UMLS overview.

Notes

  • Use the ontology versions pinned by the 2026 edition where indicated on the dataset card; matching against a different release may shift entity IRIs.
  • Correspondences use full OWL IRIs (e.g. http://purl.obolibrary.org/obo/DOID_1612).
  • OAEI Bio-ML redistributes the NCIT, DOID, and FMA ontology files with the dataset; SNOMED CT is not redistributed — obtain it under your own Affiliate Licence or by contacting us for a research-only copy (see above).