OAEI 2025::Bio-ML Track

General description

The 2025 edition involves the following ontologies:

OMIM (Online Mendelian Inheritance in Man)
ORDO (Orphanet Rare Disease Ontology)
NCIT (National Cancer Institute Thesaurus)
DOID (Human Disease Ontology)
FMA (Foundational Model of Anatomy)
SNOMED CT

A complete description is available at the Bio-ML documentation.

Resources

Dataset download: Version OAEI Bio-ML 2025
Comprehensive documentation for Bio-ML, including every piece of information you need for understanding, using, and evaluating Bio-ML
Resource paper for Bio-ML: Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching (ISWC 2022, Best Resource Paper Candidate)
Poster paper for Bio-LLM (and also the LLMap model): Exploring Large Language Models for Ontology Alignment (ISWC 2023, Poster&Demos)

Evaluation

Full details about the evaluation framework (global matching and local ranking) and the OAEI participation (result format for each setting in the main Bio-ML track and the Bio-LLM sub-track) are available at the Bio-ML documentation.

We accept direct result submission via this google forms based on trust. We will also release results for systems based on our implementations and for systems submitted via MELT. These three categories will be specified on the result tables.

Organisers

The Bio-ML track is organised by Pedro Giesteira Cotovio, Lucas Ferraz, Ernesto Jiménez-Ruiz and Catia Pesquita.