The public task data for the OAEI Bio-ML 2026 track (a larger LargeBio), over three whole-ontology pairs: NCIT–DOID, SNOMED–FMA, SNOMED–NCIT. This repository holds the redistributable pieces — the reference/candidate data as entity IRIs/CURIEs, the manifests, and the openly-licensed source ontologies (DOID, FMA, NCIT) under ontologies/. The licence-restricted SNOMED CT ontology is not re-hosted publicly (see Ontologies); the held-out test gold is organiser-side only; the scoring kit is code and lives in the GitHub repo (see Quickstart). See the evaluation metrics on the track website.

Tasks

Global equivalence alignment — submit an OAEI Alignment RDF/XML or a TSV per pair. Scored (organiser-side) with repaired coherence-aware P/R/F1 (headline) + standard P/R/F1 + Global Coherence. A public refs_equiv/train.tsv of positive mappings is provided per pair.
Local equivalence ranking — rank the 100-candidate pool per query. Scored with MRR + Hits@{1,5,10}.

Layout (per pair `NCIT-DOID/`, `SNOMED-FMA/`, `SNOMED-NCIT/`)

Path	Contents
`local.{train,valid,test}.cands.tsv`	Subtrack 2 ranking pools (100 cands/query; test is gold-stripped)
`refs_equiv/train.tsv`	Subtrack 1 public train positives (`SrcEntity, TgtEntity, Score`)
`repaired/`	the same set against the coherence-repaired reference
`evaluation/`	`sample_submission.tsv`, `submission_schema.json` (shared)
`SHA256SUMS.txt`, `release_manifest.json`, `license_manifest.json`, `resolved_versions.json`	integrity + provenance

Top-level, the ontologies/ directory holds the openly-licensed source ontologies (DOID, FMA, NCIT) with an ontologies/SHA256SUMS.txt; see Ontologies.

The scoring kit (validators + self-scorers, zero-install) is code and lives in the GitHub repository liseda-lab/OAEI-Bio-ML, not in this dataset.

Coming from the original Bio-ML?

local.*.cands.tsv corresponds to Bio-ML's refs_equiv/test.cands.tsv (now a 3-way train/valid/test split, 100 cands/query). refs_equiv/train.tsv is the supervised positive-mapping file. The openly-licensed ontologies (DOID, FMA, NCIT) are now bundled here under ontologies/; SNOMED CT remains licence-gated (see Ontologies).

Ontologies

The openly-licensed source ontologies are now included directly, under ontologies/:

Ontology	Licence	File
DOID	CC0 1.0	`ontologies/DOID-611355c44553-doid.owl`
FMA	FMA licence	`ontologies/FMA-beb3dc47979a-fma.owl`
NCIT	CC BY 4.0	`ontologies/NCIT-bd7a9a8a75e5-Thesaurus.owl`

Hosted-file checksums are in ontologies/SHA256SUMS.txt; version pins + provenance in resolved_versions.json and ontologies.md. (The NCIT-bd7a9a8a75e5-… id refers to the source Thesaurus.OWL.zip; the hosted file is the extracted .owl, whose own SHA-256 is in ontologies/SHA256SUMS.txt.)

SNOMED CT (used by the SNOMED–FMA and SNOMED–NCIT pairs) is restricted and is not published here. Obtain it either:

under your own SNOMED CT Affiliate License (via a SNOMED International Member National Release Centre), converting the pinned US Edition 2026-03-01 release to http://snomed.info/id/<id> class IRIs (View-A scheme); or
on request — researchers who already hold the required SNOMED CT licence may contact the organisers at contact@oaei-ml.org for access to the private companion repository OAEI-ML/bio-ml-private, which hosts the exact converted OWL used here.

MONDO (CC BY 4.0) underlies the reference construction and UMLS (restricted, UTS) is used only organiser-side; neither is a task ontology and neither is hosted here. See ontologies.md for pins/checksums and license_manifest.json for per-source terms.

Quickstart

The scoring kit lives in the GitHub repo — clone it for the tools, download this dataset for the data:

git clone https://github.com/liseda-lab/OAEI-Bio-ML          # provides scoring_kit/
pip install -U huggingface_hub
hf download OAEI-ML/bio-ml --repo-type dataset --revision 2026 --local-dir ./bio-ml   # data + open ontologies/
python3 OAEI-Bio-ML/scoring_kit/self_check.py --data ./bio-ml            # oracle -> perfect scores
python3 OAEI-Bio-ML/scoring_kit/validate_ranking.py bio-ml/NCIT-DOID/local.test.cands.tsv my_ranking.tsv
python3 OAEI-Bio-ML/scoring_kit/score_local.py my_ranking.tsv bio-ml/NCIT-DOID/local.valid.cands.tsv

The download includes the openly-licensed ontologies/ (DOID, FMA, NCIT); add SNOMED CT yourself (Affiliate License) or request access to OAEI-ML/bio-ml-private (see Ontologies). Submit via the CodaBench competitions (linked from the track website).

Licensing

The packaging and reference/candidate IRI data are provided for this evaluation and ontology-matching research. Underlying sources retain their licences:

DOID (CC0 1.0), NCIT (CC BY 4.0) and FMA (FMA licence) are redistributable and are published here under ontologies/;
MONDO (CC BY 4.0, reference) is linked, not hosted;
SNOMED CT (Affiliate) and UMLS (Metathesaurus) are restricted (UTS/Affiliate) and are not published here — SNOMED CT is available under your own Affiliate License or, on request to the organisers at contact@oaei-ml.org, via the private OAEI-ML/bio-ml-private repository.

Per-source details: license_manifest.json. Do not attempt to reconstruct the held-out test reference.

BioML 2026 — OAEI Bio-ML