OAEI Bio-ML 2026

Subtrack 1 — Submission Format

One OAEI Alignment RDF file per pair, with full OWL IRIs — the exact cell shape, a worked example, and a copy-paste template.

Subtrack 1 is a whole-ontology equivalence alignment over the three Bio-ML 2026 pairs:

  • NCIT-DOID
  • SNOMED-FMA
  • SNOMED-NCIT

For each pair you submit one complete alignment in the OAEI Alignment RDF format, using full OWL IRIs. Submissions are scored organiser-side against the hidden test reference — repaired, coherence-aware P/R/F1 (headline) and Global Coherence (see the task description).

File format

Root is rdf:RDF. The default namespace (xmlns=) is the OAEI Alignment namespace: http://knowledgeweb.semanticweb.org/heterogeneity/alignment. Exactly one <Alignment> with a header (<xml>yes</xml>, <level>0</level>, <type>??</type>, and <onto1> / <onto2> URIs). Each correspondence is a <map> wrapping one <Cell>:

  • <entity1 rdf:resource="IRI"/> — the source ontology entity’s full OWL IRI,
  • <entity2 rdf:resource="IRI"/> — the target ontology entity’s full OWL IRI,
  • <relation>=</relation> — equivalence,
  • <measure rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1.0</measure> — confidence in [0, 1].

Submit one file per pair. Entity IRIs MUST be absolute. The order of <map> elements is irrelevant. Submit a full alignment over the two ontologies; the organisers score the portion that lands on the hidden test entities.

Packaging the archive

Upload one zip containing the three files. Name each file after its pair slug with hyphens — ncit-doid, snomed-fma, snomed-ncit (e.g. ncit-doid.rdf, or ncit-doid.tsv for the TSV alternative).

Note that building the zip from the command line is advisable (if running macOS, using the Finder’s Compress option adds hidden __MACOSX files that may confuse the scorer).

For instance, you should compile your zip using the following command:

zip -X -j submission.zip ncit-doid.rdf snomed-fma.rdf snomed-ncit.rdf

A submission that scores 0.000 on every pair typically one of these two packaging problems; see submission support for more details.

Worked example (illustrative)

The cell below is illustrative — it shows the exact shape, using full OWL IRIs of the kind found in NCIT-DOID:

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns="http://knowledgeweb.semanticweb.org/heterogeneity/alignment"
         xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:xsd="http://www.w3.org/2001/XMLSchema#">
  <Alignment>
    <xml>yes</xml>
    <level>0</level>
    <type>??</type>
    <onto1>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl</onto1>
    <onto2>http://purl.obolibrary.org/obo/doid.owl</onto2>
    <map>
      <Cell>
        <entity1 rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3262"/>
        <entity2 rdf:resource="http://purl.obolibrary.org/obo/DOID_162"/>
        <relation>=</relation>
        <measure rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1.0</measure>
      </Cell>
    </map>
  </Alignment>
</rdf:RDF>

Minimal copy-paste template

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns="http://knowledgeweb.semanticweb.org/heterogeneity/alignment"
         xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
         xmlns:xsd="http://www.w3.org/2001/XMLSchema#">
  <Alignment>
    <xml>yes</xml>
    <level>0</level>
    <type>??</type>
    <onto1>SOURCE_ONTOLOGY_URI</onto1>
    <onto2>TARGET_ONTOLOGY_URI</onto2>
    <map>
      <Cell>
        <entity1 rdf:resource="SOURCE_IRI"/>
        <entity2 rdf:resource="TARGET_IRI"/>
        <relation>=</relation>
        <measure rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1.0</measure>
      </Cell>
    </map>
  </Alignment>
</rdf:RDF>

Validate — scoring is organiser-side

Subtrack 1 is semi-supervised: the test reference is hidden, so you cannot self-score against it. Validate the structure of each alignment file with the kit’s validate_global.py (Python 3.12+, standard library; it also checks against the bundled RelaxNG schema alignment.rng), then submit:

# structural + schema validation of one alignment file
python scoring_kit/validate_global.py  my-ncit-doid.rdf

To sanity-check your matcher before submitting, compare its output against the public refs_equiv/{train,valid}.tsv correspondences (a proxy — there is no public global scorer, and the hidden test slice is scored organiser-side). The organisers then compute the headline repaired, coherence-aware P/R/F1, the standard P/R/F1, and Global Coherence, and publish them to the Track 1 — Global Alignment leaderboard.