Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching
Ontology Matching (OM) plays an important role in many domains such as
bioinformatics and the Semantic Web, and its research is becoming increasingly
popular, especially with the application of machine learning (ML) techniques.
Although the Ontology Alignment Evaluation Initiative (OAEI) represents an
impressive effort for the systematic evaluation of OM systems, it still suffers
from several limitations including limited evaluation of subsumption mappings,
suboptimal reference mappings, and limited support for the evaluation of
ML-based systems. To tackle these limitations, we introduce five new biomedical
OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes
both equivalence and subsumption matching; the quality of reference mappings is
ensured by human curation, ontology pruning, etc.; and a comprehensive
evaluation framework is proposed to measure OM performance from various
perspectives for both ML-based and non-ML-based OM systems. We report
evaluation results for OM systems of different types to demonstrate the usage
of these resources, all of which are publicly available as part of the new
BioML track at OAEI 2022.