CMOMgen: Complex Multi-Ontology Alignment via Pattern-Guided In-Context Learning

TL;DR

CMOMgen is an innovative end-to-end method for complex multi-ontology alignment that leverages pattern-guided in-context learning to generate accurate, semantically sound mappings across multiple biomedical ontologies.

Contribution

It introduces the first end-to-end CMOM strategy that dynamically generates comprehensive mappings without restrictions on the number of ontologies or entities, enhancing semantic integration.

Findings

Outperforms baselines in class selection accuracy.

Achieves at least 63% F1-score in evaluated tasks.

46% of manual mappings scored maximum, indicating high semantic quality.

Abstract

Constructing comprehensive knowledge graphs requires the use of multiple ontologies in order to fully contextualize data into a domain. Ontology matching finds equivalences between concepts interconnecting ontologies and creating a cohesive semantic layer. While the simple pairwise state of the art is well established, simple equivalence mappings cannot provide full semantic integration of related but disjoint ontologies. Complex multi-ontology matching (CMOM) aligns one source entity to composite logical expressions of multiple target entities, establishing more nuanced equivalences and provenance along the ontological hierarchy. We present CMOMgen, the first end-to-end CMOM strategy that generates complete and semantically sound mappings, without establishing any restrictions on the number of target ontologies or entities. Retrieval-Augmented Generation selects relevant classes to compose the mapping and filters matching reference mappings to serve as examples, enhancing In-Context Learning. The strategy was evaluated in three biomedical tasks with partial reference alignments. CMOMgen outperforms baselines in class selection, demonstrating the impact of having a dedicated strategy. Our strategy also achieves a minimum of 63% in F1-score, outperforming all baselines and ablated versions in two out of three tasks and placing second in the third. Furthermore, a manual evaluation of non-reference mappings showed that 46% of the mappings achieve the maximum score, further substantiating its ability to construct semantically sound mappings.