Ontology alignment in the biomedical domain using entity definitions and context

Lucy Wang, Chandra Bhagavatula, Mark Neumann, Kyle Lo, Chris Wilhelm, Waleed Ammar
2018 Proceedings of the BioNLP 2018 workshop  
Ontology alignment is the task of identifying semantically equivalent entities from two given ontologies. Different ontologies have different representations of the same entity, resulting in a need to de-duplicate entities when merging ontologies. We propose a method for enriching entities in an ontology with external definition and context information, and use this additional information for ontology alignment. We develop a neural architecture capable of encoding the additional information
more » ... available, and show that the addition of external data results in an F1-score of 0.69 on the Ontology Alignment Evaluation Initiative (OAEI) largebio SNOMED-NCI subtask, comparable with the entitylevel matchers in a SOTA system.
doi:10.18653/v1/w18-2306 dblp:conf/bionlp/WangBNLWA18 fatcat:iqrp6lyhxnhj7inakttrpczymu