# Ontology Alignment in the Biomedical Domain Using Entity Definitions and Context

arXiv: https://arxiv.org/abs/1806.07976 · HTML: https://mlsanity.com/paper/1806.07976/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 20 Jun 2018.

## Built on by (most cited first, 10 of 10)

- [BERTMap: A BERT-based Ontology Alignment System](https://mlsanity.com/paper/2112.02682/) (2021)
- [Cross-Domain Data Integration for Named Entity Disambiguation in Biomedical Text](https://mlsanity.com/paper/2110.08228/) (2021)
- [VeeAlign: Multifaceted Context Representation using Dual Attention for Ontology Alignment](https://mlsanity.com/paper/2102.04081/) (2021)
- [Truveta Mapper: A Zero-shot Ontology Alignment Framework](https://mlsanity.com/paper/2301.09767/) (2023)
- [Matching Table Metadata with Business Glossaries Using Large Language Models](https://mlsanity.com/paper/2309.11506/) (2023)
- [MapperGPT: Large Language Models for Linking and Mapping Entities](https://mlsanity.com/paper/2310.03666/) (2023)
- [GenOM: Ontology Matching with Description Generation and Large Language Model](https://mlsanity.com/paper/2508.10703/) (2025)
- [UVA Resources for the Biomedical Vocabulary Alignment at Scale in the UMLS Metathesaurus](https://mlsanity.com/paper/2205.10575/) (2022)
- [SLHCat: Mapping Wikipedia Categories and Lists to DBpedia by Leveraging Semantic, Lexical, and Hierarchical Features](https://mlsanity.com/paper/2309.11791/) (2023)
- [Search-Optimized Quantization in Biomedical Ontology Alignment](https://mlsanity.com/paper/2507.13742/) (2025)

## Abstract (arXiv)

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 when 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 entity-level matchers in a SOTA system.