Ontology Alignment Evaluation Initiative

UMLS-based reference alignments

The original UML mapping sets were extracted from the MRCONSO.RRF file of the UMLS [1] 2009AA distribution files (see [2] for details).

In [2] it was noticed that the integration of the (formally represented) UMLS mappings together with the input ontologies was leading to numerous logical errors. To address this problem, in [2] and [3] two refinements of the UMLS mappings were presented that do not lead to such inconsistencies.

In the OAEI track we will consider the refined subset proposed in [3], since it was generated using "less aggressive" ontology repair techniques.

Please consider citing [1], [2] and [3] when you use the UMLS-based reference alignments.



  1. O. Bodenreider: The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic acids research 32 (2004) [url]
  2. E. Jimenez-Ruiz, B. Cuenca Grau, I. Horrocks, and R. Berlanga: Logic-based assessment of the compatibility of UMLS ontology sources. J Biomed. Sem. 2 (2011) [url]
  3. E. Jimenez-Ruiz, B. Cuenca Grau: Logmap: Logic-based and scalable ontology matching. In: 10th International Semantic Web Conference, 273-288 (2011) [url]