Ontology Alignment Evaluation Initiative

OAEI 2012::Large BioMed Track

UMLS-based reference alignments (OAEI 2012)

UMLS Metathesaurus [1] (2009AA) has been selected as the basis for the track reference alignments. Although the standard UMLS distribution does not directly provide sets of "mappings" (in the OAEI sense) between the integrated ontologies (e.g. FMA, NCI and SNOMED CT), it is relatively straightforward to extract mapping sets from the information provided in the MRCONSO.RRF distribution file (see [2] for details).

It was noticed, however, that the integration of the (formally represented) UMLS mappings together with the input ontologies was leading to numerous unsatisfiable classes [2].

In the OAEI 2012 we have considered two refinements of the UMLS mappings that do not lead to (many) unsatisfiable classes.

Note that LogMap and Alcomo use incomplete techniques and the refined reference alignment may still lead to unsatisfiable classes when integrated with the input ontologies.

Please consider citing [1-4] 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]
  4. Christian Meilicke. Alignment Incoherence in Ontology Matching. University of Mannheim, Chair of Artificial Intelligence (2011) [url]