UMLS Metathesaurus  (2009AA) has been selected as the basis for the track reference alignments. Although the standard UMLS distribution does not directly provide sets of "alignments" (in the OAEI sense) between the integrated ontologies (e.g. FMA, NCI and SNOMED CT), it is relatively straightforward to extract alignment sets from the information provided in the MRCONSO.RRF distribution file (see  for details).
It was noticed, however, that the integration of the (formally represented) UMLS alignments together with the input ontologies was leading to numerous unsatisfiable classes .
In the OAEI 2013, unlike previous editions, we have created an unique refinement of UMLS mappings using Alcomo (mapping) debugging system  in conjunction with LogMap's (mapping) repair facility , and manual curation when necessary. This refinement of the UMLS mappings, which does not lead to unsatisfiable classes (*), will be used as the Large BioMed reference alignment (**).
(*) Note that the refinement of the FMA-NCI alignment, since LogMap and Alcomo use incomplete techniques, was still leading to 10 unsatisfiable classes and a manual curation of the mappings was necessary. Furthermore, the ELK reasoner was used to check the class satisfiability for SNOMED-NCI, since no OWL 2 reasoner has shown to cope with the integration of SNOMED-NCI via mappings. The HermiT reasoner was used in the FMA-NCI and FMA-SNOMED cases.
(**) It is worth mentioning that some objections have been raised on the validity (and fairness) of the application of mapping repair techniques to make reference alignments coherent . For next year campaign, we intend to take into consideration their suggestions to mitigate the effect of using repair techniques. This year reference alignment already aimed at mitigating the fairness effect by combining two mapping repair techniques, however further improvement should be done in this line.
The refined UMLS-based reference alignment for the OAEI 2013 campaign can be downloaded as a zip file (RDF, OWL and TXT formats): oaei2013_umls_repaired_reference.zip [3.6Mb].
The original UMLS-based alignments, which lead to many logical errors, can also be downloaded as a zip file (RDF, OWL and TXT formats): oaei2013_umls_original_mappings.zip [4.4Mb].
Please consider citing [1-4] when you use the refined UMLS-based reference alignments.
 O. Bodenreider: The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic acids research 32 (2004) [url]
 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]
 E. Jimenez-Ruiz, B. Cuenca Grau: Logmap: Logic-based and scalable ontology matching. In: 10th International Semantic Web Conference, 273-288 (2011) [url]
 Christian Meilicke. Alignment Incoherence in Ontology Matching. University of Mannheim, Chair of Artificial Intelligence (2011) [url]
 Catia Pesquita, Daniel Faria, Emanuel Santos, Francisco M. Couto. To repair or not to repair: reconciling correctness and coherence in ontology reference alignments. In OM 2013 workshop. [pdf]