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Bioinformatics 2009 25(12):i69-i76; doi:10.1093/bioinformatics/btp194
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Alignment of the UMLS semantic network with BioTop: methodology and assessment

Stefan Schulz 1,*, Elena Beisswanger 2, László van den Hoek 3, Olivier Bodenreider 4 and Erik M. van Mulligen 3

1Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, 2Jena University Language and Information Engineering (JULIE) Lab, Germany, 3Erasmus MC, Rotterdam, The Netherlands and 4National Library of Medicine, Bethesda, MD, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: For many years, the Unified Medical Language System (UMLS) semantic network (SN) has been used as an upper-level semantic framework for the categorization of terms from terminological resources in biomedicine. BioTop has recently been developed as an upper-level ontology for the biomedical domain. In contrast to the SN, it is founded upon strict ontological principles, using OWL DL as a formal representation language, which has become standard in the semantic Web. In order to make logic-based reasoning available for the resources annotated or categorized with the SN, a mapping ontology was developed aligning the SN with BioTop.

Methods: The theoretical foundations and the practical realization of the alignment are being described, with a focus on the design decisions taken, the problems encountered and the adaptations of BioTop that became necessary. For evaluation purposes, UMLS concept pairs obtained from MEDLINE abstracts by a named entity recognition system were tested for possible semantic relationships. Furthermore, all semantic-type combinations that occur in the UMLS Metathesaurus were checked for satisfiability.

Results: The effort-intensive alignment process required major design changes and enhancements of BioTop and brought up several design errors that could be fixed. A comparison between a human curator and the ontology yielded only a low agreement. Ontology reasoning was also used to successfully identify 133 inconsistent semantic-type combinations.

Availability: BioTop, the OWL DL representation of the UMLS SN, and the mapping ontology are available at http://www.purl.org/biotop/.

Contact: stschulz{at}uni-freiburg.de


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