Journal Article

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

Stefan Schulz, Elena Beisswanger, László van den Hoek, Olivier Bodenreider and Erik M. van Mulligen

in Bioinformatics

Volume 25, issue 12, pages i69-i76
Published in print June 2009 | ISSN: 1367-4803
Published online May 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp194

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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@uni-freiburg.de

Journal Article.  6548 words. 

Subjects: Bioinformatics and Computational Biology

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