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

2009; Oxford University Press; Volume: 25; Issue: 12 Linguagem: Inglês

10.1093/bioinformatics/btp194

1367-4811

Stefan Schulz, Elena Beißwanger, L. Van Hoek, Olivier Bodenreider, Erik M. van Mulligen,

linguistics and terminology studies

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