Abstract | ||
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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. |
Year | DOI | Venue |
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2009 | 10.1093/bioinformatics/btp194 | BIOINFORMATICS |
Keywords | DocType | Volume |
computational biology,satisfiability,semantic web,semantics,unified medical language system,semantic network | Journal | 25 |
Issue | ISSN | Citations |
12 | 1367-4803 | 8 |
PageRank | References | Authors |
0.89 | 19 | 5 |
Name | Order | Citations | PageRank |
---|---|---|---|
Stefan Schulz | 1 | 29 | 5.15 |
Elena Beisswanger | 2 | 223 | 16.00 |
László van den Hoek | 3 | 12 | 1.32 |
Olivier Bodenreider | 4 | 2715 | 226.05 |
Erik M. Van Mulligen | 5 | 633 | 44.63 |