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SHR Neuro Cancer Cardio Lipid Metab Microb
Schulz, S; Beisswanger, E; van, den, Hoek, L; Bodenreider, O; van, Mulligen, EM.
Alignment of the UMLS semantic network with BioTop: methodology and assessment.
Bioinformatics. 2009; 25(12): i69-76.
Doi: 10.1093/bioinformatics/btp194
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- Leading authors Med Uni Graz
- Schulz Stefan
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- 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/.
- Find related publications in this database (using NLM MeSH Indexing)
- Computational Biology - methods
- Databases, Factual - administration & dosage
- Information Storage and Retrieval - methods
- Pattern Recognition, Automated - administration & dosage
- Semantics - administration & dosage
- Unified Medical Language System - standards
- Vocabulary, Controlled - administration & dosage