Title
Alignment of the UMLS semantic network with BioTop: methodology and assessment.
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.
Year
DOI
Venue
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 Schulz1295.15
Elena Beisswanger222316.00
László van den Hoek3121.32
Olivier Bodenreider42715226.05
Erik M. Van Mulligen563344.63