Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

Authors :: Johnson HL
Cohen KB
Baumgartner WA Jr
Lu Z
Bada M
Kester T
Kim H
Hunter L
Source :: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing [Pac Symp Biocomput] 2006, pp. 28-39.
Publication Year :: 2006
Abstract: We used exact term matching, stemming, and inclusion of synonyms, implemented via the Lucene information retrieval library, to discover relationships between the Gene Ontology and three other OBO ontologies: ChEBI, Cell Type, and BRENDA Tissue. Proposed relationships were evaluated by domain experts. We discovered 91,385 relationships between the ontologies. Various methods had a wide range of correctness. Based on these results, we recommend careful evaluation of all matching strategies before use, including exact string matching. The full set of relationships is available at compbio.uchsc.edu/dependencies.

Subjects :: Computational Biology
Databases, Factual
Linguistics
Models, Biological
Natural Language Processing
Computer Simulation

Language :: English
ISSN :: 2335-6928
Database :: MEDLINE
Journal :: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Publication Type :: Academic Journal
Accession number :: 17094225

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