title: Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.
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.
authors.affiliation: Center for Computational Pharmacology, University of Colorado School of Medicine, USA.
authors.forename: Helen L
authors.initials: HL
authors.lastname: Johnson
authors.forename: K Bretonnel
authors.initials: KB
authors.lastname: Cohen
authors.forename: William A
authors.initials: WA
authors.lastname: Baumgartner
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lu
authors.forename: Michael
authors.initials: M
authors.lastname: Bada
authors.forename: Todd
authors.initials: T
authors.lastname: Kester
authors.forename: Hyunmin
authors.initials: H
authors.lastname: Kim
authors.forename: Lawrence
authors.initials: L
authors.lastname: Hunter
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D016208:Databases, Factual; D008037:Linguistics; D008954:Models, Biological; D009323:Natural Language Processing