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