EVALUATION OF LEXICAL METHODS FOR DETECTING RELATIONSHIPS BETWEEN CONCEPTS FROM MULTIPLE ONTOLOGIES

HELEN L. JOHNSON, K. BRETONNEL COHEN, WILLIAM A. BAUMGARTNER, ZHIYONG LU, MICHAEL BADA, TODD KESTER, HYUNMIN KIM, LAWRENCE HUNTER
2005 Biocomputing 2006  
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
more » ... use, including exact string matching. The full set of relationships is available at compbio.uchsc.edu/dependencies.
doi:10.1142/9789812701626_0004 fatcat:gkxbhy2vorhxrgpjwyjjqtglsm