Annotation of Gene Products in the Literature with Gene Ontology Terms Using Syntactic Dependencies
We present a method for automatically annotating gene products in the literature with the terms of Gene Ontology (GO), which provides a dynamic but controlled vocabulary. Although GO is well-organized with such lexical relations as synonymy, ‘is-a’, and ‘part-of’ relations among its terms, GO terms show quite a high degree of morphological and syntactic variations in the literature. As opposed to the previous approaches that considered only restricted kinds of term variations, our method uncovers the syntactic dependencies between gene product names and ontological terms as well in order to deal with real-world syntactic variations, based on the observation that the component words in an ontological term usually appear in a sentence with established patterns of syntactic dependencies.
KeywordsGene Ontology Ontological Term Gene Ontology Term Main Clause Subordinate Clause
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- 4.Friedman, C., Kra, P., Yu, H., Krauthammer, M., Rzhetsky, A.: GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17(suppl. 1), S74–S82 (2001)Google Scholar
- 5.The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet. 25, 25–29 (2000)Google Scholar
- 7.Jacquemin, C.: Syntagmatic and paradigmatic representations of term variation. In: Proc. ACL, University of Maryland, pp. 341–348 (1999)Google Scholar
- 8.Milward, D.: Dynamics, dependency grammar and incremental interpretation. In: Proc. COLING, pp. 1095–1099 (1992)Google Scholar
- 10.Park, J.C., Cho, H.J.: Informed parsing for coordination with Combinatory Categorial Grammar. In: Proc. COLING, pp. 593–599 (2000)Google Scholar
- 12.Rindflesch, T.C., Tanabe, L., Weinstein, J.N., Hunter, L.: EDGAR: Extraction of drugs, genes and relations from the biomedical literature. In: Proc. Pacific Symposium on Biocomputing, pp. 517–528 (2000)Google Scholar
- 13.Stapley, B.J., Kelley, L.A., Sternberg, M.J.E.: Predicting the subcellular location of proteins from text using support vector machines. In: Proc. Pacific Symposium on Biocomputing, pp. 374–385 (2002)Google Scholar
- 14.Steedman, M.: The syntactic process. MIT Press, Cambridge (2000)Google Scholar