2003 InvestSemantSimMeasAcrossTheGeneOntoTheRelBetwSeqAndAnno

(Lord, et al., 2003) ⇒ Phillip W. Lord, Robert D. Stevens, Andy Brass, and Carole A. Goble. (2003). “Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation" In: Bioinformatics, (2003).

Subject Headings: Semantic Similarity Measure.

Notes

Cited By

~432 http://scholar.google.com/scholar?cluster=3773807094745792794

Quotes

Abstract

Motivation: Many bioinformatics data resources not only hold data in the form of sequences, but also as annotation. In the majority of cases, annotation is written as scientiﬁc natural language: this is suitable for humans, but not particularly useful for machine processing. Ontologies offer a mechanism by which knowledge can be represented in a form capable of such processing. In this paper we investigate the use of ontological annotation to measure the similarities in knowledge content or ‘semantic similarity’ between entries in a data resource. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those performed over sequences. A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repetoire of analyses. Results: We present the results from experiments that investigate the validity of using semantic similarity by comparison with sequence similarity. We show a simple extension that enables a semantic search of the knowledge held within sequence databases.

References

Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402.
Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45–48.
Blagosklonny,M.V. and Pardee,A.B. (2002). Unearthing the gems. Nature, 416, 373.
Budanitsky,A. and Hirst,G. (2001) Semantic distance in WordNet: an experimental, application-oriented evaluation of ﬁve measures. In Workshop on WordNet and Other Lexical Resources, Second meeting of the North American Chapter of the Association for Computational Linguistics. Pittsburgh.
Camon,E., Magrane,M., Barrell,D., Binns,D., Fleischmann,W., Kersey,P., Mulder,N., Oinn,T. and Apweiler,R. (2002). The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL and InterPro. Genome Res., 13, 666–672.
Chang,J., Raychaudhuri,S. and Altman,R. (2001) Including biological literature improves homology search. Pac. Symp. Biocomput., 6, 374–383
Fellbaum,C. (ed.) (1998) WordNet. An electronic lexical database. Massachusetts, Cambridge, MIT Press.
Jiang,J.J. and Conrath,D.W. (1998) Semantic similarity based on corpus statistics and lexical taxonomy. In: Proceedings of International Conference on Research in Computational Linguistics. ROCLING X, Taiwan.
Dekang Lin (1998) An information-theoretic deﬁnition of similarity. In: Proceedings of the 15th International Conference on Machine Learning. Morgan Kaufmann, San Francisco, CA, pp. 296–304.
Lord,P., Stevens,R., Brass,A. and Goble,C. (2003). Semantic similarity measures as tools for exploring the Gene Ontology. Pac. Symp. Biocomput., 8, 601–612.
MacCallum,R.M., Kelley,L.A. and Sternberg,M.J. (2000) SAWTED: structure assignment with text description–enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons. Bioinformatics, 16, 125–129.
Odell,J. (1998) Six Different Kinds of Aggregation. In advanced object-oriented analysis and design using UML. Cambridge University Press, pp. 139–149.
Rada,R., Mili,H., Bicknell,E. and Blettner,M. (1989) Development and application of a metric on semantic nets. IEEE Transaction on Systems, Man, and Cybernetics, 1, 17–30.
Resnik,P. (1999) Semantic similarity in a taxonomy: an informationbased measure and its application to problems of ambiguity in natural language. J. Artif. Intelligence Res., 11, 95–130.
Stevens,R., Goble,C. and Sean Bechhofer. (2000) Ontology-based Knowledge Representation for Bioinformatics. Brieﬁngs in Bioinformatics, 1, 398–416.
The Gene Ontology Consortium (2001) Creating the Gene Ontology resource: design and implementation. Genome Res., 11, 1425– 1433.
Wilbur,W.J. and Yang,Y. (1996) An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Comput. Biol. Med., 26, 209–222.
Winston,M., Chaffin,R. and Herrmann,D. (1987) A taxonomy of part-whole relations. Cognitive Science, 11, 417–444.

	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2003 InvestSemantSimMeasAcrossTheGeneOntoTheRelBetwSeqAndAnno	Phillip W. Lord Robert D. Stevens Andy Brass Carole A. Goble			Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation		Bioinformatics Subject Area	http://www.cs.man.ac.uk/~stevensr/papers/bioinformatics-semantic-similarity.pdf			2003