GOssTo: A stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology

Bioinformatics

Volumn 30, Issue 15, 2014, Pages 2235-2236

  Caniza, Horacio ^a   Romero, Alfonso E ^a   Heron, Samuel ^a   Yang, Haixuan ^b   Devoto, Alessandra ^a   Frasca, Marco ^c   Mesiti, Marco ^c   Valentini, Giorgio ^c   Paccanaro, Alberto ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^c UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; COMPUTER PROGRAM; CONTROLLED VOCABULARY; DATA MINING; GENE ONTOLOGY; GENETICS; INTERNET; METHODOLOGY; SEMANTICS;

DATA MINING; GENE ONTOLOGY; INTERNET; PROTEINS; SEMANTICS; SOFTWARE; VOCABULARY, CONTROLLED;

EID: 84905044212     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu144     Document Type: Article

References (11)

1. Ashburner, M. et al. (2000) Gene ontology: Tool for the unification of biology. Nat.Genet., 25, 25-29.
2. Couto, F.M. et al. (2005) Semantic similarity over the Gene Ontology: Family correlation and selecting disjunctive ancestors. In: Proceedings of the 14th ACM International Conference on Information and Knowledge Management. ACM Press, New York, NY, pp. 343-344.
3. Du, Z. et al. (2007) G-SESAME: Web tools for go term based gene similarity analysis and knowledge discovery. Nucleic Acids Res., 37, W345-W349.
4. Faria, D. et al. (2007) ProteInOn: A Web Tool for Protein Semantic Similarity. DI/ FCUL TR 07-6, Department of Informatics, University of Lisbon.
5. Ferreira, J.D. et al. (2013) Exploiting disjointness axioms to improve semantic. Bioinformatics, 29, 2781-2787.
6. Jiang, J.J. and Conrath, D.W. (1997) Semantic similarity based on corpus statistics and lexical taxonomy. In: International Conference Research on Computational Linguistics (ROCLING X), Taiwan. pp. 9008-9022.
7. Lin, D. (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.
8. Mazandu, G.K. and Mulder, N.J. (2013) Information content-based Gene Ontology semantic similarity approaches: Toward a unified framework theory. BioMed Res. Int., doi:10.1155/2013/292063.
9. Pesquita, C. et al. (2008) Metrics for GO based protein semantic similarity: A systematic evaluation. BMC Bioinform., 9 (Suppl. 5), S4.
10. Resnik, P. (1999) Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. J. Artif. Intell. Res., 11, 95-130.
11. Yang, H. et al. (2012) Improving GO semantic similarity measures using downward random walks. Bioinformatics, 28, 1383-1389.