Information-theoretic evaluation of predicted ontological annotations

Bioinformatics

Volumn 29, Issue 13, 2013, Pages

  Clark, Wyatt T ^a   Radivojac, Predrag ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BAYES THEOREM; CHEMISTRY; GENE; GENE ONTOLOGY; GENETICS; HUMAN; MOLECULAR GENETICS; PHYSIOLOGY; STATISTICAL ANALYSIS;

ALGORITHMS; BAYES THEOREM; DATA INTERPRETATION, STATISTICAL; GENE ONTOLOGY; GENES; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEINS;

EID: 84879904959     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt228     Document Type: Conference Paper

References (20)

1. Alterovitz, G. et al. (2010) Ontology engineering. Nat. Biotechnol., 28, 128-130.
2. Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Ashburner, M. et al. (2000) Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nat. Genet., 25, 25-29.
4. Clark, W.T. and Radivojac, P. (2011) Analysis of protein function and its prediction from amino acid sequence. Proteins, 79, 2086-2096.
5. Guzzi, P.H. et al. (2012) Semantic similarity analysis of protein data: Assessment with biological features and issues. Brief. Bioinform., 13, 569-585.
6. Jiang, J.J. and Conrath, D.W. (1997) Semantic similarity based on corpus statistics and lexical taxonomy. In: Proceedings of the International Conference on Research in Computational Linguistics. Taiwan. pp. 19-33.
7. Koller, D. and Friedman, N. (2009) Probabilistic Graphical Models. The MIT Press, Cambridge, MA.
8. 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.
9. Lord, P.W. et al. (2003) Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation. Bioinformatics, 19, 1275-1283.
10. Martin, D.M. et al. (2004) GOtcha: A new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics, 5, 178.
11. Pesquita, C. et al. (2009) Semantic similarity in biomedical ontologies. PLoS Comput. Biol., 5, e1000443.
12. Rada, R. et al. (1989) Development and application of a metric on semantic nets. IEEE Trans. Syst. Man Cybern., 19, 17-30.
13. Radivojac, P. et al. (2013) A large-scale evaluation of computational protein function prediction. Nat. Methods, 10, 221-227.
14. Rentzsch, R. and Orengo, C. (2009) Protein function prediction-the power of multiplicity. Trends Biotechnol., 27, 210-219.
15. Resnik, P. (1995) Using information content to evaluate semantic similarity in a taxonomy. In: Proceedings of the 14th International Joint Conference on Artificial Intelligence, Morgan Kaufmann, San Francisco, CA, pp. 448-453.
16. 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.
17. Robinson, P.N. and Bauer, S. (2011) Introduction to Bio-Ontologies. CRC Press, Boca Raton, FL, USA.
18. Schlicker, A. et al. (2006) A new measure for functional similarity of gene products based on gene ontology. BMC Bioinformatics, 7, 302.
19. Sharan, R. et al. (2007) Network-based prediction of protein function. Mol. Syst. Biol., 3, 88.
20. Verspoor, K. et al. (2006) A categorization approach to automated ontological function annotation. Protein Sci., 15, 1544-1549.