Measuring semantic similarity between Gene Ontology terms

Stevens, 2003, Ontologies in bioinformatics

Al-Shahrour, 2004, Fatigo: a web tool for finding significant associations of Gene Ontology terms with groups of genes, Bioinformatics, 20, 578, 10.1093/bioinformatics/btg455

Sevilla, 2005, Correlation between gene expression and go semantic similarity, IEEE/ACM Transactions Computational Biology Bioinformatics, 2, 330, 10.1109/TCBB.2005.50

Couto, 2006, Mining the BioLiterature: towards automatic annotation of genes and proteins

Couto, 2005, Finding genomic ontology terms in text using evidence content, BMC Bioinformatics, 6, S21, 10.1186/1471-2105-6-S1-S21

Manning, 1999

Rada, 1989, Development and application of a metric on semantic nets, IEEE Transactions on Systems, 19, 17

P. Resnik, Using information content to evaluate semantic similarity in a taxonomy, in: Proceedings of the 14th International Joint Conference on Artificial Intelligence, 1995.

J. Jiang, D. Conrath, Semantic similarity based on corpus statistics and lexical taxonomy, in: Proceedings of the 10th International Conference on Research on Computational Linguistics, 1997.

D. Lin, An information-theoretic definition of similarity, in: Proceedings of the 15th International Conference on Machine Learning, 1998.

P. Lord, R. Stevens, A. Brass, C. Goble, Semantic similarity measures as tools for exploring the Gene Ontology, in: Proceedings of the 8th Pacific Symposium on Biocomputing, 2003.

Apweiler, 2004, UniProt: the universal protein knowledgebase, Nucleic Acids Research, 32, D115, 10.1093/nar/gkh131

A. Budanitsky, G. Hirst, Semantic distance in WordNet: An experimental, application-oriented evaluation of five measures, in: Proceedings of the Workshop on WordNet and Other Lexical Resources co-located with the 2nd North American Chapter of the Association for Computational Linguistics, 2001.

Lord, 2003, Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation, Bioinformatics, 19, 1275, 10.1093/bioinformatics/btg153

Devos, 2001, Intrinsic errors in genome annotation, Trends Genetics, 17, 429, 10.1016/S0168-9525(01)02348-4

Camon, 2004, The Gene Ontology Annotations (GOA) database: sharing knowledge in UniProt with Gene Ontology, Nucleic Acids Research, 32, 262, 10.1093/nar/gkh021

Bateman, 2004, The Pfam protein families database, Nucleic Acids Research, 32, D138, 10.1093/nar/gkh121

Gruber, 1993, A translation approach to portable ontologies, Knowledge Acquisition, 5, 199, 10.1006/knac.1993.1008

GO-Consortium, The Gene Ontology (GO) database and informatics resource, Nucleic Acids Research 32 (Database issue) (2004) D258–D261.

F. Couto, M. Silva, P. Coutinho, Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors, in: Proceedings of the ACM Conference in Information and Knowledge Management as a short paper, 2005.

Doerks, 1998, Protein annotation: detective work for function prediction, Trends Genetics, 14, 248, 10.1016/S0168-9525(98)01486-3

Fellbaum, 1998

F. Couto, M. Silva, P. Coutinho, Implementation of a functional semantic similarity measure between gene-products, DI/FCUL TR 03–29, Department of Informatics, University of Lisbon, November 2003.