A shortest-path graph kernel for estimating gene product semantic similarity

Journal of Biomedical Semantics

Volumn 2, Issue 1, 2011, Pages

  Alvarez, Marco A ^a   Qi, Xiaojun ^a   Yan, Changhui ^b  

^a Department of Computer Science ^*  (United States)

^b North Dakota State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84891725921     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-2-3     Document Type: Article

References (25)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038/75556.
2. Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R: The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucl Acids Res. 2009, 37: D396-403. 10.1093/nar/gkn803.
3. Wang JZ, Du Z, Payattakool R, Yu PS, Chen C-F: A new method to measure the semantic similarity of go terms. Bioinformatics. 2007, 23: 1274-1281. 10.1093/bioinformatics/btm087.
4. Sheehan B, Quigley A, Gaudin B, Dobson S: A relation based measure of semantic similarity for gene ontology annotations. BMC Bioinformatics. 2008, 9: 468-10.1186/1471-2105-9-468.
5. Nagar A, Al-Mubaid H: A new path length measure based on go for gene similarity with evaluation using sgd pathways. Proceedings of IEEE International Symposium on Computer-Based Medical Systems. 2008, 590-595.
6. Du Z, Li L, Chen C-F, Yu PS, Wang JZ: G-sesame: web tools for go-term-based gene similarity analysis and knowledge discovery. Nucl Acids Res. 2009, 37: W345-349. 10.1093/nar/gkp463.
7. Xu T, Du L, Zhou Y: Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. BMC Bioinformatics. 2008, 9: 472-10.1186/1471-2105-9-472.
8. Sevilla JL, Segura V, Podhorski A, Guruceaga E, Mato JM, Martinez-Cruz LA, Corrales FJ, Rubio A: Correlation between gene expression and go semantic similarity. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2005, 2: 330-338. 10.1109/TCBB.2005.50.
9. Pesquita C, Faria D, Bastos H, Ferreira AE, Falcão AO, Couto FM: Metrics for go based protein semantic similarity: a systematic evaluation. BMC Bioinformatics. 2008, 9: 5-10.1186/1471-2105-9-5.
10. Mistry M, Pavlidis P: Gene ontology term overlap as a measure of gene functional similarity. BMC Bioinformatics. 2008, 9: 327-10.1186/1471-2105-9-327.
11. Lord PW, Stevens RD, Brass A, Goble CA: Investigating semantic similarity measures across the gene ontology: the relationship between sequence and annotation. Bioinformatics. 2003, 19: 1275-1283. 10.1093/bioinformatics/btg153.
12. Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S: Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology. PLoS ONE. 2009, 4: e4619-10.1371/journal.pone.0004619.
13. Couto FM, Silva MJ, Coutinho PM: Measuring semantic similarity between gene ontology terms. Data and Knowledge Engineering. 2007, 16: 137-152.
14. Schlicker A, Domingues F, Rahnenfuhrer J, Lengauer T: A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics. 2006, 7: 302-10.1186/1471-2105-7-302.
15. Alvarez M, Qi X, Yan C: GO-Based Term Semantic Similarity. Ontology Learning and Knowledge Discovery Using the Web: Challenges and Recent Advances. Edited by: Wong W, Liu W, Bennamoun M. 2011, Pennsylvania: IGI-Global, 174-185.
16. Pesquita C, Faria D, Falcão AO, Lord P, Couto FM: Semantic similarity in biomedical ontologies. PLOS Computational Biology. 2009, 5: e1000443-10.1371/journal.pcbi.1000443.
17. Cheng J, Cline M, Martin J, Finkelstein D, Awad T, Kulp D, Siani-Rose MA: A knowledge-based clustering algorithm driven by gene ontology. J Biopharm Stat. 2004, 14: 687-700. 10.1081/BIP-200025659.
18. Wu X, Zhu L, Guo J, Zhang D-Y, Lin K: Prediction of yeast proteinprotein interaction network: insights from the gene ontology and annotations. Nucl Acids Res. 2006, 34: 2137-2150. 10.1093/nar/gkl219.
19. The UniProt Consortium: The Universal Protein Resource (UniProt) in 2010. Nucl Acids Res. 2010, 38: D142-148.
20. Borgwardt KM, Ong CS, Schonauer S, Vishwanathan SVN, Smola AJ, Kriegel H-P: Protein function prediction via graph kernels. Bioinformatics. 2005, 21: i47-56. 10.1093/bioinformatics/bti1007.
21. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, H-R Hotz, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A: The pfam protein families database. Nucl Acids Res. 2008, 36: D281-288. 10.1093/nar/gkn226.
22. Pesquita C, Pessoa D, Faria D, Couto F: CESSM: Collaborative Evaluation of Semantic Similarity Measures. Proceedings of JB2009: Challenges in Bioinformatics Lisbon, Portugal. 2009
23. Resnik P: Using information content to evaluate semantic similarity in a taxonomy. Proceedings of International Joint Conference on Artificial Intelligent. 1995, 448-453.
24. Lin D: An information-theoretic definition of similarity. Proceedings of International Conference on Machine Learning. 1998, 296-304.
25. Jiang JJ, Conrath DW: Semantic similarity based on corpus statistics and lexical taxonomy. Proceedings of International Conference Research on Computational Linguistics. 1997, 19-33.