Using semantic web rules to reason on an ontology of pseudogenes

Bioinformatics

Volumn 26, Issue 12, 2010, Pages

  Holford, Matthew E ^a   Khurana, Ekta ^a   Cheung, Kei Hoi ^a,b,c   Gerstein, Mark ^a,b  

^a YALE UNIVERSITY   (United States)

^b Yale University   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FACTUAL DATABASE; INFORMATION RETRIEVAL; INTERNET; LINGUISTICS; METHODOLOGY; PSEUDOGENE; SEMANTICS;

DATABASES, FACTUAL; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PSEUDOGENES; SEMANTICS; VOCABULARY, CONTROLLED;

EID: 77954195925     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq173     Document Type: Article

References (22)

1. Bailey, J.A. and Eichler, E.E. (2006) Primate segmental duplications: crucibles of evolution, diversity and disease. Nat. Rev. Genet., 7, 552-564.
2. Bechhofer, S. and Philip Lord, R.V. (2003) Cooking the semantic web with the OWL API. In ISWC 2003, Springer, Berlin, pp. 659-675.
3. Ding, Z. and Peng, Y. (2004) A probabilistic extension to ontology language owl. In Proceedings of the 37th Hawaii International Conference On System Sciences (HICSS-37), IEEE., Big Island.
4. Duplication, S. (2010) Available at http://humanparalogy.gs.washington.edu/build36/build36.htm (last accessed date January 8, 2010).
5. Eilbeck, K. and Lewis, S.E. (2004) Sequence ontology annotation guide. Comp. Funct. Genomics, 5, 642-647.
6. Eilbeck, K. et al. (2005) The sequence ontology: a tool for the unification of genome annotations. Genome Biol., 6, 1-12.
7. Hubbard, T. et al. (2002) The ensembl genome database project. Nucleic Acids Res., 30, 38-41.
8. KAON (2010) Available at http://kaon2.semanticweb.org.
9. Karro, J.E. et al. (2007) Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res., 35, D55-D60.
10. Lam, H.Y.K. et al. (2009) Pseudofam: the pseudogene families database. Nucleic Acids Res., 37, D738-D743.
11. Mungall, C.J. et al. (2007) A chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23, i337-i346.
12. OWL2 (2009) Available at http://www.w3.org/TR/owl2-profiles/ (last accessed date February 1, 2010).
13. Rubin, D.L. et al. (1997) Biomedical ontologies: a functional perspective. Brief. Bioinformatics, 9, 75-90.
14. Sirin, E. et al. (2007) Pellet: A practical owl-dl reasoner. Web Semant., 5, 51-53.
15. Smith, B. et al. (2007) The obo foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. biotechnol., 25, 1251-1255.
16. SPARQL (2008) Available at http://www.w3.org/tr/rdf-sparql-query (last accessed date January 23, 2010).
17. SWRL (2005) Available at http://www.w3.org/submission/swrl (last accessed date January 8, 2010).
18. SWRLTab (2010) Available at http://protege.cim3.net/cgi-bin/wiki.pl?swrltab (last accessed date December 23, 2009).
19. Tsarkov, D. and Horrocks, I. (2006) Fact++ description logic reasoner: system description. In Automated Reasoning, Springer, Berlin, pp. 292-297.
20. Virtuoso (2010) Available at virtuoso-openlinksw.com (last accessed date January 8, 2010).
21. Winston, M.E. etal. (1987) A taxonomy of part-whole relations. Cogn. Sci., 11, 417-444.
22. Zhang, Z. and Gerstein, M. (2003) Patterns of nucleotide subsitution, insertion and deltion in the human genome inferred from pseudogenes. Nucleic Acids Res., 31, 5338-5348.