INOH: Ontology-based highly structured database of signal transduction pathways

Database

Volumn 2011, Issue , 2011, Pages

  Yamamoto, Satoko ^a   Sakai, Noriko ^a   Nakamura, Hiromi ^b   Fukagawa, Hiroshi ^c   Fukuda, Ken ^d   Takagi, Toshihisa ^e  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b Information and Mathematical Science Laboratory Inc   (Japan)

^c INTEC Inc   (Japan)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; MAMMALIA; XENOPUS LAEVIS;

ANIMAL; ARTICLE; BIOLOGY; CAENORHABDITIS ELEGANS; COMPUTER INTERFACE; DROSOPHILA MELANOGASTER; FACTUAL DATABASE; MAMMAL; METABOLISM; METHODOLOGY; NOMENCLATURE; SIGNAL TRANSDUCTION; XENOPUS LAEVIS;

ANIMALS; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DROSOPHILA MELANOGASTER; MAMMALS; METABOLIC NETWORKS AND PATHWAYS; SIGNAL TRANSDUCTION; TERMINOLOGY AS TOPIC; USER-COMPUTER INTERFACE; XENOPUS LAEVIS;

EID: 84864037265     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bar052     Document Type: Article

References (28)

1. Bader, G. D., Cary, M. P. and Sander, C. (2006) Pathguide: A pathway resource list. Nucleic Acids Res., 34, D504-D506.
2. Demir, E., Cary, M. P., Paley, S. et al. (2010) The BioPAX community standard for pathway data sharing. Nat. Biotechnol., 28, 935-942.
3. Kerrien, S., Orchard, S., Montecchi-Palazzi, L. et al. (2007) Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol., 5 44.
4. Hucka, M., Finney, A., Sauro, H. M. et al. (2003) The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531. (Pubitemid 36336519)
5. Fukuda, K. and Takagi, T. (2001) Knowledge representation of signal transduction pathways. Bioinformatics, 17, 829-837. (Pubitemid 32970481)
6. Yamamoto, S., Asanuma, T., Takagi, T. et al. (2004) The molecule role ontology: An ontology for annotation of signal transduction pathway molecules in the scientific literature. Comp. Funct. Genomics, 5, 528-536. (Pubitemid 40207551)
7. Kushida, T., Takagi, T. and Fukuda, K. I. (2006) Event ontology: A pathway-centric ontology for biological processes. Pac. Symp. Biocomput., 11, 152-163.
8. Vastrik, I., D'Eustachio, P., Schmidt, E. et al. (2007) Reactome: A knowledge base of biologic pathways and processes. Genome Biol., 8, R39.
9. Schaefer, C. F., Anthony, K., Krupa, S. et al. (2009) PID: The Pathway Interaction Database. Nucleic Acids Res., 37, D674-D679.
10. Thomas, P. D., Kejariwal, A., Campbell, M. J. et al. (2003) PANTHER: A browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res., 31, 334-341. (Pubitemid 36150398)
11. Gough, N. R. (2002) Science's signal transduction knowledge environment: The connections maps database. Ann. N Y Acad. Sci., 971, 585-587. (Pubitemid 35305362)
12. Kandasamy, K., Mohan, S., Raju, R. et al. (2010) NetPath: A public resource of curated signal transduction pathways. Genome Biol., 11, R3.
13. Kanehisa, M., Goto, S., Furumichi, M. et al. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
14. Demir, E., Babur, O., Dogrusoz, U. et al. (2004) An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics, 20, 349-356. (Pubitemid 38262766)
15. Ashburner, M., Ball, C. A., Blake, J. A. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
16. Day-Richter, J., Harris, M. A., Haendel, M. et al. (2007) OBO-Edit-an ontology editor for biologists. Bioinformatics, 23, 2198-2200.
17. The UniProt Consortium. (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 39, D214-D219.
18. Eilbeck, K., Lewis, S. E., Mungall, C. J. et al. (2005) The Sequence Ontology: A tool for the unification of genome annotations. Genome Biol., 6, R44.
19. Natale, D. A., Arighi, C. N., Barker, W. C. et al. (2007) Framework for a Protein Ontology. BMC Bioinformatics, 8, S1.
20. Smith, B., Ashburner, M., Rosse, C. et al. (2007) The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251-1255. (Pubitemid 350076511)
21. Noy, N. F., Shah, N. H., Whetzel, P. L. et al. (2009) BioPortal: Ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res., 37, W170-W173.
22. Scheer, M., Grote, A., Chang, A. et al. (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res., 39, D670-D676.
23. Cote, R. G., Jones, P., Apweiler, R. et al. (2006) The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics, 7, 97.
24. Tsesmetzis, N., Couchman, M., Higgins, J. et al. (2008) Arabidopsis reactome: A foundation knowledgebase for plant systems biology. Plant Cell, 20, 1426-1436. (Pubitemid 352844154)
25. Renkonen,J, Mattila,P, Parviainen, V. et al. (2010) A network analysis of the single nucleotide polymorphisms in acute allergic diseases. Allergy, 65, 40-47.
26. Shannon,P, Markiel,A, Ozier, O. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504. (Pubitemid 37428274)
27. Pico, A. R., Kelder, T., van Iersel, M. P. et al. (2008) WikiPathways: Pathway editing for the people. PLoS Biol., 6, e184.
28. Kamburov, A., Pentchev, K., Galicka, H. et al. (2011) ConsensusPathDB: Toward a more complete picture of cell biology. Nucleic Acids Res., 39, D712-D717.