DcGO: Database of domain-centric ontologies on functions, phenotypes, diseases and more

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Fang, Hai ^a   Gough, Julian ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER PREDICTION; DATA MINING; DCGO DATABASE; GENE ONTOLOGY; GENOME; INFORMATION RETRIEVAL; INFORMATION SERVICE; INTERNET; METAGENOME; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; SEQUENCE HOMOLOGY; WEB BROWSER;

ALGORITHMS; ANIMALS; DATABASES, PROTEIN; DISEASE; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PHENOTYPE; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN; VOCABULARY, CONTROLLED;

EID: 84876528480     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1080     Document Type: Article

References (32)

1. Friedberg, I. (2006) Automated protein function prediction - the genomic challenge. Brief. Bioinform., 7, 225-242.
2. Thorisson, G.A., Muilu, J. and Brookes, A.J. (2009) Genotype-phenotype databases: challenges and solutions for the post-genomic era. Nat. Rev. Genet., 10, 9-18.
3. Butler, D. (2010) Human genome at ten: science after the sequence. Nature, 465, 1000-1001.
4. de Lima Morais, D.A., Fang, H., Rackham, O.J., Wilson, D., Pethica, R., Chothia, C. and Gough, J. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res., 39, D427-D434.
5. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251-1255.
6. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
7. Barrell, D., Dimmer, E., Huntley, R.P., Binns, D., O'Donovan, C. and Apweiler, R. (2009) The GOA database in 2009 - an integrated Gene Ontology Annotation resource. Nucleic Acids Res., 37, D396-D403.
8. Fleischmann, A., Darsow, M., Degtyarenko, K., Fleischmann, W., Boyce, S., Axelsen, K.B., Bairoch, A., Schomburg, D., Tipton, K.F. and Apweiler, R. (2004) IntEnz, the integrated relational enzyme database. Nucleic Acids Res., 32, D434-D437.
9. Morgat, A., Coissac, E., Coudert, E., Axelsen, K.B., Keller, G., Bairoch, A., Bridge, A., Bougueleret, L., Xenarios, I. and Viari, A. (2012) UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res., 40, D761-D769.
10. Bairoch, A., Apweiler, R., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154-D159.
11. Smith, C.L. and Eppig, J.T. (2009) The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip. Rev. Syst. Biol. Med., 1, 390-399.
12. Schindelman, G., Fernandes, J.S., Bastiani, C.A., Yook, K. and Sternberg, P.W. (2011) Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics, 12, 32.
13. Engel, S.R., Balakrishnan, R., Binkley, G., Christie, K.R., Costanzo, M.C., Dwight, S.S., Fisk, D.G., Hirschman, J.E., Hitz, B.C., Hong, E.L. et al. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res., 38, D433-D436.
14. Grumbling, G. and Strelets, V. (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res., 34, D484-D488.
15. Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Howe, D.G., Knight, J., Mani, P., Martin, R., Moxon, S.A. et al. (2011) ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res., 39, D822-D829.
16. Bowes, J.B., Snyder, K.A., Segerdell, E., Jarabek, C.J., Azam, K., Zorn, A.M. and Vize, P.D. (2009) Xenbase: gene expression and improved integration. Nucleic Acids Res., 38, D607-D612.
17. Ilic, K., Kellogg, E.A., Jaiswal, P., Zapata, F., Stevens, P.F., Vincent, L.P., Avraham, S., Reiser, L., Pujar, A., Sachs, M.M. et al. (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol., 143, 587-599.
18. Robinson, P.N., Kohler, S., Bauer, S., Seelow, D., Horn, D. and Mundlos, S. (2008) The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet., 83, 610-615.
19. Schriml, L.M., Arze, C., Nadendla, S., Chang, Y.W., Mazaitis, M., Felix, V., Feng, G. and Kibbe, W.A. (2012) Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res., 40, D940-D946.
20. Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V. et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res., 39, D1035-D1041.
21. Davis, M.J., Sehgal, M.S. and Ragan, M.A. (2010) Automatic, context-specific generation of Gene Ontology slims. BMC Bioinformatics, 11, 498.
22. Andreeva, A., Howorth, D., Chandonia, J.M., Brenner, S.E., Hubbard, T.J., Chothia, C. and Murzin, A.G. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425.
23. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
24. Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.
25. The UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
26. Wilson, D., Madera, M., Vogel, C., Chothia, C. and Gough, J. (2007) The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res., 35, D308-D313.
27. Wilson, D., Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M., Chothia, C. and Gough, J. (2009) SUPERFAMILY - sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res., 37, D380-D386.
28. Washington, N.L., Haendel, M.A., Mungall, C.J., Ashburner, M., Westerfield, M. and Lewis, S.E. (2009) Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol., 7, e1000247.
29. Hoehndorf, R., Schofield, P.N. and Gkoutos, G.V. (2011) PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res., 39, e119.
30. Mungall, C.J., Gkoutos, G.V., Smith, C.L., Haendel, M.A., Lewis, S.E. and Ashburner, M. (2010) Integrating phenotype ontologies across multiple species. Genome Biol., 11, R2.
31. Han, H.J., Russo, J., Kohwi, Y. and Kohwi-Shigematsu, T. (2008) SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis. Nature, 452, 187-193.
32. Velankar, S., Alhroub, Y., Alili, A., Best, C., Boutselakis, H.C., Caboche, S., Conroy, M.J., Dana, J.M., van Ginkel, G., Golovin, A. et al. (2011) PDBe: Protein Data Bank in Europe. Nucleic Acids Res., 39, D402-D410.