Nucleic Acids Research Advance Access originally published online on November 4, 2007
Nucleic Acids Research 2008 36(Database issue):D440-D444; doi:10.1093/nar/gkm883
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, Database issue D440-D444
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
The Gene Ontology project in 2008
*To whom correspondence should be addressed: Tel: +44(0)1223 494667; Fax: +44(0)1223 494468; Email: midori{at}ebi.ac.uk
Received September 14, 2007. Accepted October 1, 2007.
The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ontologies have been implemented. To improve the quantity and quality of gene product annotations available from its public repository, the GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of ‘reference’ genomes, including human and several key model organisms. Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. M. Gould, F. Diella, A. Via, P. Puntervoll, C. Gemund, S. Chabanis-Davidson, S. Michael, A. Sayadi, J. C. Bryne, C. Chica, et al. ELM: the status of the 2010 eukaryotic linear motif resource Nucleic Acids Res., November 17, 2009; (2009) gkp1016v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Marsico, K. Scheubert, A. Tuukkanen, A. Henschel, C. Winter, R. Winnenburg, and M. Schroeder MeMotif: a database of linear motifs in {alpha}-helical transmembrane proteins Nucleic Acids Res., November 12, 2009; (2009) gkp1042v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Y. Kim, L. Von Weymarn, O. Larsson, D. Fan, J. M. Underwood, M. S. Peterson, S. S. Hecht, V. A. Polunovsky, and P. B. Bitterman Eukaryotic Initiation Factor 4E Binding Protein Family of Proteins: Sentinels at a Translational Control Checkpoint in Lung Tumor Defense Cancer Res., November 1, 2009; 69(21): 8455 - 8462. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. M. Markowitz, I-M. A. Chen, K. Palaniappan, K. Chu, E. Szeto, Y. Grechkin, A. Ratner, I. Anderson, A. Lykidis, K. Mavromatis, et al. The integrated microbial genomes system: an expanding comparative analysis resource Nucleic Acids Res., October 28, 2009; (2009) gkp887v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Bult, J. A. Kadin, J. E. Richardson, J. A. Blake, J. T Eppig, and the Mouse Genome Database Group The Mouse Genome Database: enhancements and updates Nucleic Acids Res., October 27, 2009; (2009) gkp880v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, A. T. Ghanbarian, S. Kerrien, J. Khadake, et al. The IntAct molecular interaction database in 2010 Nucleic Acids Res., October 22, 2009; (2009) gkp878v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Duan, R. Li, D. Cheng, W. Fan, X. Zha, T. Cheng, Y. Wu, J. Wang, K. Mita, Z. Xiang, et al. SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology Nucleic Acids Res., September 30, 2009; (2009) gkp801v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Richardson, S. Venkataraman, P. Stevenson, Y. Yang, N. Burton, J. Rao, M. Fisher, R. A. Baldock, D. R. Davidson, and J. H. Christiansen EMAGE mouse embryo spatial gene expression database: 2010 update Nucleic Acids Res., September 18, 2009; (2009) gkp763v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. M. Markowitz, K. Mavromatis, N. N. Ivanova, I-M. A. Chen, K. Chu, and N. C. Kyrpides IMG ER: a system for microbial genome annotation expert review and curation Bioinformatics, September 1, 2009; 25(17): 2271 - 2278. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Glez-Pena, G. Gomez-Lopez, D. G. Pisano, and F. Fdez-Riverola WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis Nucleic Acids Res., July 1, 2009; 37(suppl_2): W329 - W334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. C. Tsoi, M. Boehnke, R. L. Klein, and W. J. Zheng Evaluation of genome-wide association study results through development of ontology fingerprints Bioinformatics, May 15, 2009; 25(10): 1314 - 1320. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. I. Wolf, P. S. Novichkov, G. P. Karev, E. V. Koonin, and D. J. Lipman Inaugural Article: The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages PNAS, May 5, 2009; 106(18): 7273 - 7280. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. C. Costanzo, M. S. Skrzypek, R. Nash, E. Wong, G. Binkley, S. R. Engel, B. Hitz, E. L. Hong, J. M. Cherry, and the Saccharomyces Genome Database Project New mutant phenotype data curation system in the Saccharomyces Genome Database Database, March 26, 2009; 2009(0): bap001 - bap001. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Dumontier and N. Villanueva-Rosales Towards pharmacogenomics knowledge discovery with the semantic web Brief Bioinform, March 1, 2009; 10(2): 153 - 163. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Diella, S. Chabanis, K. Luck, C. Chica, C. Ramu, C. Nerlov, and T. J. Gibson KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors Bioinformatics, January 1, 2009; 25(1): 1 - 5. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Ogata, N. Sakurai, K. Aoki, H. Suzuki, K. Okazaki, K. Saito, and D. Shibata KAGIANA: An Excel-Based Tool for Retrieving Summary Information on Arabidopsis Genes Plant Cell Physiol., January 1, 2009; 50(1): 173 - 177. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Lima, A. H. Auchincloss, E. Coudert, G. Keller, K. Michoud, C. Rivoire, V. Bulliard, E. de Castro, C. Lachaize, D. Baratin, et al. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot Nucleic Acids Res., January 1, 2009; 37(suppl_1): D471 - D478. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi-Sutherland, A. Schroeder, R. Seal, et al. FlyBase: enhancing Drosophila Gene Ontology annotations Nucleic Acids Res., January 1, 2009; 37(suppl_1): D555 - D559. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Nogales-Cadenas, F. Abascal, J. Diez-Perez, J. M. Carazo, and A. Pascual-Montano CentrosomeDB: a human centrosomal proteins database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D175 - D180. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Fey, P. Gaudet, T. Curk, B. Zupan, E. M. Just, S. Basu, S. N. Merchant, Y. A. Bushmanova, G. Shaulsky, W. A. Kibbe, et al. dictyBase--a Dictyostelium bioinformatics resource update Nucleic Acids Res., January 1, 2009; 37(suppl_1): D515 - D519. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Blake, C. J. Bult, J. T. Eppig, J. A. Kadin, J. E. Richardson, and the Mouse Genome Database Group The Mouse Genome Database genotypes::phenotypes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D712 - D719. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Chang, M. Scheer, A. Grote, I. Schomburg, and D. Schomburg BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D588 - D592. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Richardson, Q. Gao, C. Mitsopoulous, M. Zvelebil, L. H. Pearl, and F. M. G. Pearl MoKCa database--mutations of kinases in cancer Nucleic Acids Res., January 1, 2009; 37(suppl_1): D824 - D831. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. R. Dwinell, E. A. Worthey, M. Shimoyama, B. Bakir-Gungor, J. DePons, S. Laulederkind, T. Lowry, R. Nigram, V. Petri, J. Smith, et al. The Rat Genome Database 2009: variation, ontologies and pathways Nucleic Acids Res., January 1, 2009; 37(suppl_1): D744 - D749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Vinogradov Modularity of cellular networks shows general center-periphery polarization Bioinformatics, December 15, 2008; 24(24): 2814 - 2817. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. A. Reeves, K. Eilbeck, M. Magrane, C. O'Donovan, L. Montecchi-Palazzi, M. A. Harris, S. Orchard, R. C. Jimenez, A. Prlic, T. J. P. Hubbard, et al. The Protein Feature Ontology: a tool for the unification of protein feature annotations Bioinformatics, December 1, 2008; 24(23): 2767 - 2772. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. L. Hughes and R. Friedman Genome Size Reduction in the Chicken Has Involved Massive Loss of Ancestral Protein-Coding Genes Mol. Biol. Evol., December 1, 2008; 25(12): 2681 - 2688. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Yu, P. Braun, M. A. Yildirim, I. Lemmens, K. Venkatesan, J. Sahalie, T. Hirozane-Kishikawa, F. Gebreab, N. Li, N. Simonis, et al. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network Science, October 3, 2008; 322(5898): 104 - 110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hakenberg, C. Plake, R. Leaman, M. Schroeder, and G. Gonzalez Inter-species normalization of gene mentions with GNAT Bioinformatics, August 15, 2008; 24(16): i126 - i132. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Menda, R. M. Buels, I. Tecle, and L. A. Mueller A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes Plant Physiology, August 1, 2008; 147(4): 1788 - 1799. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. J. Lee, I. Paulsen, and P. Karp Annotation-based inference of transporter function Bioinformatics, July 1, 2008; 24(13): i259 - i267. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. G. Cote, P. Jones, L. Martens, R. Apweiler, and H. Hermjakob The Ontology Lookup Service: more data and better tools for controlled vocabulary queries Nucleic Acids Res., July 1, 2008; 36(suppl_2): W372 - W376. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Brohee, K. Faust, G. Lima-Mendez, O. Sand, R. Janky, G. Vanderstocken, Y. Deville, and J. van Helden NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways Nucleic Acids Res., July 1, 2008; 36(suppl_2): W444 - W451. [Abstract] [Full Text] [PDF]
|
|