The GOA database: Gene Ontology annotation updates for 2015

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D1057-D1063

  Huntley, Rachael P ^a   Sawford, Tony ^a   Mutowo Meullenet, Prudence ^a   Shypitsyna, Aleksandra ^a   Bonilla, Carlos ^a   Martin, Maria J ^a   O'Donovan, Claire ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; GENE ONTOLOGY; GENE ONTOLOGY ANNOTATION; GENETIC DATABASE; INFORMATION PROCESSING; MOLECULAR GENETICS; PRIORITY JOURNAL; PROTEIN DATABASE; QUALITY CONTROL; TAXONOMY; WEB BROWSER; COMPUTER PROGRAM; GENETICS; HUMAN; INTERNET;

PROTEIN;

DATABASES, PROTEIN; GENE ONTOLOGY; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; SOFTWARE;

EID: 84946023145     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1113     Document Type: Article

References (24)

1. Dimmer, E. C., Huntley, R. P., Alam-Faruque, Y., Sawford, T., O'Donovan, C., Martin, M. J., Bely, B., Browne, P., Mun Chan, W., Eberhardt, R. et al. (2011) The UniProt-GO Annotation database in 2011. Nucleic Acids Res., 40, D565-D570.
2. Balakrishnan, R., Harris, M. A., Huntley, R., Van Auken, K. and Cherry, J. M. (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database, 2013, doi:10.1093/database/bat054.
3. Burge, S., Kelly, E., Lonsdale, D., Mutowo-Muellenet, P., McAnulla, C., Mitchell, A., Sangrador-Vegas, A., Yong, S. Y., Mulder, N. and Hunter, S. (2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database, 2012, doi:10.1093/database/bar068.
4. 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.
5. 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.
6. Vilella, A. J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R. and Birney, E. (2009) EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res., 19, 327-335.
7. Alam-Faruque, Y., Hill, D. P., Dimmer, E. C., Harris, M. A., Foulger, R. E., Tweedie, S., Attrill, H., Howe, D. G., Thomas, S. R., Davidson, D. et al. (2014) Representing kidney development using the gene ontology. PLoS One, 9, e99864.
8. Mutowo-Meullenet, P., Huntley, R. P., Dimmer, E. C., Alam-Faruque, Y., Sawford, T., Jesus Martin, M., O'Donovan, C. and Apweiler, R. (2013) Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database, 2013, doi: 10.1093/database/bas062.
9. Wass, M. N., Mooney, S. D., Linial, M., Radivojac, P. and Friedberg, I. (2014) The automated function prediction SIG looks back at 2013 and prepares for 2014. Bioinformatics, 30, 2091-2092.
10. Huntley, R. P., Harris, M. A., Alam-Faruque, Y., Blake, J. A., Carbon, S., Dietze, H., Dimmer, E. C., Foulger, R. E., Hill, D. P., Khodiyar, V. K. et al. (2014) A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics, 15, 155.
11. Meehan, T. F., Masci, A. M., Abdulla, A., Cowell, L. G., Blake, J. A., Mungall, C. J. and Diehl, A. D. (2011) Logical development of the cell ontology. BMC Bioinformatics, 12, 6.
12. Cerqueira, G. C., Arnaud, M. B., Inglis, D. O., Skrzypek, M. S., Binkley, G., Simison, M., Miyasato, S. R., Binkley, J., Orvis, J., Shah, P. et al. (2014) The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res., 42, D705-D710.
13. Winsor, G. L., Lam, D. K. W., Fleming, L., Lo, R., Whiteside, M. D., Yu, N. Y., Hancock, R. E. W. and Brinkman, F. S. L. (2011) Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res., 39, D596-D600.
14. Logan-Klumpler, F. J., De Silva, N., Boehme, U., Rogers, M. B., Velarde, G., McQuillan, J. A., Carver, T., Aslett, M., Olsen, C., Subramanian, S. et al. (2012) GeneDB - an annotation database for pathogens. Nucleic Acids Res., 40, D98-D108.
15. Alam-Faruque, Y., Huntley, R. P., Khodiyar, V. K., Camon, E. B., Dimmer, E. C., Sawford, T., Martin, M. J., O'Donovan, C., Talmud, P. J., Scambler, P. et al. (2011) The impact of focused Gene Ontology curation of specific mammalian systems. PLoS One, 6, e27541.
16. Lovering, R. C., Dimmer, E., Khodiyar, V. K., Barrell, D. G., Scambler, P., Hubank, M., Apweiler, R. and Talmud, P. J. (2008) Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics, 8, 1950-1953.
17. Binns, D., Dimmer, E., Huntley, R., Barrell, D., O'Donovan, C. and Apweiler, R. (2009) QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics, 25, 3045-3046.
18. Chibucos, M. C., Mungall, C. J., Balakrishnan, R., Christie, K. R., Huntley, R. P., White, O., Blake, J. A., Lewis, S. E. and Giglio, M. (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database, 2014, doi:10.1093/database/bau075.
19. Harris, T. W., Baran, J., Bieri, T., Cabunoc, A., Chan, J., Chen, W. J., Davis, P., Done, J., Grove, C., Howe, K. et al. (2014) WormBase 2014: new views of curated biology. Nucleic Acids Res., 42, D789-D793.
20. Costanzo, M. C., Engel, S. R., Wong, E. D., Lloyd, P., Karra, K., Chan, E. T., Weng, S., Paskov, K. M., Roe, G. R., Binkley, G. et al. (2014) Saccharomyces genome database provides new regulation data. Nucleic Acids Res., 42, D717-D725.
21. Basu, S., Fey, P., Pandit, Y., Dodson, R., Kibbe, W. A. and Chisholm, R. L. (2013) DictyBase 2013: integrating multiple Dictyostelid species. Nucleic Acids Res., 41, D676-D683.
22. Meldal, B. H. M., Forner-Martinez, O., Costanzo, M. C., Dana, J., Demeter, J., Dumousseau, M., Dwight, S. S., Gaulton, A., Licata, L., Melidoni, A. N. et al. (2014) The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res., doi:10.1093/nar/gku975.
23. Bateman, A., Agrawal, S., Birney, E., Bruford, E. A., Bujnicki, J. M., Cochrane, G., Cole, J. R., Dinger, M. E., Enright, A. J., Gardner, P. P. et al. (2011) RNAcentral: a vision for an international database of RNA sequences. RNA, 17, 1941-1946.
24. Huntley, R. P., Sawford, T., Martin, M. J. and O'Donovan, C. (2014) Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. Gigascience, 3, 4.