The Integr8 project - A resource for genomic and proteomic data

In Silico Biology

Volumn 5, Issue 2, 2005, Pages 179-185

  Pruess, Manuela ^a   Kersey, Paul ^a   Apweiler, Rolf ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Bioinformatics; Database integration; Genomes; Molecular biology databases; Nucleotide sequences; Protein sequences; Proteomics

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; EUROPE; GENE SEQUENCE; GENOMICS; INTEGR8 DATABASE; INTERNET; PROTEOMICS; SEQUENCE DATABASE; TAXONOMY;

COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; GENOMICS; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; PROTEOMICS;

EID: 22144452209     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (21)

1. Apweiler, R., Bairoch, A., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Natale, D. A., O'Donovan, C., Redaschi, N. and Yeh, L. L. (2004). UniProt: The Universal Protein knowledgebase. Nucleic Acids Res. 32, D115-D119.
2. 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. Nature Genet. 25, 25-29.
3. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. and Wheeler, D. L. (2004). GenBank: Update. Nucleic Acids Res. 32, D23-D26.
4. Birney, E., Andrews, T. D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., Down, T., Eyras, E., Fernandez-Suarez, X. M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H. R., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, K. C., Cameron, G., Durbin, R., Cox, A., Hubbard, T. and Clamp, M. (2004). An Overview of Ensembl. Genome Res. 14, 925-928.
5. Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G. G., Oezcimen, A., Rocca-Serra, P. and Sansone, S. A. (2003). ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68-71.
6. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R. and Apweiler, R. (2004). The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32, D262-D266.
7. Golovin, A., Oldfield, T. J., Tate, J. G., Velankar, S., Barton, G. J., Boutselakis, H., Dimitropoulos, D., Fillon, J., Hussain, A., Ionides, J. M., John, M., Keller, P. A., Krissinel, E., McNeil, P., Naim, A., Newman, R., Pajon, A., Pineda, J., Rachedi, A., Copeland, J., Sitnov, A., Sobhany, S., Suarez-Uruena, A., Swaminathan, G. J., Tagari, M., Tromm, S., Vranken, W. and Henrick, K. (2004). E-MSD: An integrated data resource for bioinformatics. Nucleic Acids Res. 32, D211-D216.
8. Harris, T. W., Chen, N., Cunningham, F., Tello-Ruiz, M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Chan, J., Chen, C. K., Chen, W. J., Davis, P., Kenny, E., Kishore, R., Lawson, D., Lee, R., Muller, H. M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Sabo, A., Schwarz, E. M., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, P. W. and Stein, L. D. (2004). WormBase: A multi-species resource for nematode biology and genomics. Nucleic Acids Res. 32, D411-D417.
9. Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T. and Birney, E. (2004). EnsMart: A Generic System for Fast and Flexible Access to Biological Data. Genome Res. 14, 160-169.
10. Kersey, P. J., Morris, L., Hermjakob, H. and Apweiler, R. (2003). Integr8: Enhanced Inter-Operability of European Molecular Biology Databases. Methods Inf. Med. 42, 154-160.
11. Kersey, P. J, Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E. and Apweiler, R. (2004). The International Protein Index: An integrated database for proteomics experiments. Proteomics 4, 1985-1988.
12. Kriventseva, E. V., Servant, F. and Apweiler, R. (2003). Improvements to CluSTr: The database of Swiss-Prot+TrEMBL protein clusters. Nucleic Acids Res. 31, 388-389.
13. Kulikova, T., Aldebert, P., Althorpe, N., Baker, W., Bates, K., Browne, P., Van Den Broek, A., Cochrane, G., Duggan, K., Eberhardt, R., Faruque, N., Garcia-Pastor, M., Harte, N., Kanz, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., Mancuso, R., McHale, M., Nardone, F., Silventoinen, V., Stoehr, P., Stoesser, G., Tuli, M.A., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W. and Apweiler R. (2004). The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 32, D27-D30.
14. Leinonen, R., Diez, F. G., Binns, D., Fleischmann, W., Lopez, R. and Apweiler, R. (2004). UniProt Archive. Bioinformatics 20, 3236-3237.
15. Miyazaki, S., Sugawara, H., Ikeo, K., Gojobori, T. and Tateno, Y. (2004). DDBJ in the stream of various biological data. Nucleic Acids Res. 32, D31-D34.
16. Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R. R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S. E., Pagni, M., Peyruc, D., Ponting, C. P., Selengut, J. D, Servant, F., Sigrist, C. J. A., Vaughan, R. and Zdobnov, E. M. (2003). The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31, 315-318.
17. Pruess, M., Fleischmann, W., Kanapin, A., Karavidopoulou, Y., Kersey, P., Kriventseva, E., Mittard, V., Mulder, N., Phan, I., Servant, F. and Apweiler, R. (2003). The Proteome Analysis database: A tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31, 414-417.
18. Pruitt, K. D., Tatusova, T. and Maglott, D. R. (2003). NCBI Reference Sequence project: Update and current status. Nucleic Acids Res. 31, 34-37.
19. The FlyBase Consortium (2003). The FlyBase database of the Drosophila, genome projects and community literature. Nucleic Acids Res. 31, 172-175.
20. Westbrook, J., Feng, Z., Chen, L., Yang, H. and Berman, H. M. (2003). The Protein Data Bank and structural genomics. Nucleic Acids Res. 31, 489-491.
21. Wheeler, D. L., Church, D. M., Edgar, R., Federhen, S., Helmberg, W., Madden, T. L., Pontius, J. U., Schuler, G. D., Schriml, L. M., Sequeira, E., Suzek, T. O., Tatusova, T. A. and Wagner, L. (2004): Database resources of the National Center for Biotechnology Information: Update. Nucleic Acids Res. 32, D35-D40.