Bioinformatics database infrastructure for biotechnology research

Journal of Biotechnology

Volumn 124, Issue 4, 2006, Pages 629-639

  Whitfield, Eleanor J ^a   Pruess, Manuela ^a   Apweiler, Rolf ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Bioinformatics; Genomics database; Nucleic acid database; Protein database; Proteome database

Indexed keywords

DATABASE SYSTEMS; GENES; INTEGRATED CIRCUITS; NUCLEIC ACIDS; PROTEINS; RESOURCE ALLOCATION;

BIOINFORMATICS; GENOMICS DATABASE; NUCLEIC ACID DATABASE; PROTEIN DATABASE; PROTEOME DATABASE;

BIOTECHNOLOGY;

AMINO ACID SEQUENCE; BIOINFORMATICS; BIOTECHNOLOGY; DATA BASE; DNA DATA BANK OF JAPAN; EMBL NUCLEOTIDE SEQUENCE DATABASE; GENBANK; GENE; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; ORGANISM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; REVIEW;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; HUMANS;

EID: 33746113370     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2006.04.006     Document Type: Review

References (49)

1. Allen F.H. The Cambridge structural database: a quarter of a million crystal structures and rising. Acta Crystallogr. B 58 (2002) 380-388
2. Ashurst J.L., Chen C.-K., Gilbert J.G.R., Jekosch K., Keenan S., Meidl P., Searle S.M., Stalker J., Storey R., Trevanion S., Wilming L., and Hubbard T. The vertebrate genome annotation (Vega) database. Nucl. Acids Res. 33 (2005) D459-D465
3. Attwood T.K., Bradley P., Gaulton A., Maudling N., Mitchell A.L., and Moulton G. The PRINTS protein fingerprint database: functional and evolutionary applications. In: Dunn M., Jorde L., Little P., and Subramaniam A. (Eds). Encyclopaedia of Genomics (2004), Proteomics and Bioinformatics
4. Bairoch A. The ENZYME database in 2000. Nucl. Acids Res. 28 (2000) 304-305
5. Bairoch A., Apweiler R., 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.-S.L. The universal protein resource (UniProt). Nucl. Acids Res. 33 (2005) D154-D159
6. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L.L., et al. The Pfam protein families database. Nucl. Acids Res. 32 (2004) D138-D141
7. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucl. Acids Res. 28 (2000) 235-242
8. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., and Wheeler D.L. GenBank. Nucl. Acids Res. 33 (2005) D34-D38
9. Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., et al. The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003. Nucl. Acids Res. 31 (2003) 365-370
10. Brooksbank C., Cameron G., and Thornton J. The European Bioinformatics Institute's data resources: towards systems biology. Nucl. Acids Res. 33 (2005) D46-D53
11. Bru C., Courcelle E., Carrère S., Beausse Y., Dalmar S., and Kahn D. The ProDom database of protein domain families: more emphasis on 3D. Nucl. Acids Res. 33 (2005) D212-D215
12. Camon E., Magrane M., Barrell D., Lee V., Dimmer E., Maslen J., Binns D., Harte N., Lopez R., and Apweiler R. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucl. Acids Res. 32 (2004) D262-D266
13. Chen N., Harris T.W., Antoshechkin I., Bastiani C., Bieri T., Blasiar D., Bradnam K., Canaran P., Chan J., Chen C.-K., et al. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucl. Acids Res. 33 (2005) D383-D389
14. Dowell R.D., Jokerst R.M., Day A., Eddy S.R., and Stein L. The distributed annotation system. BMC Bioinformatics 2 (2001) 7
15. Drysdale R.A., Crosby M.A., and The FlyBase Consortium. FlyBase: genes and gene models. Nucl. Acids Res. 33 (2005) D390-D395
16. Eppig J.T., Bult C.J., Kadin J.A., Richardson J.E., Blake J.A., and The Mouse Genome Database Group. The Mouse Genome Database (MGD): from genes to mice-a community resource for mouse biology. Nucl. Acids Res. 33 (2005) D471-D475
17. Fleischmann A., Darsow M., Degtyarenko K., Fleischmann W., Boyce S., Axelsen K.B., Bairoch A., Schomburg D., Tipton K.F., and Apweiler R. IntEnz, the integrated relational enzyme database. Nucl. Acids Res. 32 (2004) D434-D437
18. Garavelli J.S. The RESID database of protein modifications as a resource and annotation tool. Proteomics 4 (2004) 1527-1533
19. Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucl. Acids Res. 32 (2004) D258-D261
20. Gough J., and Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucl. Acids Res. 30 (2002) 268-272
21. Haft D.H., Selengut J.D., and White O. The TIGRFAMs database of protein families. Nucl. Acids Res. 31 (2003) 371-373
22. Hermjakob H., Montecchi-Palazzi L., Lewington C., Mudali S., Kerrien S., Orchard S., Vingron M., Roechert B., Roepstorff P., Valencia A., et al. IntAct: an open source molecular interaction database. Nucl. Acids Res. 32 (2004) D452-D455
23. Höld K.M., Sirisoma N.S., Ikeda T., Narahashi T., and Casida J.E. Alpha-thujone (the active component of absinthe): gamma-aminobutyric acid type A receptor modulation and metabolic detoxification. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 3826-3831
24. Hoogland C., Mostaguir K., Sanchez J.-C., Hochstrasser D.F., and Appel R.D. SWISS-2DPAGE, ten years later. Proteomics (2004) 4
25. Huang H., Barker W.C., Chen Y., and Wu C.H. iProClass: an integrated database of protein family, function and structure information. Nucl. Acids Res. 31 (2003) 390-392
26. Hubbard T., Andrews D., Caccamo M., Cameron G., Chen Y., Clamp M., Clarke L., Coates G., Cox T., Cunningham F., et al. Ensembl 2005. Nucl. Acids Res. 33 (2005) D447-D453
27. Hulo N., Sigrist C.J.A., Le Saux V., Langendijk-Genevaux P.S., Bordoli L., Gattiker A., De Castro E., Bucher P., and Bairoch A. Recent improvements to the PROSITE database. Nucl. Acids Res. 32 (2004) D134-D137
28. Kanz C., Aldebert P., Althorpe N., Baker W., Baldwin A., Bates K., Browne P., van den Broek A., Castro M., Cochrane G., et al. The EMBL nucleotide sequence database. Nucl. Acids Res. 33 (2005) D29-D33
29. Karolchik D., Baertsch R., Diekhans M., Furey T.S., Hinrichs A., Lu Y.T., Roskin K.M., Schwartz M., Sugnet C.W., Thomas D.J., Weber R.J., Haussler D., and Kent W.J. The UCSC genome browser database. Nucl. Acids Res. 31 (2003) 51-54
30. Kash T.L., Trudell J.R., and Harrison N.L. Structural elements involved in activation of the gamma-aminobutyric acid type A (GABAA) receptor. Biochem. Soc. Trans. 32 (2004) 540-548
31. Kersey P.J., Duarte J., Williams A., Karavidopoulou Y., Birney E., and Apweiler R. The International Protein Index: an integrated database for proteomics experiments. Proteomics 4 (2004) 1985-1988
32. Kersey P.J., Bower L., Morris L., Horne A., Petryszak R., Kanz C., Kanapin A., Das U., Michoud K., Phan I., et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucl. Acids Res. 33 (2005) D297-D302
33. Lefranc M.-P., Giudicelli V., Kaas Q., Duprat E., Jabado-Michaloud J., Scaviner D., Ginestoux C., Clément O., Chaume D., and Lefranc G. IMGT, the international ImMunoGeneTics information system. Nucl. Acids Res. 33 (2005) D593-D597
34. Leinonen R., Diez F.G., Binns D., Fleischmann W., Lopez R., and Apweiler R. UniProt archive. Bioinformatics 20 (2004) 3236-3237
35. Letunic I., Copley R.R., Schmidt S., Ciccarelli F.D., Doerks T., Schultz J., Ponting C.P., and Bork P. SMART 4.0: towards genomic data integration. Nucl. Acids Res. 32 (2004) D142-D144
36. Martens, L., Hermjakob, H., Jones, P., Taylor, C., Gevaert, J., Vandekerckhove, J., Apweiler, R., in press. PRIDE: The PRoteomics IDEntifications database Proteomics, PPP Special Issue.
37. Matys V., Fricke E., Geffers R., Gossling E., Haubrock M., Hehl R., Hornischer K., Karas D., Kel A.E., Kel-Margoulis O.V., Kloos D.U., Land S., Lewicki-Potapov B., Michael H., Munch R., Reuter I., Rotert S., Saxel H., Scheer M., Thiele S., and Wingender E. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucl. Acids Res. 31 (2003) 374-378
38. Mi H., Lazareva-Ulitsky B., Loo R., Kejariwal A., Vandergriff J., Rabkin S., Guo N., Mruganujan A., Doremieux O., Campbell M.J., Kitano H., and Thomas P.D. The PANTHER database of protein families, subfamilies, functions and pathways. Nucl. Acids Res. 33 (2005) D284-D288
39. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bradley P., Bork P., Bucher P., Cerutti L., et al. InterPro, progress and status in 2005. Nucl. Acids Res. 33 (2005) D201-D205
40. Pearl F., Todd A., Sillitoe I., Dibley M., Redfern O., Lewis T., Bennett C., Marsden R., Grant A., Lee D., et al. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucl. Acids Res. 33 (2005) D247-D251
41. Pruitt K.D., Tatusova T., and Maglott D.R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucl. Acids Res. 33 (2005) D501-D504
42. Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., and Lopez R. InterProScan: protein domains identifier. Nucl. Acids Res. 33 (2005) W116-W120
43. Schmid C.D., Praz V., Delorenzi M., Périer R., and Bucher P. The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucl. Acids Res. 32 (2004) D82-D85
44. Schomburg I., Chang A., Ebeling C., Gremse M., Heldt C., Huhn G., and Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucl. Acids Res. 32 (2004) D431-D433
45. Tateno Y., Saitou N., Okubo K., Sugawara H., and Gojobori T. DDBJ in collaboration with mass-sequencing teams on annotation. Nucl. Acids Res. 33 (2005) D25-D28
46. Twigger S., Lu J., Shimoyama M., Chen D., Pasko D., Long H., Ginster J., Chen C.F., Nigam R., Kwitek A., et al. Nucl. Acids Res. 30 (2002) 125-128
47. Wain H.M., Lush M., Ducluzeau F., and Povey S. Nucl. Acids Res. 30 (2002) 169-171
48. Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Church D.M., DiCuccio M., Edgar R., Federhen S., Helmberg W., et al. Database resources of the National Centre for Biotechnology Information. Nucl. Acids Res. 33 (2005) D39-D45
49. Wu C.H., Yeh L.S., Huang H., Arminski L., Castro-Alvear J., Chen Y., Hu Z., Kourtesis P., Ledley R.S., Suzek B.E., et al. The protein information resource. Nucl. Acids Res. 31 (2003) 345-347