Genomic information infrastructure after the deluge

Genome Biology

Volumn 11, Issue 7, 2010, Pages

  Parkhill, Julian ^a   Birney, Ewan ^b   Kersey, Paul ^b  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL ACTIVITY; CHROMATIN IMMUNOPRECIPITATION; COMMUNICATION SOFTWARE; COMPARATIVE GENOMIC HYBRIDIZATION; DATA ANALYSIS SOFTWARE; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FUNDING; GENE TECHNOLOGY; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION DISSEMINATION; LETTER; MUTAGENESIS; NONHUMAN; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; RNA SEQUENCE; SEQUENCE ANALYSIS; STRUCTURAL BIOINFORMATICS; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS; ANIMAL; ARABIDOPSIS; ECONOMICS; FINANCIAL MANAGEMENT; GENETICS; GENOME; GENOMICS; INTERPERSONAL COMMUNICATION; METHODOLOGY; NUCLEIC ACID DATABASE; SACCHAROMYCES CEREVISIAE;

ANIMALS; ARABIDOPSIS; COMMUNICATION; DATABASES, NUCLEIC ACID; GENOME; GENOMICS; RESEARCH SUPPORT AS TOPIC; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA;

EID: 77957768333     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-7-402     Document Type: Letter

References (25)

1. Drysdale R. FlyBase: a database for the Drosophila research community. Methods Mol Biol 2008, 420:45-59. full_text, 18641940.
2. Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller H, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res 2010, 38:D463-D467. 10.1093/nar/gkp952, 2808986, 19910365.
3. Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM. Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res 2010, 38:D433-D436. 10.1093/nar/gkp917, 2808950, 19906697.
4. Ed L, Nomi H, Mark G, Raymond C, Suzanna L. Apollo: a community resource for genome annotation editing. Bioinformatics 2009, 25:1836-1837. 10.1093/bioinformatics/btp314, 2705230, 19439563.
5. Zhou P, Emmert D, Zhang P. Using Chado to store genome annotation data. Curr Protoc Bioinformatics 2006, Chapter 9(Unit 9.6).
6. Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell BG, Parkhill J, Rajandream M. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008, 24:2672-2676. 10.1093/bioinformatics/btn529, 2606163, 18845581.
7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2010, 38:D46-D51. 10.1093/nar/gkp1024, 2808980, 19910366.
8. Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G. Improvements to services at the European Nucleotide Archive. Nucleic Acids Res 2010, 38:D39-D45. 10.1093/nar/gkp998, 2808951, 19906712.
9. Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T, Nakamura Y. DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res 2010, 38:D33-D38. 10.1093/nar/gkp847, 2808917, 19850725.
10. Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, et al. Ensembl's 10th year. Nucleic Acids Res 2010, 38:D557-D562. 10.1093/nar/gkp972, 2808936, 19906699.
11. Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, 37:D32-D36. 10.1093/nar/gkn721, 2686572, 18927115.
12. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 2010, 38:D613-D619. 10.1093/nar/gkp939, 2808870, 19906737.
13. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2010, 38:D5-D16. 10.1093/nar/gkp967, 2808881, 19910364.
14. Brooksbank C, Cameron G, Thornton J. The European Bioinformatics Institute's data resources. Nucleic Acids Res 2010, 38:D17-D25. 10.1093/nar/gkp986, 2808956, 19934258.
15. Poole RL. The TAIR database. Methods Mol Biol 2007, 406:179-212. full_text, 18287693.
16. Giles PF, Soanes DM, Talbot NJ. A relational database for the discovery of genes encoding amino acid biosynthetic enzymes in pathogenic fungi. Comp Funct Genomics 2003, 4:4-15. 10.1002/cfg.236, 2447380, 18629094.
17. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res 2002, 12:1599-1610. 10.1101/gr.403602, 187535, 12368253.
18. Aslett M, Mooney P, Adlem E, Berriman M, Berry A, Hertz-Fowler C, Ivens AC, Kerhornou A, Parkhill J, Peacock CS, Wood V, Rajandream M, Barrell B, Tivey A. Integration of tools and resources for display and analysis of genomic data for protozoan parasites. Int J Parasitol 2005, 35:481-493. 10.1016/j.ijpara.2005.01.011, 15826641.
19. Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ, Thibodeau R, Treatman C, Wang H. EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res 2010, 38:D415-D419. 10.1093/nar/gkp941, 2808945, 19914931.
20. Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH. VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res 2009, 37:D583-D587. 10.1093/nar/gkn857, 2686483, 19028744.
21. Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, Hance M, Huntington KI, Jukneliene D, Koziski J, Mackasmiel L, Mane SP, Nguyen V, Purkayastha A, Shallom J, Yu G, Guo Y, Gabbard J, Hix D, Azad AF, Baker SC, et al. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res 2007, 35:D401-406. 10.1093/nar/gkl858, 1669763, 17142235.
22. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005, 15:1451-1455. 10.1101/gr.4086505, 1240089, 16169926.
23. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, 37:D885-D890. 10.1093/nar/gkn764, 2686538, 18940857.
24. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone S, et al. ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 2009, 37:D868-D872. 10.1093/nar/gkn889, 2686529, 19015125.
25. Wixon J, Wood V. Tools and resources for Sz. pombe: a report from the 2006 European Fission Yeast Meeting. Yeast 2006, 23:901-903. 10.1002/yea.1421, 17072880.