PomBase: a comprehensive online resource for fission yeast

被引：228

作者：

Wood, Valerie ^{[1
,2
,3
]}

Harris, Midori A. ^{[1
,2
]}

McDowall, Mark D. ^{[4
]}

Rutherford, Kim ^{[1
,2
]}

Vaughan, Brendan W. ^{[4
]}

Staines, Daniel M. ^{[4
]}

Aslett, Martin ^{[5
]}

Lock, Antonia ^{[6
,7
]}

Baehler, Juerg ^{[6
,7
]}

Kersey, Paul J. ^{[4
]}

Oliver, Stephen G. ^{[1
,2
]}

机构：

[1] Univ Cambridge, Cambridge Syst Biol Ctr, Cambridge CB2 1GA, England

[2] Univ Cambridge, Dept Biochem, Cambridge CB2 1GA, England

[3] London Res Inst, Cell Cycle Lab, Canc Res UK, London WC2A 3LY, England

[4] European Bioinformat Inst, Hinxton CB10 1SD, Cambs, England

[5] Wellcome Trust Sanger Inst, Hinxton CB10 1SA, Cambs, England

[6] UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England

[7] UCL, UCL Canc Inst, London WC1E 6BT, England

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

基金：

英国惠康基金;

关键词：

ONTOLOGY; SEQUENCE; ENSEMBL; ARTEMIS;

D O I：

10.1093/nar/gkr853

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance.

引用

页码：D695 / D699

页数：5

共 20 条

[1]

Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[2]

The GOA database in 2009-an integrated Gene Ontology Annotation resource [J].

Barrell, Daniel ;

Dimmer, Emily ;

Huntley, Rachael P. ;

Binns, David ;

O'Donovan, Claire ;

Apweiler, Rolf .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D396-D403

[3]

The Gene Ontology in 2010: extensions and refinements The Gene Ontology Consortium [J].

Berardini, Tanya Z. ;

Li, Donghui ;

Huala, Eva ;

Bridges, Susan ;

Burgess, Shane ;

McCarthy, Fiona ;

Carbon, Seth ;

Lewis, Suzanna E. ;

Mungall, Christopher J. ;

Abdulla, Amina ;

Wood, Valerie ;

Feltrin, Erika ;

Valle, Giorgio ;

Chisholm, Rex L. ;

Fey, Petra ;

Gaudet, Pascale ;

Kibbe, Warren ;

Basu, Siddhartha ;

Bushmanova, Yulia ;

Eilbeck, Karen ;

Siegele, Deborah A. ;

McIntosh, Brenley ;

Renfro, Daniel ;

Zweifel, Adrienne ;

Hu, James C. ;

Ashburner, Michael ;

Tweedie, Susan ;

Alam-Faruque, Yasmin ;

Apweiler, Rolf ;

Auchinchloss, Andrea ;

Bairoch, Amos ;

Barrell, Daniel ;

Binns, David ;

Blatter, Marie-Claude ;

Bougueleret, Lydie ;

Boutet, Emmanuel ;

Breuza, Lionel ;

Bridge, Alan ;

Browne, Paul ;

Chan, Wei Mun ;

Coudert, Elizabeth ;

Daugherty, Louise ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Estreicher, Anne ;

Famiglietti, Livia ;

Ferro-Rojas, Serenella ;

Feuermann, Marc ;

Foulger, Rebecca ;

Gruaz-Gumowski, Nadine .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D331-D335

[4]

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database [J].

Carver, Tim ;

Berriman, Matthew ;

Tivey, Adrian ;

Patel, Chinmay ;

Bohme, Ulrike ;

Barrell, Barclay G. ;

Parkhill, Julian ;

Rajandream, Marie-Adele .

BIOINFORMATICS, 2008, 24 (23) :2672-2676

[5]

Chemical Entities of Biological Interest: an update [J].

de Matos, Paula ;

Alcantara, Rafael ;

Dekker, Adriano ;

Ennis, Marcus ;

Hastings, Janna ;

Haug, Kenneth ;

Spiteri, Inmaculada ;

Turner, Steve ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D249-D254

[6]

Egel R., 2004, The Molecular Biology of Schizosaccharomyces pombeed

[7]

The Sequence Ontology: a tool for the unification of genome annotations [J].

Eilbeck, K ;

Lewis, SE ;

Mungall, CJ ;

Yandell, M ;

Stein, L ;

Durbin, R ;

Ashburner, M .

GENOME BIOLOGY, 2005, 6 (05)

[8]

Ensembl 2011 [J].

Flicek, Paul ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Chen, Yuan ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gordon, Leo ;

Hendrix, Maurice ;

Hourlier, Thibaut ;

Johnson, Nathan ;

Kaehaeri, Andreas ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Kokocinski, Felix ;

Kulesha, Eugene ;

Larsson, Pontus ;

Longden, Ian ;

McLaren, William ;

Overduin, Bert ;

Pritchard, Bethan ;

Riat, Harpreet Singh ;

Rios, Daniel ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sobral, Daniel ;

Spudich, Giulietta ;

Tang, Y. Amy ;

Trevanion, Stephen ;

Vandrovcova, Jana ;

Vilella, Albert J. ;

White, Simon ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Zamora, Jorge ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard ;

Fernandez-Suarez, Xose M. ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Parker, Anne ;

Proctor, Glenn .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D800-D806

[9]

Using ontologies to describe mouse phenotypes [J].

Georgios V Gkoutos ;

Eain CJ Green ;

Ann-Marie Mallon ;

John M Hancock ;

Duncan Davidson .

Genome Biology, 6 (1)

[10]

Ensembl Genomes: Extending Ensembl across the taxonomic space [J].

Kersey, P. J. ;

Lawson, D. ;

Birney, E. ;

Derwent, P. S. ;

Haimel, M. ;

Herrero, J. ;

Keenan, S. ;

Kerhornou, A. ;

Koscielny, G. ;

Kaehaeri, A. ;

Kinsella, R. J. ;

Kulesha, E. ;

Maheswari, U. ;

Megy, K. ;

Nuhn, M. ;

Proctor, G. ;

Staines, D. ;

Valentin, F. ;

Vilella, A. J. ;

Yates, A. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D563-D569

← 1 2 →