WormBase 2016: expanding to enable helminth genomic research

被引：257

作者：

Howe, Kevin L. ^{[1
]}

Bolt, Bruce J. ^{[1
]}

Cain, Scott ^{[2
]}

Chan, Juancarlos ^{[3
]}

Chen, Wen J. ^{[3
]}

Davis, Paul ^{[1
]}

Done, James ^{[3
]}

Down, Thomas ^{[1
]}

Gao, Sibyl ^{[2
]}

Grove, Christian ^{[3
]}

Harris, Todd W. ^{[2
]}

Kishore, Ranjana ^{[3
]}

Lee, Raymond ^{[3
]}

Lomax, Jane ^{[4
]}

Li, Yuling ^{[3
]}

Muller, Hans-Michael ^{[3
]}

Nakamura, Cecilia ^{[3
]}

Nuin, Paulo ^{[2
]}

Paulini, Michael ^{[1
]}

Raciti, Daniela ^{[3
]}

Schindelman, Gary ^{[3
]}

Stanley, Eleanor ^{[4
]}

Tuli, Mary Ann ^{[3
]}

Van Auken, Kimberly ^{[3
]}

Wang, Daniel ^{[3
]}

Wang, Xiaodong ^{[3
]}

Williams, Gary ^{[1
]}

Wright, Adam ^{[2
]}

Yook, Karen ^{[3
]}

Berriman, Matthew ^{[4
]}

Kersey, Paul ^{[1
]}

Schedl, Tim ^{[5
]}

Stein, Lincoln ^{[2
]}

Sternberg, Paul W. ^{[2
,6
]}

机构：

[1] European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England

[2] Ontario Inst Canc Res, Informat & Biocomp Platform, Toronto, ON M5G0A3, Canada

[3] CALTECH, Div Biol & Biol Engn 156 29, Pasadena, CA 91125 USA

[4] Wellcome Trust Sanger Inst, Wellcome Trust Genome Campus, Cambridge CB10 1SA, England

[5] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA

[6] CALTECH, Howard Hughes Med Inst, Pasadena, CA 91125 USA

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

基金：

英国生物技术与生命科学研究理事会; 英国医学研究理事会;

关键词：

DATABASE; ONTOLOGY; MODEL; PREDICTION; BROWSER; ACCESS; SYSTEM; GENES; API;

D O I：

10.1093/nar/gkv1217

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.

引用

页码：D774 / D780

页数：7

共 43 条

[1] OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders [J].

Amberger, Joanna S. ;

Bocchini, Carol A. ;

Schiettecatte, Francois ;

Scott, Alan F. ;

Hamosh, Ada .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D789-D798

[2]

[Anonymous], 1997, C ELEGANS

[3] The arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome [J].

Berardini, Tanya Z. ;

Reiser, Leonore ;

Li, Donghui ;

Mezheritsky, Yarik ;

Muller, Robert ;

Strait, Emily ;

Huala, Eva .

GENESIS, 2015, 53 (08) :474-485

[4]

BRENNER S, 1974, GENETICS, V77, P71

[5]

Cast V., 1994, TAROT INDIVIDUATION, pi

[6] Saccharomyces genome database provides new regulation data [J].

Costanzo, Maria C. ;

Engel, Stacia R. ;

Wong, Edith D. ;

Lloyd, Paul ;

Karra, Kalpana ;

Chan, Esther T. ;

Weng, Shuai ;

Paskov, Kelley M. ;

Roe, Greg R. ;

Binkley, Gail ;

Hitz, Benjamin C. ;

Cherry, Michael .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D717-D725

[7] Ensembl 2015 [J].

Cunningham, Fiona ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Billis, Konstantinos ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Giron, Carlos Garcia ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah E. ;

Janacek, Sophie H. ;

Johnson, Nathan ;

Juettemann, Thomas ;

Kaehaeri, Andreas K. ;

Keenan, Stephen ;

Martin, Fergal J. ;

Maurel, Thomas ;

McLaren, William ;

Murphy, Daniel N. ;

Nag, Rishi ;

Overduin, Bert ;

Parker, Anne ;

Patricio, Mateus ;

Perry, Emily ;

Pignatelli, Miguel ;

Riat, Harpreet Singh ;

Sheppard, Daniel ;

Taylor, Kieron ;

Thormann, Anja ;

Vullo, Alessandro ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Aken, Bronwen L. ;

Birney, Ewan ;

Harrow, Jennifer ;

Kinsella, Rhoda ;

Muffato, Matthieu ;

Ruffier, Magali ;

Searle, Stephen M. J. ;

Spudich, Giulietta ;

Trevanion, Stephen J. ;

Yates, Andy ;

Zerbino, Daniel R. ;

Flicek, Paul .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D662-D669

[8] ChEMBL web services: streamlining access to drug discovery data and utilities [J].

Davies, Mark ;

Nowotka, Michal ;

Papadatos, George ;

Dedman, Nathan ;

Gaulton, Anna ;

Atkinson, Francis ;

Bellis, Louisa ;

Overington, John P. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W612-W620

[9]

De Ley P., 2006, WORMBOOK, P1, DOI [DOI 10.1895/WORMBOOK.1.178.1, DOI 10.1895/WORMBOOK.1.41.1]

[10] FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations [J].

dos Santos, Gilberto ;

Schroeder, Andrew J. ;

Goodman, Joshua L. ;

Strelets, Victor B. ;

Crosby, Madeline A. ;

Thurmond, Jim ;

Emmert, David B. ;

Gelbart, William M. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D690-D697

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