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PMID: 24194605 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

WormBase 2014: new views of curated biology.

Nucleic acids research ·Vol. 42 ·No. Database issue ·2014-01-00 ·Pages D789-93

Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW

Abstract

WormBase (http://www.wormbase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest.

MeSH Terms
Animals Caenorhabditis elegans/genetics Databases, Genetic Genome, Helminth Internet Molecular Sequence Annotation Nematoda/genetics
Authors & Affiliations
33 authors, click to expand affiliations / ORCID
Harris Todd W
Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, Genome Sequencing Center, Washington University, School of Medicine, St Louis, MO 63108, USA, Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, CA 91125, USA, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Genetics Campus, Washington University School of Medicine, St. Louis, MO 63110, USA, Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
Baran Joachim
Bieri Tamberlyn
Cabunoc Abigail
Chan Juancarlos
Chen Wen J
Davis Paul
Done James
Grove Christian
Howe Kevin
Kishore Ranjana
Lee Raymond
Li Yuling
Muller Hans-Michael
Nakamura Cecilia
Ozersky Philip
Paulini Michael
Raciti Daniela
Schindelman Gary
Tuli Mary Ann
Van Auken Kimberly
Wang Daniel
Wang Xiaodong
Williams Gary
Wong J D
Yook Karen
Schedl Tim
Hodgkin Jonathan
Berriman Matthew
Kersey Paul
Spieth John
Stein Lincoln
Sternberg Paul W
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
Published
2014-01-00
Epub
2013-00-04
Pages
D789-93
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3965043
Subset
IM
Grants
Medical Research Council · G070119 · United Kingdom
Howard Hughes Medical Institute · United States
Medical Research Council · MR/L001020/1 · United Kingdom
NHGRI NIH HHS · P41 HG002223 · United States
NHGRI NIH HHS · U41 HG002223 · United States
NHGRI NIH HHS · U41-HG002223 · United States
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