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WormBase 2012: more genomes, more data, new website

Yook, Karen and Chan, Juancarlos and Chen, Wen J. and Fang, Ruihua and Ganesan, Uma and Grove, Christian and Kadam, Snehalata and Kishore, Ranjana and Lee, Raymond and Li, Yuling and Muller, Hans-Michael and Nakamura, Cecilia and Rangarajan, Arun and Schindelman, Gary and Schwarz, Erich M. and Van Auken, Kimberly and Wang, Xiaodong and Sternberg, Paul W. and Raciti, Daniela and Wang, Daniel (2012) WormBase 2012: more genomes, more data, new website. Nucleic Acids Research, 40 (D1). D735-D741. ISSN 0305-1048. PMCID PMC3245152. https://resolver.caltech.edu/CaltechAUTHORS:20120214-071150526

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Abstract

Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1093/nar/gkr954 DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245152/PubMed CentralArticle
ORCID:
AuthorORCID
Yook, Karen0000-0002-4457-6787
Chan, Juancarlos0000-0002-7259-8107
Grove, Christian0000-0001-9076-6015
Lee, Raymond0000-0002-8151-7479
Nakamura, Cecilia0000-0002-4689-7314
Schwarz, Erich M.0000-0003-3151-4381
Van Auken, Kimberly0000-0002-1706-4196
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© 2011 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Received September 14, 2011; Accepted October 12, 2011. First published online: November 8, 2011. This work is supported by the US National Institutes of Health (Grant no. P41 HG02223); US National Human Genome Research Institute (Grant no. P41-HG02223) to WormBase; and British Medical Research Council (Grant no. G070119) to WormBase; P.W.S. is an investigator with the Howard Hughes Medical Institute. Funding for open access charge: US National Human Genome Research Institute (Grant no. P41-HG02223). Conflict of interest statement. None declared.
Funders:
Funding AgencyGrant Number
NIHP41 HG02223
Medical Research Council (UK)G070119
NIHP41-HG02223
Issue or Number:D1
PubMed Central ID:PMC3245152
Record Number:CaltechAUTHORS:20120214-071150526
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20120214-071150526
Official Citation: Karen Yook, Todd W. Harris, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, Norie de la Cruz, Adrian Duong, Ruihua Fang, Uma Ganesan, Christian Grove, Kevin Howe, Snehalata Kadam, Ranjana Kishore, Raymond Lee, Yuling Li, Hans-Michael Muller, Cecilia Nakamura, Bill Nash, Philip Ozersky, Michael Paulini, Daniela Raciti, Arun Rangarajan, Gary Schindelman, Xiaoqi Shi, Erich M. Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Jonathan Hodgkin, Matthew Berriman, Richard Durbin, Paul Kersey, John Spieth, Lincoln Stein, and Paul W. Sternberg WormBase 2012: more genomes, more data, new website Nucl. Acids Res. (2012) 40(D1): D735-D741 doi:10.1093/nar/gkr954
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:29264
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:14 Feb 2012 15:56
Last Modified:29 Oct 2019 19:35

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