WormBase 2014: New views of curated biology

Todd W. Harris; Joachim Baran; Tamberlyn Bieri; Abigail Cabunoc; Juancarlos Chan; Wen J. Chen; Paul Davis; James Done; Christian Grove; Kevin Howe; Ranjana Kishore; Raymond Lee; Yuling Li; Hans Michael Muller; Cecilia Nakamura; Philip Ozersky; Michael Paulini; Daniela Raciti; Gary Schindelman; Mary Ann Tuli; Kimberly Van Auken; Daniel Wang; Xiaodong Wang; Gary Williams; J. D. Wong; Karen Yook; Tim Schedl; Jonathan Hodgkin; Matthew Berriman; Paul Kersey; John Spieth; Lincoln Stein; Paul W. Sternberg

doi:10.1093/nar/gkt1063

WormBase 2014: New views of curated biology

Todd W. Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian Grove, Kevin Howe, Ranjana Kishore, Raymond Lee, Yuling Li, Hans Michael Muller, Cecilia Nakamura, Philip Ozersky, Michael Paulini, Daniela Raciti, Gary Schindelman, Mary Ann TuliKimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, J. D. Wong, Karen Yook, Tim Schedl, Jonathan Hodgkin, Matthew Berriman, Paul Kersey, John Spieth, Lincoln Stein, Paul W. Sternberg

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127 Scopus citations

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.

Original language	English
Pages (from-to)	D789-D793
Journal	Nucleic acids research
Volume	42
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkt1063
State	Published - Jan 1 2014

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Harris, T. W., Baran, J., Bieri, T., Cabunoc, A., Chan, J., Chen, W. J., Davis, P., Done, J., Grove, C., Howe, K., Kishore, R., Lee, R., Li, Y., Muller, H. M., Nakamura, C., Ozersky, P., Paulini, M., Raciti, D., Schindelman, G., ... Sternberg, P. W. (2014). WormBase 2014: New views of curated biology. Nucleic acids research, 42(D1), D789-D793. https://doi.org/10.1093/nar/gkt1063

@article{1c04377ea2a44ee0ae4af4110e1450fe,

title = "WormBase 2014: New views of curated biology",

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.",

author = "Harris, {Todd W.} and Joachim Baran and Tamberlyn Bieri and Abigail Cabunoc and Juancarlos Chan and Chen, {Wen J.} and Paul Davis and James Done and Christian Grove and Kevin Howe and Ranjana Kishore and Raymond Lee and Yuling Li and Muller, {Hans Michael} and Cecilia Nakamura and Philip Ozersky and Michael Paulini and Daniela Raciti and Gary Schindelman and Tuli, {Mary Ann} and Auken, {Kimberly Van} and Daniel Wang and Xiaodong Wang and Gary Williams and Wong, {J. D.} and Karen Yook and Tim Schedl and Jonathan Hodgkin and Matthew Berriman and Paul Kersey and John Spieth and Lincoln Stein and Sternberg, {Paul W.}",

year = "2014",

month = jan,

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doi = "10.1093/nar/gkt1063",

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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, Auken, KV, Wang, D, Wang, X, Williams, G, Wong, JD, Yook, K, Schedl, T, Hodgkin, J, Berriman, M, Kersey, P, Spieth, J, Stein, L & Sternberg, PW 2014, 'WormBase 2014: New views of curated biology', Nucleic acids research, vol. 42, no. D1, pp. D789-D793. https://doi.org/10.1093/nar/gkt1063

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T2 - New views of curated biology

AU - Harris, Todd W.

AU - Baran, Joachim

AU - Bieri, Tamberlyn

AU - Cabunoc, Abigail

AU - Chan, Juancarlos

AU - Chen, Wen J.

AU - Davis, Paul

AU - Done, James

AU - Grove, Christian

AU - Howe, Kevin

AU - Kishore, Ranjana

AU - Lee, Raymond

AU - Li, Yuling

AU - Muller, Hans Michael

AU - Nakamura, Cecilia

AU - Ozersky, Philip

AU - Paulini, Michael

AU - Raciti, Daniela

AU - Schindelman, Gary

AU - Tuli, Mary Ann

AU - Auken, Kimberly Van

AU - Wang, Daniel

AU - Wang, Xiaodong

AU - Williams, Gary

AU - Wong, J. D.

AU - Yook, Karen

AU - Schedl, Tim

AU - Hodgkin, Jonathan

AU - Berriman, Matthew

AU - Kersey, Paul

AU - Spieth, John

AU - Stein, Lincoln

AU - Sternberg, Paul W.

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N2 - 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.

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DO - 10.1093/nar/gkt1063

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VL - 42

SP - D789-D793

JO - Nucleic acids research

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WormBase 2014: New views of curated biology

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