WormBase: A modern Model Organism Information Resource

Todd W. Harris; Valerio Arnaboldi; Scott Cain; Juancarlos Chan; Wen J. Chen; Jaehyoung Cho; Paul Davis; Sibyl Gao; Christian A. Grove; Ranjana Kishore; Raymond Y.N. Lee; Hans Michael Muller; Cecilia Nakamura; Paulo Nuin; Michael Paulini; Daniela Raciti; Faye H. Rodgers; Matthew Russell; Gary Schindelman; Kimberly V. Auken; Qinghua Wang; Gary Williams; Adam J. Wright; Karen Yook; Kevin L. Howe; Tim Schedl; Lincoln Stein; Paul W. Sternberg

doi:10.1093/nar/gkz920

WormBase: A modern Model Organism Information Resource

Todd W. Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J. Chen, Jaehyoung Cho, Paul Davis, Sibyl Gao, Christian A. Grove, Ranjana Kishore, Raymond Y.N. Lee, Hans Michael Muller, Cecilia Nakamura, Paulo Nuin, Michael Paulini, Daniela Raciti, Faye H. Rodgers, Matthew Russell, Gary Schindelman, Kimberly V. AukenQinghua Wang, Gary Williams, Adam J. Wright, Karen Yook, Kevin L. Howe, Tim Schedl, Lincoln Stein, Paul W. Sternberg

Research output: Contribution to journal › Article › peer-review

197 Scopus citations

Abstract

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.

Original language	English
Pages (from-to)	D762-D767
Journal	Nucleic acids research
Volume	48
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkz920
State	Published - Jan 1 2020

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Harris, T. W., Arnaboldi, V., Cain, S., Chan, J., Chen, W. J., Cho, J., Davis, P., Gao, S., Grove, C. A., Kishore, R., Lee, R. Y. N., Muller, H. M., Nakamura, C., Nuin, P., Paulini, M., Raciti, D., Rodgers, F. H., Russell, M., Schindelman, G., ... Sternberg, P. W. (2020). WormBase: A modern Model Organism Information Resource. Nucleic acids research, 48(D1), D762-D767. https://doi.org/10.1093/nar/gkz920

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title = "WormBase: A modern Model Organism Information Resource",

abstract = "WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.",

author = "Harris, {Todd W.} and Valerio Arnaboldi and Scott Cain and Juancarlos Chan and Chen, {Wen J.} and Jaehyoung Cho and Paul Davis and Sibyl Gao and Grove, {Christian A.} and Ranjana Kishore and Lee, {Raymond Y.N.} and Muller, {Hans Michael} and Cecilia Nakamura and Paulo Nuin and Michael Paulini and Daniela Raciti and Rodgers, {Faye H.} and Matthew Russell and Gary Schindelman and Auken, {Kimberly V.} and Qinghua Wang and Gary Williams and Wright, {Adam J.} and Karen Yook and Howe, {Kevin L.} and Tim Schedl and Lincoln Stein and Sternberg, {Paul W.}",

note = "Publisher Copyright: {\textcopyright} 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2020",

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doi = "10.1093/nar/gkz920",

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Harris, TW, Arnaboldi, V, Cain, S, Chan, J, Chen, WJ, Cho, J, Davis, P, Gao, S, Grove, CA, Kishore, R, Lee, RYN, Muller, HM, Nakamura, C, Nuin, P, Paulini, M, Raciti, D, Rodgers, FH, Russell, M, Schindelman, G, Auken, KV, Wang, Q, Williams, G, Wright, AJ, Yook, K, Howe, KL, Schedl, T, Stein, L & Sternberg, PW 2020, 'WormBase: A modern Model Organism Information Resource', Nucleic acids research, vol. 48, no. D1, pp. D762-D767. https://doi.org/10.1093/nar/gkz920

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AU - Harris, Todd W.

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AU - Cain, Scott

AU - Chan, Juancarlos

AU - Chen, Wen J.

AU - Cho, Jaehyoung

AU - Davis, Paul

AU - Gao, Sibyl

AU - Grove, Christian A.

AU - Kishore, Ranjana

AU - Lee, Raymond Y.N.

AU - Muller, Hans Michael

AU - Nakamura, Cecilia

AU - Nuin, Paulo

AU - Paulini, Michael

AU - Raciti, Daniela

AU - Rodgers, Faye H.

AU - Russell, Matthew

AU - Schindelman, Gary

AU - Auken, Kimberly V.

AU - Wang, Qinghua

AU - Williams, Gary

AU - Wright, Adam J.

AU - Yook, Karen

AU - Howe, Kevin L.

AU - Schedl, Tim

AU - Stein, Lincoln

AU - Sternberg, Paul W.

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ER -

WormBase: A modern Model Organism Information Resource

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