Cargando…

WormBase: a modern Model Organism Information Resource

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 face...

Descripción completa

Detalles Bibliográficos
Autores principales: Harris, Todd W, Arnaboldi, Valerio, Cain, Scott, Chan, Juancarlos, Chen, Wen J, Cho, Jaehyoung, Davis, Paul, Gao, Sibyl, Grove, Christian A, Kishore, Ranjana, Lee, Raymond Y N, Muller, Hans-Michael, Nakamura, Cecilia, Nuin, Paulo, Paulini, Michael, Raciti, Daniela, Rodgers, Faye H, Russell, Matthew, Schindelman, Gary, Auken, Kimberly V, Wang, Qinghua, Williams, Gary, Wright, Adam J, Yook, Karen, Howe, Kevin L, Schedl, Tim, Stein, Lincoln, Sternberg, Paul W
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145598/
https://www.ncbi.nlm.nih.gov/pubmed/31642470
http://dx.doi.org/10.1093/nar/gkz920
_version_ 1783520021837774848
author Harris, Todd W
Arnaboldi, Valerio
Cain, Scott
Chan, Juancarlos
Chen, Wen J
Cho, Jaehyoung
Davis, Paul
Gao, Sibyl
Grove, Christian A
Kishore, Ranjana
Lee, Raymond Y N
Muller, Hans-Michael
Nakamura, Cecilia
Nuin, Paulo
Paulini, Michael
Raciti, Daniela
Rodgers, Faye H
Russell, Matthew
Schindelman, Gary
Auken, Kimberly V
Wang, Qinghua
Williams, Gary
Wright, Adam J
Yook, Karen
Howe, Kevin L
Schedl, Tim
Stein, Lincoln
Sternberg, Paul W
author_facet Harris, Todd W
Arnaboldi, Valerio
Cain, Scott
Chan, Juancarlos
Chen, Wen J
Cho, Jaehyoung
Davis, Paul
Gao, Sibyl
Grove, Christian A
Kishore, Ranjana
Lee, Raymond Y N
Muller, Hans-Michael
Nakamura, Cecilia
Nuin, Paulo
Paulini, Michael
Raciti, Daniela
Rodgers, Faye H
Russell, Matthew
Schindelman, Gary
Auken, Kimberly V
Wang, Qinghua
Williams, Gary
Wright, Adam J
Yook, Karen
Howe, Kevin L
Schedl, Tim
Stein, Lincoln
Sternberg, Paul W
author_sort Harris, Todd W
collection PubMed
description 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.
format Online
Article
Text
id pubmed-7145598
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-71455982020-04-13 WormBase: a modern Model Organism Information Resource Harris, Todd W Arnaboldi, Valerio Cain, Scott Chan, Juancarlos Chen, Wen J Cho, Jaehyoung Davis, Paul Gao, Sibyl Grove, Christian A Kishore, Ranjana Lee, Raymond Y N Muller, Hans-Michael Nakamura, Cecilia Nuin, Paulo Paulini, Michael Raciti, Daniela Rodgers, Faye H Russell, Matthew Schindelman, Gary Auken, Kimberly V Wang, Qinghua Williams, Gary Wright, Adam J Yook, Karen Howe, Kevin L Schedl, Tim Stein, Lincoln Sternberg, Paul W Nucleic Acids Res Database Issue 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. Oxford University Press 2020-01-08 2019-10-23 /pmc/articles/PMC7145598/ /pubmed/31642470 http://dx.doi.org/10.1093/nar/gkz920 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Harris, Todd W
Arnaboldi, Valerio
Cain, Scott
Chan, Juancarlos
Chen, Wen J
Cho, Jaehyoung
Davis, Paul
Gao, Sibyl
Grove, Christian A
Kishore, Ranjana
Lee, Raymond Y N
Muller, Hans-Michael
Nakamura, Cecilia
Nuin, Paulo
Paulini, Michael
Raciti, Daniela
Rodgers, Faye H
Russell, Matthew
Schindelman, Gary
Auken, Kimberly V
Wang, Qinghua
Williams, Gary
Wright, Adam J
Yook, Karen
Howe, Kevin L
Schedl, Tim
Stein, Lincoln
Sternberg, Paul W
WormBase: a modern Model Organism Information Resource
title WormBase: a modern Model Organism Information Resource
title_full WormBase: a modern Model Organism Information Resource
title_fullStr WormBase: a modern Model Organism Information Resource
title_full_unstemmed WormBase: a modern Model Organism Information Resource
title_short WormBase: a modern Model Organism Information Resource
title_sort wormbase: a modern model organism information resource
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145598/
https://www.ncbi.nlm.nih.gov/pubmed/31642470
http://dx.doi.org/10.1093/nar/gkz920
work_keys_str_mv AT harristoddw wormbaseamodernmodelorganisminformationresource
AT arnaboldivalerio wormbaseamodernmodelorganisminformationresource
AT cainscott wormbaseamodernmodelorganisminformationresource
AT chanjuancarlos wormbaseamodernmodelorganisminformationresource
AT chenwenj wormbaseamodernmodelorganisminformationresource
AT chojaehyoung wormbaseamodernmodelorganisminformationresource
AT davispaul wormbaseamodernmodelorganisminformationresource
AT gaosibyl wormbaseamodernmodelorganisminformationresource
AT grovechristiana wormbaseamodernmodelorganisminformationresource
AT kishoreranjana wormbaseamodernmodelorganisminformationresource
AT leeraymondyn wormbaseamodernmodelorganisminformationresource
AT mullerhansmichael wormbaseamodernmodelorganisminformationresource
AT nakamuracecilia wormbaseamodernmodelorganisminformationresource
AT nuinpaulo wormbaseamodernmodelorganisminformationresource
AT paulinimichael wormbaseamodernmodelorganisminformationresource
AT racitidaniela wormbaseamodernmodelorganisminformationresource
AT rodgersfayeh wormbaseamodernmodelorganisminformationresource
AT russellmatthew wormbaseamodernmodelorganisminformationresource
AT schindelmangary wormbaseamodernmodelorganisminformationresource
AT aukenkimberlyv wormbaseamodernmodelorganisminformationresource
AT wangqinghua wormbaseamodernmodelorganisminformationresource
AT williamsgary wormbaseamodernmodelorganisminformationresource
AT wrightadamj wormbaseamodernmodelorganisminformationresource
AT yookkaren wormbaseamodernmodelorganisminformationresource
AT howekevinl wormbaseamodernmodelorganisminformationresource
AT schedltim wormbaseamodernmodelorganisminformationresource
AT steinlincoln wormbaseamodernmodelorganisminformationresource
AT sternbergpaulw wormbaseamodernmodelorganisminformationresource