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WormBase: a comprehensive resource for nematode research

Todd W. Harris, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Juancarlos Chan, Wen J. Chen, Norie De La Cruz, Paul Davis, Margaret Duesbury, Ruihua Fang, Jolene Fernandes, Michael Han (+20 others)
2009 Nucleic Acids Research  
ABSTRACT WormBase (http://www.wormbase.org) is a central data repository for nematode biology.  ...  INTEGRATION WITH THIRD-PARTY RESOURCES Although the data housed at WormBase is extensive, it is not comprehensive.  ... 
doi:10.1093/nar/gkp952 pmid:19910365 pmcid:PMC2808986 fatcat:msx6exctxvfvnaurwn2fr4fd7a

WormBase 2017: molting into a new stage

Raymond Y N Lee, Kevin L Howe, Todd W Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J Chen, Paul Davis, Sibyl Gao, Christian Grove, Ranjana Kishore, Hans-Michael Muller (+18 others)
2017 Nucleic Acids Research  
WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide.  ...  To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive  ...  INTRODUCTION WormBase is a critically important public information resource for nematode research.  ... 
doi:10.1093/nar/gkx998 pmid:29069413 pmcid:PMC5753391 fatcat:5rholx7nqvaurox74fnyrulgs4

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 (+21 others)
2013 Nucleic Acids Research  
Researchers who come to the WormBase Web site with a particular goal of understanding how nematode research has informed a particular field of study are now able to explore WormBase data from a perspective  ...  Working in collaboration with the filariasis community via FR3 (NIAID Filariasis Research Reagent Resource Center), targets for manual curation were identified based on their likely importance to the research  ... 
doi:10.1093/nar/gkt1063 pmid:24194605 pmcid:PMC3965043 fatcat:lh2mkgbydvfwrdngdv7nz3icme

WormBase 2012: more genomes, more data, new website

K. Yook, T. W. Harris, T. Bieri, A. Cabunoc, J. Chan, W. J. Chen, P. Davis, N. de la Cruz, A. Duong, R. Fang, U. Ganesan, C. Grove (+27 others)
2011 Nucleic Acids Research  
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  ...  Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing.  ...  INTRODUCTION Caenorhabditis elegans is a millimeter long, free-living, soil nematode used as a model organism for biology research for nearly four decades [(1,2) ; http://www.wormbook.org].  ... 
doi:10.1093/nar/gkr954 pmid:22067452 pmcid:PMC3245152 fatcat:4jkq3undtzc6lporuvo3nteium

WormBase 2016: expanding to enable helminth genomic research

Kevin L. Howe, Bruce J. Bolt, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Thomas Down, Sibyl Gao, Christian Grove, Todd W. Harris, Ranjana Kishore (+22 others)
2015 Nucleic Acids Research  
WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes.  ...  WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.  ...  ACKNOWLEDGEMENTS After many years working closely with WormBase as the guardian and authority for C. elegans genetic nomenclature, Jonathan Hodgkin has now stepped down from this role.  ... 
doi:10.1093/nar/gkv1217 pmid:26578572 pmcid:PMC4702863 fatcat:h3yxwojkojgszivof7ahs6fprq

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics

N. Chen
2004 Nucleic Acids Research  
WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth.  ...  Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. To accommodate this  ...  evolution from a data repository into a resource for all biologists to use in order to maximize the value of model organism research in C.elegans and its relatives.  ... 
doi:10.1093/nar/gki066 pmid:15608221 pmcid:PMC540020 fatcat:ffmlelkm4zcv3h5al6d7gsbbcq

Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes [chapter]

Christian Grove, Scott Cain, Wen J. Chen, Paul Davis, Todd Harris, Kevin L. Howe, Ranjana Kishore, Raymond Lee, Michael Paulini, Daniela Raciti, Mary Ann Tuli, Kimberly Van Auken (+1 others)
2018 Msphere  
WormBase (www.wormbase.org) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes.  ...  As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to  ...  Community Resources WormBase offers a number of services to support the C. elegans research community.  ... 
doi:10.1007/978-1-4939-7737-6_14 pmid:29761466 fatcat:pmvjwlblwrf6fkwid5fm272sfq

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

K. Van Auken, P. Fey, T. Z. Berardini, R. Dodson, L. Cooper, D. Li, J. Chan, Y. Li, S. Basu, H.-M. Muller, R. Chisholm, E. Huala (+1 others)
2012 Database: The Journal of Biological Databases and Curation  
Wimpfheimer for assistance with the figures. The members of the WormBase Consortium are M. Berriman and R. Durbin  ...  Arighi for advice and support regarding the Task III evaluation.  ...  WormBase (http://www.wormbase.org) is a model organism database that curates data about Caenorhabditis elegans and other nematodes (4) .  ... 
doi:10.1093/database/bas040 pmid:23160413 pmcid:PMC3500519 fatcat:xm263mzjpferrgyn4augokxkgm

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

2020 Database: The Journal of Biological Databases and Curation  
WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline.  ...  The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed curation  ...  We also thank Gary Ruvkun for the permission to use his name in Figure 3 .  ... 
doi:10.1093/database/baaa006 pmid:32185395 pmcid:PMC7078066 fatcat:rqgg4d73ufb5xmkusxfyhj6tzi

Unraveling worm biology in the post-genomic era

Chang-Su Lim
2001 Genome Biology  
Many international biologists and bioinformaticians contribute to WormBase. It is the most comprehensive site for genomic information in C. elegans and contains a vast amount of information.  ...  Best feature It is fantastic that one can simply navigate around a comprehensive resource of biological information on C. elegans, including genomics.  ... 
doi:10.1186/gb-2001-3-1-reports2005 fatcat:s5d54jwtvnfhhkjedc42szzqly

Caenorhabditis elegans: nature and nurture gift to nematode parasitologists

Gustavo Salinas, Gastón Risi
2017 Parasitology  
How emerging technologies being used in C. elegans can pave the way for parasitic nematode research is discussed.  ...  The use of C. elegans relating to parasitic nematodes from a basic biology standpoint or an applied perspective has increased in recent years.  ...  We thank all members of the Worm Biology Lab for helpful discussions (Institut Pasteur de Montevideo).  ... 
doi:10.1017/s0031182017002165 pmid:29208057 fatcat:atjsdg6ksndefpxjqx5djg4zfm

WormBook: the online review of Caenorhabditis elegans biology

L. R. Girard, T. J. Fiedler, T. W. Harris, F. Carvalho, I. Antoshechkin, M. Han, P. W. Sternberg, L. D. Stein, M. Chalfie
2007 Nucleic Acids Research  
WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field.  ...  WormBook also serves as the text companion to WormBase, the C.elegans model organism database.  ...  Funding for WormBook has been provided by a grant to WormBase from the US National Human Genome Research Institute (P41 HG02223), the Genetics Society, the Society for Developmental Biology, as well as  ... 
doi:10.1093/nar/gkl894 pmid:17099225 pmcid:PMC1669767 fatcat:yqijfizk2ngnhfxn73l6mlffg4

Toward 959 nematode genomes

Sujai Kumar, Georgios Koutsovoulos, Gaganjot Kaur, Mark Blaxter
2012 Worm  
goals of any nematode research program a less daunting prospect.  ...  The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model  ...  K. is funded by a School of Biological Sciences PhD studentship and the Overseas Research Student Awards Scheme at the University of Edinburgh; G.  ... 
doi:10.4161/worm.19046 pmid:24058822 pmcid:PMC3670170 fatcat:bnsl3sgtx5bxnelky6lnvfccui

Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes

T. Wylie
2004 Nucleic Acids Research  
Nematode.net (www.nematode.net) is a web accessible resource for investigating gene sequences from nematode genomes.  ...  Nematodes or roundworms are members of an ancient phylum that accounts for perhaps four out of every five individual animals in the world ( 1 ).  ...  of medical and economic importance as a route toward research on new anthelmintic drugs, vaccines, safe pesticides and resistant plants.  ... 
doi:10.1093/nar/gkh010 pmid:14681448 pmcid:PMC308745 fatcat:alqmlkbvfng3zm36kcgfknephu

Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data

J. Martin, S. Abubucker, E. Heizer, C. M. Taylor, M. Mitreva
2011 Nucleic Acids Research  
Nematode.net (http://nematode.net) has been a publicly available resource for studying nematodes for over a decade.  ...  Organism-centric portals containing dynamically generated data are available for over 56 different nematode species.  ...  We would like to thank Gaia Remerowski for technical advice and John Spieth, who heads the Wormbase efforts at the TGI.  ... 
doi:10.1093/nar/gkr1194 pmid:22139919 pmcid:PMC3245159 fatcat:3cg4tlli5ree3lmiz54chz5ngi
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