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WormBase: a cross-species database for comparative genomics

T. W. Harris
2003 Nucleic Acids Research  
WormBase ( is a webaccessible central data repository for information about Caenorhabditis elegans and related nematodes.  ...  These advances have expanded WormBase beyond the obvious target audience of C. elegans researchers, to include researchers wishing to explore problems in functional and comparative genomics within the  ...  ACKNOWLEDGEMENTS WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute and the British  ... 
doi:10.1093/nar/gkg053 pmid:12519966 pmcid:PMC165500 fatcat:73j36qtk2fcobkvh263qweseae

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  
We provide a consistent and familiar user interface for each species at WormBase.  ...  WormBase objects referenced in WormBook chapters are cross-linked to their corresponding entries at WormBase.  ... 
doi:10.1093/nar/gkp952 pmid:19910365 pmcid:PMC2808986 fatcat:msx6exctxvfvnaurwn2fr4fd7a

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 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.  ...  New genomes Initially housing just the C. elegans genome, WormBase now has genomic sequences for seven Caenorhabditis species with the recent integration of C. angaria (9) , and C. sp. 11.  ... 
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 ( is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes.  ...  The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic  ...  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 (, 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  ...  More recently, the availability of the whole C.briggsae genome sequence (12) , in addition to that of C.elegans, has established WormBase as a platform for comparative genomics among the Caenorhabditides  ... 
doi:10.1093/nar/gki066 pmid:15608221 pmcid:PMC540020 fatcat:ffmlelkm4zcv3h5al6d7gsbbcq

Methods and strategies for gene structure curation in WormBase

G. W. Williams, P. A. Davis, A. S. Rogers, T. Bieri, P. Ozersky, J. Spieth
2011 Database: The Journal of Biological Databases and Curation  
The Caenorhabditis elegans genome sequence was published over a decade ago; this was the first published genome of a multi-cellular organism and now the WormBase project has had a decade of experience  ...  In one of its roles as a central repository for nematode biology, WormBase continues to refine the gene structure annotations using sequence similarity and other computational methods, as well as information  ...  The UWGC group uses it on other species in the WormBase database apart from C. elegans.  ... 
doi:10.1093/database/baq039 pmid:21543339 pmcid:PMC3092607 fatcat:nptcyaxhirhwpatcl6aylqeb5u

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 ( 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  ...  Comparative Genomics Other Nematode Genomes WormBase contains genomic data from many nematode species beyond C. elegans (http://  ... 
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.  ...  Although WormBase is largely a gene-centric database, it warehouses, in addition to genomic sequence and gene function curation, information about additional aspects of nematode biology, including anatomy  ... 
doi:10.1093/database/bas040 pmid:23160413 pmcid:PMC3500519 fatcat:xm263mzjpferrgyn4augokxkgm

Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

Gary Schindelman, Jolene S Fernandes, Carol A Bastiani, Karen Yook, Paul W Sternberg
2011 BMC Bioinformatics  
Conclusions: We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species comparisons within the nematode community.  ...  In the larger scientific community, the WPO will permit data integration, and interoperability across the different Model Organism Databases (MODs) and other biological databases.  ...  suggestions; Norie de la Cruz for his work on the phenotype ontology search tool and fellow curators at WormBase for their valuable input.  ... 
doi:10.1186/1471-2105-12-32 pmid:21261995 pmcid:PMC3039574 fatcat:j7nmqr5wirfxpnxd65zx3lfmay

Meta Analysis of Human AlzGene Database: Benefits and Limitations of Using C. elegans for the Study of Alzheimer's Disease and Co-morbid Conditions

Behrad Vahdati Nia, Christine Kang, Michelle G. Tran, Deborah Lee, Shin Murakami
2017 Frontiers in Genetics  
genes identified in the C. elegans database, WormBase.  ...  We also validated 680 of the AD genes as a unique gene from the AlzGene database, including 431 genes (63%) that are predicted to have orthologs in C. elegans.  ...  They, as Alzheimer's patients, have used their valuable time for comments and advice on the work. We also thank members of Murakami Laboratory for helpful discussion and comments on the manuscript.  ... 
doi:10.3389/fgene.2017.00055 pmid:28553317 pmcid:PMC5427079 fatcat:dk6xruu2hzg6zaamrsern2ojo4

RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects

K. C. Gunsalus
2004 Nucleic Acids Research  
RNA interference (RNAi) is being used in large-scale genomic studies as a rapid way to obtain in vivo functional information associated with speci®c genes.  ...  RNAiDB could serve as a model database for distributing and navigating in vivo functional information from large-scale systematic phenotypic analyses in different organisms.  ...  their experience with BioGraphics, and Lincoln Stein for his help with RNAiDB and ePCR and for authoring extremely useful open-source software for web and genome applications.  ... 
doi:10.1093/nar/gkh110 pmid:14681444 pmcid:PMC308844 fatcat:m54y25kvuzhbfhgzmndiyjq7we

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

Sabine P Schrimpf, Manuel Weiss, Lukas Reiter, Christian H Ahrens, Marko Jovanovic, Johan Malmström, Erich Brunner, Sonali Mohanty, Martin J Lercher, Peter E Hunziker, Ruedi Aebersold, Christian von Mering (+2 others)
2009 PLoS Biology  
Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster).  ...  This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins.  ...  Acknowledgments We thank Frank Potthast and Christian Panse for the database searches; Bernd Roschitzki, Mike Scott, Bertran Gerrits, and René Brunisholz for technical support; Ralph Schlapbach for access  ... 
doi:10.1371/journal.pbio.1000048 pmid:19260763 pmcid:PMC2650730 fatcat:q36mg362zbg3hhjjrq6kw2xphu

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.  ...  We advocate the use of C. elegans as a model to study helminth metabolism, a neglected area ready to advance.  ...  We thank all members of the Worm Biology Lab for helpful discussions (Institut Pasteur de Montevideo).  ... 
doi:10.1017/s0031182017002165 pmid:29208057 fatcat:atjsdg6ksndefpxjqx5djg4zfm

HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology

Ying-fu Zhong, Peter W. H. Holland
2011 Evolution & Development  
HomeoDB2 includes all homeobox loci from 10 animal genomes (human, mouse, chicken, frog, zebrafish, amphioxus, nematode, fruitfly, beetle, honeybee) plus tools for downloading sequences, comparing between  ...  Homeobox gene database (HomeoDB), a manually curated database of homeobox genes and their classification, has been well received since its release in 2008.  ...  ACKNOWLEDGMENTS This research was supported by a Marie Curie International Incoming Fellowship to YFZ within the 7th European Community Framework Programme.  ... 
doi:10.1111/j.1525-142x.2011.00513.x pmid:23016940 pmcid:PMC3399086 fatcat:dzz4cgpmknhevbbj3qwfz7yuby

WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp

L. Basten Snoek, K. Joeri Van der Velde, Danny Arends, Yang Li, Antje Beyer, Mark Elvin, Jasmin Fisher, Alex Hajnal, Michael O. Hengartner, Gino B. Poulin, Miriam Rodriguez, Tobias Schmid (+5 others)
2012 Nucleic Acids Research  
Here, we present WormQTL (http://www.wormqtl. org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp.  ...  ACKNOWLEDGEMENTS We thank Wormbase for being an easy accessible and versatile data source.  ...  We also thank Mark Sterken and Rita Volkers for helpful suggestions, Konrad Zych for graphics design and testing and many members of the C. elegans community for their comments and ideas.  ... 
doi:10.1093/nar/gks1124 pmid:23180786 pmcid:PMC3531126 fatcat:m4flp7y6ave7tdkeuhsvymoyc4
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