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'''WormBase''' is an online [[bioinformatics]] [[database]] of the biology and genome of the [[model organism]] ''[[Caenorhabditis elegans|Caenorhabditis elegans]]'' and related nematodes<ref name="Harris">{{cite journal
#REDIRECT [[Wormbase]] {{R from other capitalisation}}
| last = Harris
| first = TW
| authorlink =
| coauthors = et al.
| title = WormBase: a comprehensive resource for nematode research.
| journal = Nucleic Acids Res
| volume = 38
| issue =
| pages = D463-7
| date = 2009-11-12
| url = http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D463
| id =
| doi = 10.1093/nar/gkp952
| accessdate = 2010-04-26}}</ref>
. It is used by the ''C. elegans'' research community both as an information resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis.

WormBase is one of the organizations participating in the [[Generic Model Organism Database]] (GMOD) project.

==Contents==

WormBase comprises the following main data sets:

*The annotated genomes of ''[[Caenorhabditis elegans|C. elegans]]'', ''[[Caenorhabditis briggsae|C. briggsae]]'', and ''[[Caenorhabditis remanei|C. remanei]]'';
*Hand-curated annotations describing the function of ~20,000 ''C. elegans'' genes;
*Gene families;
*Comprehensive information on mutant alleles and their phenotypes;
*Whole-genome [[RNAi]] (''RNA interference'') screens;
*Genetic maps, markers and polymorphisms;
*The ''C. elegans'' physical map;
*Gene expression profiles (stage, tissue and cell) from microarrays, SAGE analysis and GFP promoter fusions;
*The complete cell lineage of the worm;
*The wiring diagram of the worm nervous system;
*Protein-protein interaction [[Interactome]] data;
*Genetic regulatory relationships;
*Details of intra- and inter-specific sequence [[homology (biology)|homologies]] (with links to other model organism databases).

In addition, WormBase contains an up-to-date searchable bibliography of ''C. elegans'' research and is linked to the [[WormBook]] project.

==Tools==
WormBase offers many ways of searching and retrieving data from the database:

* [http://www.wormbase.org/biomart/martview WormMart] - a tool for retrieving varied information on many genes (or the sequences of those genes). This is the WormBase implementation of [http://www.biomart.org BioMart]<ref>http://www.wormbase.org/wiki/index.php/Data_mining:WormMart</ref>.
** [http://www.youtube.com/watch?v=BrbMAbxUseo WormMart Tutorial]
* [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ Genome Browser] - browse the genes of ''C. elegans'' (and other species) in their genomic context
* [http://www.textpresso.org/cgi-bin/wb/tfw.cgi TextPresso] - a search tool that queries published ''C. elegans'' literature (including meeting abstracts)

==WormBase Management==
WormBase is a collaboration among the [[Wellcome Trust Sanger Institute]], [http://www.oicr.on.ca Ontario Institute for Cancer Research], [[Washington University in St. Louis]], and the [[California Institute of Technology]]. It is supported by grants from the [[National Institutes of Health]] and the [[Medical Research Council (UK)|British Medical Research Council]] .<ref>http://www.wormbase.org/wiki/index.php/WormBaseWiki:Copyrights</ref>

==References==
{{reflist}}

==External links==
* [http://www.wormbase.org/ WormBase]
* [http://www.wormbook.org/ The WormBook website], the online textbook companion to WormBase.
* [http://www.textpresso.org/ Textpresso], search engine for C. elegans and other biological literature.
* [http://www.wormbase.org/wiki/index.php/Main_Page WormBase Wiki]
* [http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/release_notes.txt Release notes], details of the latest WormBase release
* [http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=16381915 WormBase: better software, richer content] Nucleic Acids Research article describing WormBase (2006).

[[Category:Bioinformatics]]
[[Category:Cell biology]]
[[Category:WikiProject Molecular and Cellular Biology articles]]
[[Category:Caenorhabditis elegans]]
[[Category:Proteins]]
[[Category:Developmental biology]]
[[Category:Model organism databases]]

Revision as of 13:13, 27 April 2010

WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes[1] . It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. The database is constantly updated and new versions are released on a monthly basis.

WormBase is one of the organizations participating in the Generic Model Organism Database (GMOD) project.

Contents

WormBase comprises the following main data sets:

  • The annotated genomes of C. elegans, C. briggsae, and C. remanei;
  • Hand-curated annotations describing the function of ~20,000 C. elegans genes;
  • Gene families;
  • Comprehensive information on mutant alleles and their phenotypes;
  • Whole-genome RNAi (RNA interference) screens;
  • Genetic maps, markers and polymorphisms;
  • The C. elegans physical map;
  • Gene expression profiles (stage, tissue and cell) from microarrays, SAGE analysis and GFP promoter fusions;
  • The complete cell lineage of the worm;
  • The wiring diagram of the worm nervous system;
  • Protein-protein interaction Interactome data;
  • Genetic regulatory relationships;
  • Details of intra- and inter-specific sequence homologies (with links to other model organism databases).

In addition, WormBase contains an up-to-date searchable bibliography of C. elegans research and is linked to the WormBook project.

Tools

WormBase offers many ways of searching and retrieving data from the database:

  • WormMart - a tool for retrieving varied information on many genes (or the sequences of those genes). This is the WormBase implementation of BioMart[2].
  • Genome Browser - browse the genes of C. elegans (and other species) in their genomic context
  • TextPresso - a search tool that queries published C. elegans literature (including meeting abstracts)

WormBase Management

WormBase is a collaboration among the Wellcome Trust Sanger Institute, Ontario Institute for Cancer Research, Washington University in St. Louis, and the California Institute of Technology. It is supported by grants from the National Institutes of Health and the British Medical Research Council .[3]

References

  1. ^ Harris, TW (2009-11-12). "WormBase: a comprehensive resource for nematode research". Nucleic Acids Res. 38: D463-7. doi:10.1093/nar/gkp952. Retrieved 2010-04-26. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  2. ^ http://www.wormbase.org/wiki/index.php/Data_mining:WormMart
  3. ^ http://www.wormbase.org/wiki/index.php/WormBaseWiki:Copyrights
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