BioGRID

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital. It strives to provide a comprehensive resource of protein–protein interactions for all major species while attempting to remove redundancy to create a single mapping of protein interactions. Users of The BioGRID can search for their protein of interest and retrieve annotation, as well as physical and genetic interaction data as reported, by the primary literature and compiled by in house large scale curation efforts. The BioGRID is hosted in Toronto, Ontario, Canada and is partnered with the Saccharomyces Genome Database.

History

The BioGRID was originally published and released as simply the General Repository for Interaction Datasets but was later renamed to the BioGRID in order to more concisely describe the project, and help distinguish it from several unrelated projects with a similar name. Originally separated into organism specific databases, the newest version now provides a unified front end allowing for searches across several organisms simultaneously.

Abstract

The Biological General Repository for Interaction Datasets (BioGRID) database (http://www.thebiogrid.org) was developed to house and distribute collections of protein and genetic interactions from major model organism species. BioGRID currently contains over 198 000 interactions from six different species, as derived from both high-throughput studies and conventional focused studies. Through comprehensive curation efforts, BioGRID now includes a virtually complete set of interactions reported to date in the primary literature for both the budding yeast "Saccharomyces cerevisiae" and the fission yeast "Schizosaccharomyces pombe". A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management system to coordinate curation across different locations. The BioGRID provides interaction data with monthly updates to Saccharomyces Genome Database, Flybase and Entrez Gene. Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction.

upported Organisms

The following organisms are currently supported within the BioGRID, but not all may contain interactions in the most recent build:
* Homo sapiens - Human
* Drosophila melanogaster - Fruit Fly
* Mus musculus - House Mouse
* Caenorhabditis elegans - Nematode Worm
* Rattus norvegicus - Norway Rat
* Danio rerio - Zebrafish
* Saccharomyces cerevisiae - Budding Yeast
* Schizosaccharomyces pombe - Fission Yeast
* Takifugu rubripes - Torafugu
* Arabidopsis thaliana - Thale Cress
* Bos taurus - Cow
* Canis familiaris - Dog
* Xenopus laevis - African Clawed Frog
* Bacillus subtilis
* Escherichia coli
* Oryza sativa - Rice
* Gallus gallus - Chicken
* Pan troglodytes - Chimpanzee
* Equus caballus - Horse
* Macaca mulatta - Rhesus Monkey
* Nematostella vectensis - Starlet Sea Anemone
* Strongylocentrotus purpuratus - Purple Sea Urchin

References

* Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael Livstone, Rose Oughtred, Daniel Lackner, Jurg Bähler, Valerie Wood, Kara Dolinski and Mike Tyers. The BioGRID Interaction Database: 2008 Update [http://nar.oxfordjournals.org/ Nucleic Acids Res] . 2008 Jan;36:D637-40. [http://nar.oxfordjournals.org/cgi/reprint/36/suppl_1/D637.pdf PDF]
* Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, and Mike Tyers. BioGRID: A General Repository for Interaction Datasets. [http://nar.oxfordjournals.org/ Nucleic Acids Res] . 2006 Jan1;34:D535-9.
* Bobby-Joe Breitkreutz, Chris Stark, and Mike Tyers. The GRID: The General Repository for Interaction Datasets. [http://www.genomebiology.com Genome Biology] 2003;3(12). [http://genomebiology.com/content/pdf/gb-2002-3-12-preprint0013.pdf PDF] .

External links

* [http://www.thebiogrid.org BioGRID: Homepage]
* [http://www.mshri.on.ca/tyers Mike Tyers Lab Homepage]
* [http://www.mshri.on.ca/ Samuel Lunenfeld Research Institute]
* [http://www.flybase.org/ Flybase]
* [http://www.yeastgenome.org/ The Saccharomyces Genome Database]
* [http://www.geneontology.org/ Gene Ontology]
* [http://www.genedb.org/ GeneDB]