BioGRID
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| BioGRID | |
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| Developer: | Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Mike Tyers |
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| Latest release: | 2.0.19 / |
| OS: | MS-Windows, Unix, Mac, MS-Windows |
| Use: | Bioinformatics tool |
| Licence: | Free |
| Website: | [1] |
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.
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[edit] 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.
[edit] Abstract
Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at [2]. BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.
[edit] Supported Organisms
The following organisms are currently supported within the BioGRID, but not all may contain interactions in the most recent build:
- Homo sapiens
- Drosophila melanogaster
- Mus musculus
- Caenorhabditis elegans
- Rattus norvegicus
- Danio rerio
- Saccharomyces cerevisiae
- Schizosaccharomyces pombe
- Takifugu rubripes
- Arabidopsis thaliana
- Bos taurus
- Canis familiaris
- Xenopus laevis
[edit] References
- Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, and Mike Tyers. BioGRID: A General Repository for Interaction Datasets. Nucleic Acids Res. Jan1;34:D535-9.
- Bobby-Joe Breitkreutz, Chris Stark, and Mike Tyers. The GRID: The General Repository for Interaction Datasets. Genome Biology 2003;3(12). PDF.
