BioGRID

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BioGRID
Biogrid logo.png
Content
Description BioGRID is an online biological interaction repository with data compiled through comprehensive curation efforts.
Data types
captured
Protein Interactions, Genetic Interactions, Chemical Interactions, Post-Translational Modifications.
Organisms All
Contact
Research center Université de Montréal, Princeton University, Mount Sinai Hospital, University of Edinburgh
Laboratory Institut de Recherche en Immunologie et en Cancérologie, Lewis-Sigler Institute for Integrative Genomics, Lunenfeld-Tanenbaum Research Institute, Wellcome Trust Center for Cell Biology
Authors Lorrie Boucher, Ashton Breitkreutz, Bobby-Joe Breitkreutz, Christie Chang, Andrew Chatr-Aryamontri, Kara Dolinski, Sven Heinicke, Nadine Kolas, Lara O'Donnell, Sara Oster, Rose Oughtred, Jennifer Rust, Adnane Sellam, Chris Stark, Jean Tang, Chandra Theesfeld, Mike Tyers.
Primary citation Stark & al. (2006)[1]
Access
Data format Custom flat files, PSI-MI, MITAB
Website thebiogrid.org
Download URL thebiogrid.org/download.php
Web service URL Yes - wiki.thebiogrid.org/doku.php/biogridrest
Tools
Web Advanced search, integrated network viewer, custom downloads, bulk retrieval/download
Miscellaneous
Versioning Yes
Data release
frequency
Monthly (4 Weeks)
Version 3.4.125; 1 June 2015; 23 months ago (2015-06-01)
Curation policy Yes - manual; Also focused curation efforts.
Bookmarkable
entities
Yes - both individual results and searches,

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID)[2] by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital. It strives to provide a comprehensive curated resource for all major model organism species while attempting to remove redundancy to create a single mapping of data. Users of The BioGRID can search for their protein or publication of interest and retrieve annotation, as well as curated 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 Dallas, Texas, United States and is partnered with the Saccharomyces Genome Database. The BioGRID is funded by the BBSRC, NIH, and CIHR. BioGRID is a member of the International Molecular Exchange Consortium (IMEx).

History[edit]

The BioGRID was originally published and released as simply the General Repository for Interaction Datasets[2] but was later renamed to the BioGRID[1] in order to more concisely describe the project, and help distinguish it from several GRID Computing 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. The BioGRID was developed initially as a project at the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital but has since expanded to include teams at the Institut de Recherche en Immunologie et en Cancérologie at the Université de Montréal, the Lewis-Sigler Institute for Integrative Genomics at Princeton University, and the Wellcome Trust Center for Cell Biology at the University of Edinburgh. The BioGRID's original focus was on curation of binary protein-protein and genetic interactions, but has expanded over several updates[1][3][4][5][6] to incorporate curated post-translational modification data,[7][8] chemical interaction data, and complex multi-gene/protein interactions. Moreover, on a monthly basis, the BioGRID continues to expand curated data and also develop and release new tools,[7][8][9][10] data from comprehensive targeted curation projects,[11] and perform targeted scientific analysis.[12]

Abstract[edit]

The Biological General Repository for Interaction Datasets (BioGRID) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of 1 September 2014,[3] the BioGRID contains 749,912 interactions as drawn from 43,149 publications that represent 30 model organisms. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control. Through comprehensive curation efforts, BioGRID now includes a virtually complete set of interactions reported to date in the primary literature for budding yeast (Saccharomyces cerevisiae), thale cress (Arabidopsis thaliana), and fission yeast (Schizosaccharomyces pombe).

Supported Organisms[edit]

The following organisms are currently supported within the BioGRID, and each has curated interaction data available according to the latest statistics.

Funding for BioGRID[edit]

BioGRID is funded by grants from the National Institutes of Health, Canadian Institutes of Health Research, and the Biotechnology and Biological Sciences Research Council.

References[edit]

  1. ^ a b c Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (Jan 2006). "BioGRID: A General Repository for Interaction Datasets". Nucleic Acids Research. 34: 535–539. doi:10.1093/nar/gkj109. PMC 1347471Freely accessible. PMID 16381927. 
  2. ^ a b Breitkreutz BJ, Stark C, Tyers M (Jan 2003). "The GRID: the General Repository for Interaction Datasets.". Genome Biology. 4: R23. doi:10.1186/gb-2003-4-3-r23. PMC 153463Freely accessible. PMID 12620108. 
  3. ^ a b Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M (Jan 2015). "The BioGRID interaction database: 2015 update.". Nucleic Acids Research. 43: 470–478. doi:10.1093/nar/gku1204. PMC 4383984Freely accessible. PMID 25428363. 
  4. ^ Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O'Donnell L, Reguly T, Breitkreutz A, Sellam A, Chen D, Chang C, Rust JM, Livstone MS, Oughtred R, Dolinski K, Tyers M (Jan 2013). "The BioGRID interaction database: 2013 update.". Nucleic Acids Research. 41: 816–823. doi:10.1093/nar/gks1158. PMC 3531226Freely accessible. PMID 23203989. 
  5. ^ Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M (Jan 2011). "The BioGRID Interaction Database: 2011 update.". Nucleic Acids Research. 39: 698–704. doi:10.1093/nar/gkq1116. PMC 3013707Freely accessible. PMID 21071413. 
  6. ^ Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M (Jan 2008). "The BioGRID Interaction Database: 2008 update.". Nucleic Acids Research. 36: 637–640. doi:10.1093/nar/gkm1001. PMC 2238873Freely accessible. PMID 18000002. 
  7. ^ a b Stark C, Ting-Cheng Su, Breitkreutz A, Lourenco P, Dahabieh M, Breitkreutz BJ, Tyers M, Sadowski I (Jan 2010). "PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.". Database. 2010: bap026. doi:10.1093/database/bap026. PMC 2860897Freely accessible. PMID 20428315. 
  8. ^ a b Sadowski I, Breitkreutz BJ, Stark C, Su TC, Dahabieh M, Raithatha S, Bernhard W, Oughtred R, Dolinski K, Barreto K, Tyers M (May 2013). "The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.". Database. 2013: bat026. doi:10.1093/database/bat026. PMC 3653121Freely accessible. PMID 23674503. 
  9. ^ Winter AG, Wildenhain J, Tyers M (April 2011). "BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID.". Bioinformatics. 27 (7): 1043–1044. doi:10.1093/bioinformatics/btr062. PMC 3065694Freely accessible. PMID 21300700. 
  10. ^ Breitkreutz BJ, Stark C, Tyers M (January 2003). "Osprey: a network visualization system.". Genome Biology. 4 (3): R22. doi:10.1186/gb-2003-4-3-r22. PMC 153462Freely accessible. PMID 12620107. 
  11. ^ Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M (2006). "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.". The Journal of Biological Chemistry. 5 (4): 11. doi:10.1186/jbiol36. PMC 1561585Freely accessible. PMID 16762047. 
  12. ^ Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M (May 2010). "A global protein kinase and phosphatase interaction network in yeast.". Science. 328 (5981): 1043–1046. doi:10.1126/science.1176495. PMC 3983991Freely accessible. PMID 20489023. 

External links[edit]