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BioGRID

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BioGRID
Content
DescriptionBioGRID is a biomedical interaction repository with data compiled through comprehensive curation efforts.
Data types
captured		Protein Interactions, Genetic Interactions, Chemical Interactions, Post-Translational Modifications.
Organisms80
Contact
Research centerUniversité de Montréal, Princeton University, Mount Sinai Hospital (Toronto)
LaboratoryInstitut de Recherche en Immunologie et en Cancérologie, Lewis-Sigler Institute for Integrative Genomics, Lunenfeld-Tanenbaum Research Institute
AuthorsLorrie 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 citationStark & al. (2006)[1]
Access
Data formatCustom flat files, PSI-MI, MITAB
Websitethebiogrid.org
Download URLdownloads.thebiogrid.org/BioGRID
Web service URLYes - wiki.thebiogrid.org/doku.php/biogridrest
Tools
WebAdvanced search, integrated network viewer, custom downloads, bulk retrieval/download
Miscellaneous
VersioningYes
Data release
frequency		Monthly (4 Weeks)
Version4.2.193; 1 January 2021; 3 years ago (2021-01-01)
Curation policyYes - 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, chemical 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, FlyBase, WormBase, PomBase, and the Alliance of Genome Resources. The BioGRID is funded by the NIH and CIHR. BioGRID is an observer member of the International Molecular Exchange Consortium (IMEx).

History

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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 and the Lewis-Sigler Institute for Integrative Genomics at Princeton University. 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][7][8] to incorporate curated post-translational modification data,[9][10] 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,[9][10][11][12] data from comprehensive targeted curation projects,[13] and perform targeted scientific analysis.[14]

Curation of Genetic, Protein, and Chemical Interactions

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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 18 October 2020,[15] the BioGRID contains 1,928 million interactions as drawn from 63,083 publications that represent 71 model organisms. At the start of 2021 it already contained more than 2,0 million biological interactions, 29,023 chemical-protein interactions, and 506,485 post-translational modifications collectively curated from 75,988 publications for more than 80 species.[16] BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. 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).

Themed Curation Projects

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Due to the overwhelming size of published scientific literature containing human (Homo sapiens) gene, protein, and chemical interactions, BioGRID has taken a targeted, project-based approach to curation of human interaction data in manageable collections of high impact data. These themed curation projects represent central biological processes with disease relevance such as chromatin modification, autophagy, and the ubiquitin-proteasome system or diseases of interest including glioblastoma, Fanconi Anemia, and COVID-19. As of 18 October 2020,[15] BioGRID themed curation project efforts have resulted in the extraction of 424,631 interactions involving 2,361 proteins from more than 37,000 scientific articles.

Curation of Genome-Wide CRISPR Screens

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CRISPR-based genetic screens have now been reported in numerous publications that link gene function to cell viability, chemical and stress resistance, and other phenotypes. To increase the accessibility of CRISPR screen data and facilitate assignment of protein function, BioGRID has developed an embedded resource called the Open Repository of CRISPR Screens (ORCS)[7][15] to house and distribute manually curated, comprehensive collections of CRISPR screen datasets using Cas9 and other CRISPR nucleases. As of 18 October 2020,[15] BioGRID-ORCS contains more than 1,042 CRISPR screens curated from 114 publications representing more than 60,000 unique genes across three species human (Homo sapiens), fruit fly (Drosophila melanogaster), and house mouse (Mus musculus) in over 670 cell lines and 17 phenotypes.

Supported Organisms

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

Funding for BioGRID

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BioGRID is funded by grants from the National Institutes of Health and the Canadian Institutes of Health Research

References

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  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 (90001): 535–539. doi:10.1093/nar/gkj109. PMC 1347471. PMID 16381927.
  2. ^ a b Breitkreutz BJ, Stark C, Tyers M (Jan 2003). "The GRID: the General Repository for Interaction Datasets". Genome Biology. 4 (3): R23. doi:10.1186/gb-2003-4-3-r23. PMC 153463. PMID 12620108.
  3. ^ 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 (Database issue): 470–478. doi:10.1093/nar/gku1204. PMC 4383984. 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 (Database issue): 816–823. doi:10.1093/nar/gks1158. PMC 3531226. 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 (Database issue): 698–704. doi:10.1093/nar/gkq1116. PMC 3013707. 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 (Database issue): 637–640. doi:10.1093/nar/gkm1001. PMC 2238873. PMID 18000002.
  7. ^ a b Chatr-Aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K.; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris (2017-01-04). "The BioGRID interaction database: 2017 update". Nucleic Acids Research. 45 (D1): D369–D379. doi:10.1093/nar/gkw1102. ISSN 1362-4962. PMC 5210573. PMID 27980099.
  8. ^ Oughtred, Rose; Stark, Chris; Breitkreutz, Bobby-Joe; Rust, Jennifer; Boucher, Lorrie; Chang, Christie; Kolas, Nadine; O'Donnell, Lara; Leung, Genie; McAdam, Rochelle; Zhang, Frederick (2019-08-01). "The BioGRID interaction database: 2019 update". Nucleic Acids Research. 47 (D1): D529–D541. doi:10.1093/nar/gky1079. ISSN 1362-4962. PMC 6324058. PMID 30476227.
  9. ^ 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 2860897. PMID 20428315.
  10. ^ 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 3653121. PMID 23674503.
  11. ^ 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 3065694. PMID 21300700.
  12. ^ 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 153462. PMID 12620107.
  13. ^ 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 1561585. PMID 16762047.
  14. ^ 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. Bibcode:2010Sci...328.1043B. doi:10.1126/science.1176495. PMC 3983991. PMID 20489023.
  15. ^ a b c d Oughtred, Rose; Rust, Jennifer; Chang, Christie; Breitkreutz, Bobby-Joe; Stark, Chris; Willems, Andrew; Boucher, Lorrie; Leung, Genie; Kolas, Nadine; Zhang, Frederick; Dolma, Sonam (2020-10-18). "The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions". Protein Science. 30 (1): 187–200. doi:10.1002/pro.3978. ISSN 1469-896X. PMC 7737760. PMID 33070389.
  16. ^ "Build Statistics (4.2.193) - January 2021 | BioGRID". wiki.thebiogrid.org. Retrieved 2021-01-26.
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