BioGRID

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).

BioGRID
Content
DescriptionBioGRID 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.
Organisms71
Contact
Research centerUniversité de Montréal, Princeton University, Mount Sinai Hospital, University of Edinburgh
LaboratoryInstitut de Recherche en Immunologie et en Cancérologie, Lewis-Sigler Institute for Integrative Genomics, Lunenfeld-Tanenbaum Research Institute, Wellcome Trust Center for Cell Biology
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 URLthebiogrid.org/download.php
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)
Version3.4.165; 25 September 2018 (2018-09-25)
Curation policyYes - manual; Also focused curation efforts.
Bookmarkable
entities		Yes - both individual results and searches,

History

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

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. At the start of 2019 it already contained up to 1,6 million biological interactions from 55,809 publications for 71 species.[13] 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

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

Funding for BioGRID

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

gollark: You need to block the easy outcome of "no computation received" somehow, and if you do that then you'll either get the answer or bizarre failure modes.
gollark: Receive solution from the future, check if it's correct, if it is then send it back so it's received.
gollark: For problems which are easy to check and hard to solve.
gollark: If time travel requires "fixed history", then you can use the universe's built in paradox resolver magic thing to either do your computation for you, or cause bizarre failure modes.
gollark: Actually, it's even better.

References
  1. 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. 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. 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.
  8. 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.
  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 3065694. 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 153462. 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 1561585. 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. Bibcode:2010Sci...328.1043B. doi:10.1126/science.1176495. PMC 3983991. PMID 20489023.
  13. Oughtred, Rose; Stark, Chris; Breitkreutz, Bobby-Joe; Rust, Jennifer; Boucher, Lorrie; Chang, Christie; Kolas, Nadine; O’Donnell, Lara; Leung, Genie; McAdam, Rochelle; Zhang, Frederick; Dolma, Sonam; Willems, Andrew; Coulombe-Huntington, Jasmin; Chatr-aryamontri, Andrew; Dolinski, Kara; Tyers, Mike (8 January 2019). "The BioGRID interaction database: 2019 update". Nucleic Acids Research. 47 (Database issue): D529–D541. doi:10.1093/nar/gky1079. ISSN 0305-1048. PMC 6324058. PMID 30476227.
This article is issued from Wikipedia. The text is licensed under Creative Commons - Attribution - Sharealike. Additional terms may apply for the media files.