BioGRID

The Biological General Repository for

Interaction Datasets (BioGRID) is a curated
BioGRID
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 Content
organism species while attempting to remove Description BioGRID is a biomedical
redundancy to create a single mapping of data. interaction repository with data
Users of The BioGRID can search for their protein, compiled through
chemical or publication of interest and retrieve
comprehensive curation
annotation, as well as curated data as reported, by
efforts.
the primary literature and compiled by in house
large-scale curation efforts. The BioGRID is hosted Data types Protein Interactions, Genetic
in Toronto, Ontario, Canada and Dallas, Texas, captured Interactions, Chemical
United States and is partnered with the Interactions, Post-
Saccharomyces Genome Database, FlyBase, Translational Modifications.
WormBase, PomBase, and the Alliance of Genome
Organisms 80
Resources. The BioGRID is funded by the NIH and
CIHR. BioGRID is an observer member of the Contact
International Molecular Exchange Consortium (http Research center Université de Montréal,
s://imex.sourceforge.net/) (IMEx).
Princeton University, Mount
Sinai Hospital (Toronto)
History Laboratory Institut de Recherche en
Immunologie et en
The BioGRID was originally published and
Cancérologie, Lewis-Sigler
released as simply the General Repository for
Institute for Integrative
Interaction Datasets[2] but was later renamed to the
Genomics, Lunenfeld-
BioGRID[1] in order to more concisely describe the
Tanenbaum Research Institute
project, and help distinguish it from several GRID
Computing projects with a similar name. Originally Authors Lorrie Boucher, Ashton
separated into organism specific databases, the Breitkreutz, Bobby-Joe
newest version now provides a unified front end Breitkreutz, Christie Chang,
allowing for searches across several organisms Andrew Chatr-Aryamontri,
simultaneously. The BioGRID was developed Kara Dolinski, Sven Heinicke,
initially as a project at the Lunenfeld-Tanenbaum
Nadine Kolas, Lara O'Donnell,
Research Institute at Mount Sinai Hospital but has
Sara Oster, Rose Oughtred,
since expanded to include teams at the Institut de
Recherche en Immunologie et en Cancérologie at Jennifer Rust, Adnane Sellam,
the Université de Montréal and the Lewis-Sigler Chris Stark, Jean Tang,
Institute for Integrative Genomics at Princeton
University. The BioGRID's original focus was on Chandra Theesfeld, Mike
curation of binary protein-protein and genetic Tyers.
interactions, but has expanded over several
Primary citation Stark & al. (2006)[1]
updates[1][3][4][5][6][7][8] to incorporate curated post-
translational modification data,[9][10] chemical Access
interaction data, and complex multi-gene/protein Data format Custom flat files, PSI-MI,
interactions. Moreover, on a monthly basis, the MITAB
BioGRID continues to expand curated data and also
Website thebiogrid.org (https://thebiogr
develop and release new tools,[9][10][11][12] data
id.org)
from comprehensive targeted curation projects,[13]
and perform targeted scientific analysis.[14] Download URL downloads.thebiogrid.org
/BioGRID (https://downloads.t
hebiogrid.org/BioGRID)
Curation of Genetic, Protein,
Web service URL Yes - wiki.thebiogrid.org/doku
and Chemical Interactions .php/biogridrest (https://wiki.th
ebiogrid.org/doku.php/biogridr
The Biological General Repository for Interaction est)
Datasets (BioGRID) is an open access database that
houses genetic and protein interactions curated from Tools
the primary biomedical literature for all major model Web Advanced search, integrated
organism species and humans. As of network viewer, custom
18  October  2020, [15] the BioGRID contains 1,928 downloads, bulk
million interactions as drawn from 63,083 retrieval/download
publications that represent 71 model organisms. At
the start of 2021 it already contained more than 2,0 Miscellaneous
million biological interactions, 29,023 chemical- Versioning Yes
protein interactions, and 506,485 post-translational Data release Monthly (4 Weeks)
modifications collectively curated from 75,988
frequency
publications for more than 80 species.[16] BioGRID
data are freely distributed through partner model Version 4.2.193; 1 January 2021
organism databases and meta-databases and are Curation policy Yes - manual; Also focused
directly downloadable in a variety of formats. curation efforts.
BioGRID curation is coordinated through an
Interaction Management System (IMS) that Bookmarkable Yes - both individual results
facilitates the compilation interaction records entities and searches,
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

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

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
The following organisms are currently supported within the BioGRID, and each has curated interaction
data available according to the latest statistics (https://wiki.thebiogrid.org/doku.php/statistics).

Anopheles gambiae PEST (African malaria mosquito)

Apis mellifera (honey bee)
Arabidopsis thaliana (thale cress)
Bacillus subtilis 168
Bos taurus (cow)
Caenorhabditis elegans (nematode worm)
Candida albicans SC5314
Canis familiaris (dog)
Cavia porcellus (guinea pig)
Chlamydomonas reinhardtii (green algae)
Chlorocebus sabaeus (green monkey)
Cricetulus griseus (Chinese hamster)
Danio rerio (zebrafish)
Dictyostelium discoideum AX4 (slime mold)
Drosophila melanogaster (fruit fly)
Emericella nidulans FGSC A4
Equus caballus (horse)
Escherichia coli (E. coli)
Felis catus (cat)
Gallus gallus (chicken)
Glycine max (soybean)
Hepatitis C Virus
Homo sapiens (human)
Human Herpesvirus (1,2,3,4,5,6A,6B,7,8)
Human Immunodeficiency Virus 1 (HIV-1)
Human Immunodeficiency Virus 2 (HIV-2)
 Human Papillomavirus (HPV, 10, 16, 32, 5, 6B, 7, 9)
Leishmania major
Macaca mulatta (rhesus monkey)
Meleagris gallopavo (turkey)
Middle East respiratory syndrome–related coronavirus (MERS-CoV)
Monodelphis domestica (gray short-tailed opossum)
Mus musculus (house mouse)
Mycobacterium tuberculosis H37Rv
Mycoplasma pneumoniae M129
Neurospora crassa OR74A
Nicotiana tomentosiformis
Oryctolagus cuniculus (rabbit)
Oryza sativa Japonica (Japanese rice)
Ovis aries (sheep)
Pan troglodytes (chimpanzee)
Pediculus humanus (a type louse that infects humans)
Plasmodium falciparum 3D7 (malaria parasite)
Rattus norvegicus (Norway rat)
Ricinus communis (castor bean)
Saccharomyces cerevisiae (budding yeast)
Schizosaccharomyces pombe (fission yeast)
Selaginella moellendorffii
Severe acute respiratory syndrome coronavirus (SARS-CoV)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Simian Immunodeficiency Virus
Solanum lycopersicum (tomato)
Solanum tuberosum (potato)
Sorghum bicolor (sorghum)
Streptococcus pneumoniae (pneumococcus)
Strongylocentrotus purpuratus (purple urchin)
Sus scrofa (pig)
Tobacco Mosaic Virus
Ustilago maydis 521 (corn smut)
Vaccinia Virus
Vitis vinifera (common grape vine)
Xenopus laevis (African clawed frog)
Zea mays (corn)

Funding for BioGRID

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

References
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External links
Official website (https://thebiogrid.org)
BioGRID-ORCS CRISPR Database (https://orcs.thebiogrid.org)
Themed Curation Projects (https://thebiogrid.org/projectslist.php)
Mike Tyers Lab Homepage (https://web.archive.org/web/20100417133520/http://www.tyersla
b.com/)
International Molecular Exchange Consortium (https://imex.sourceforge.net/)
Lunenfeld-Tanenbaum Research Institute (http://www.lunenfeld.ca/)
Institut de Recherche en iImmunologie et en Cancérologie (http://www.iric.ca/)
Princeton University (https://web.archive.org/web/20140126142529/http://www.princeton.ed
u/main/)

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