The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open‐access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID...
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| Published in | Protein science Vol. 30; no. 1; pp. 187 - 200 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Hoboken, USA
John Wiley & Sons, Inc
01.01.2021
Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0961-8368 1469-896X 1469-896X |
| DOI | 10.1002/pro.3978 |
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| Abstract | The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open‐access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low‐throughput studies and large high‐throughput datasets. BioGRID also captures protein post‐translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built‐in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin‐proteasome system, as well as specific disease areas, such as for the SARS‐CoV‐2 virus that causes COVID‐19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome‐wide CRISPR/Cas9‐based genetic screens. BioGRID‐ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta‐databases. |
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| AbstractList | The BioGRID (Biological General Repository for Interaction Datasets,
thebiogrid.org
) is an open‐access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low‐throughput studies and large high‐throughput datasets. BioGRID also captures protein post‐translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built‐in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin‐proteasome system, as well as specific disease areas, such as for the SARS‐CoV‐2 virus that causes COVID‐19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS,
orcs.thebiogrid.org
), captures single mutant phenotypes and genetic interactions from published high throughput genome‐wide CRISPR/Cas9‐based genetic screens. BioGRID‐ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta‐databases. The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open‐access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low‐throughput studies and large high‐throughput datasets. BioGRID also captures protein post‐translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built‐in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin‐proteasome system, as well as specific disease areas, such as for the SARS‐CoV‐2 virus that causes COVID‐19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome‐wide CRISPR/Cas9‐based genetic screens. BioGRID‐ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta‐databases. The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open-access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low-throughput studies and large high-throughput datasets. BioGRID also captures protein post-translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built-in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin-proteasome system, as well as specific disease areas, such as for the SARS-CoV-2 virus that causes COVID-19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome-wide CRISPR/Cas9-based genetic screens. BioGRID-ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta-databases.The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open-access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low-throughput studies and large high-throughput datasets. BioGRID also captures protein post-translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built-in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin-proteasome system, as well as specific disease areas, such as for the SARS-CoV-2 virus that causes COVID-19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome-wide CRISPR/Cas9-based genetic screens. BioGRID-ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta-databases. |
| Author | Boucher, Lorrie Dolma, Sonam Dolinski, Kara Zhang, Frederick Kolas, Nadine Coulombe‐Huntington, Jasmin Chang, Christie Leung, Genie Rust, Jennifer Willems, Andrew Chatr‐aryamontri, Andrew Stark, Chris Tyers, Mike Oughtred, Rose Breitkreutz, Bobby‐Joe |
| AuthorAffiliation | 4 Institute for Research in Immunology and Cancer Université de Montréal Quebec Canada 2 The Lunenfeld‐Tanenbaum Research Institute Mount Sinai Hospital Toronto Ontario Canada 3 Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell Biology The Hospital for Sick Children Toronto Ontario Canada 1 Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton New Jersey USA |
| AuthorAffiliation_xml | – name: 4 Institute for Research in Immunology and Cancer Université de Montréal Quebec Canada – name: 2 The Lunenfeld‐Tanenbaum Research Institute Mount Sinai Hospital Toronto Ontario Canada – name: 3 Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell Biology The Hospital for Sick Children Toronto Ontario Canada – name: 1 Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton New Jersey USA |
| Author_xml | – sequence: 1 givenname: Rose surname: Oughtred fullname: Oughtred, Rose organization: Princeton University – sequence: 2 givenname: Jennifer surname: Rust fullname: Rust, Jennifer organization: Princeton University – sequence: 3 givenname: Christie surname: Chang fullname: Chang, Christie organization: Princeton University – sequence: 4 givenname: Bobby‐Joe surname: Breitkreutz fullname: Breitkreutz, Bobby‐Joe organization: Mount Sinai Hospital – sequence: 5 givenname: Chris surname: Stark fullname: Stark, Chris organization: Mount Sinai Hospital – sequence: 6 givenname: Andrew surname: Willems fullname: Willems, Andrew organization: Mount Sinai Hospital – sequence: 7 givenname: Lorrie surname: Boucher fullname: Boucher, Lorrie organization: Mount Sinai Hospital – sequence: 8 givenname: Genie surname: Leung fullname: Leung, Genie organization: Mount Sinai Hospital – sequence: 9 givenname: Nadine surname: Kolas fullname: Kolas, Nadine organization: Mount Sinai Hospital – sequence: 10 givenname: Frederick surname: Zhang fullname: Zhang, Frederick organization: The Hospital for Sick Children – sequence: 11 givenname: Sonam surname: Dolma fullname: Dolma, Sonam organization: The Hospital for Sick Children – sequence: 12 givenname: Jasmin surname: Coulombe‐Huntington fullname: Coulombe‐Huntington, Jasmin organization: Université de Montréal – sequence: 13 givenname: Andrew surname: Chatr‐aryamontri fullname: Chatr‐aryamontri, Andrew organization: Université de Montréal – sequence: 14 givenname: Kara orcidid: 0000-0002-7010-0264 surname: Dolinski fullname: Dolinski, Kara email: dolinski@princeton.edu organization: Princeton University – sequence: 15 givenname: Mike orcidid: 0000-0002-9713-9994 surname: Tyers fullname: Tyers, Mike email: md.tyers@umontreal.ca organization: Université de Montréal |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33070389$$D View this record in MEDLINE/PubMed |
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| Keywords | COVID-19 phenotype biological network ubiquitin-proteasome system protein interaction CRISPR screen chemical interaction post-translational modification drug target genetic interaction |
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| Notes | Funding information Canada Research Chair in Systems and Synthetic Biology; Stand Up To Cancer Canada; Genomics Technology Platform Award; Rapid Response Initiative Award; Genome Canada and Genome Quebec; Canadian Institutes of Health Research, Grant/Award Number: FDN‐167277; National Center For Advancing Translational Sciences of the National Institutes of Health, Grant/Award Number: OT3TR002026; National Institutes of Health Office of Research Infrastructure Programs, Grant/Award Number: R01OD010929 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Rose Oughtred, Jennifer Rust, and Christie Chang are joint first authors. Funding information Canada Research Chair in Systems and Synthetic Biology; Stand Up To Cancer Canada; Genomics Technology Platform Award; Rapid Response Initiative Award; Genome Canada and Genome Quebec; Canadian Institutes of Health Research, Grant/Award Number: FDN‐167277; National Center For Advancing Translational Sciences of the National Institutes of Health, Grant/Award Number: OT3TR002026; National Institutes of Health Office of Research Infrastructure Programs, Grant/Award Number: R01OD010929 |
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| SubjectTerms | Animals Annotations biological network Cell lines chemical interaction Chemical interactions COVID-19 COVID-19 - genetics COVID-19 - virology CRISPR CRISPR screen Databases, Factual Datasets drug target genetic interaction Genetic screening Genomes Humans Mice phenotype Phenotypes post‐translational modification Proteasomes protein interaction Protein Interaction Mapping Proteins Proteins - genetics Repositories Respiratory diseases SARS-CoV-2 - genetics SARS-CoV-2 - pathogenicity Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Tools for Protein Science Ubiquitin ubiquitin‐proteasome system User-Computer Interface Viral diseases Viruses Yeast Zebrafish |
| Title | The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions |
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