The BioGRID interaction database: 2019 update

By Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, J. Rust, Lorrie Boucher, Christie S. Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam and 7 more. Nucleic Acids Res., 2018

1,296 citations recorded by the source corpus.

Abstract The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2018 (build 3.4.164), BioGRID contains records for 1 598 688 biological interactions manually annotated from 55 809 publications for 71 species, as classified by an updated set of controlled vocabularies for experimental detection methods. BioGRID also houses records for >700 000 post-translational modification sites. BioGRID now captures chemical interaction data, including chemical–protein interactions for human drug targets drawn from the DrugBank database and manually curated bioactive compounds reported in the literature. A new dedicated aspect of BioGRID annotates genome-wide CRISPR/Cas9-based screens that report gene–phenotype and gene–gene relationships. An extension of the BioGRID resource called the Open Repository for CRISPR Screens (ORCS) database (https://orcs.thebiogrid.org) currently contains over 500 genome-wide screens carried out in human or mouse cell lines. All data in BioGRID is made freely available without restriction, is directly downloadable in standard formats and can be readily incorporated into existing applications via our web service platforms. BioGRID data are also freely distributed through partner model organism databases and meta-databases.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8035e5002b7b0898ca7fa8263d09fe4454c6e4fd

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Citations in the corpus

Post-translational modifications in proteins: resources, tools and prediction methods (2021, background): “In addition to protein and genetic interactions, it also holds data on ∼726000 phosphorylation sites in ∼72000 proteins, which were extracted from 4742 publications for 71 major model organisms (126).”
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis (2020, neutral): “Or for the resulting networks used to make the conclusions it would be good to show the number of resources from which the nodes/data points were extracted, to make the case that this integrated resource is necessary for this analysis.”
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, background): “This includes biochemical, bio-physical and genetic experiments; all such interaction evidence is imported from the curated interaction database organized in the iMEX consortium (39), plus BioGRID (40).”
Alliance of Genome Resources Portal: unified model organism research platform (2019, background): “org/) (17) and the IMEx consortium (http:// www.”
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions (2020, methodology): “The BioGRID record structure, database architecture, and curation pipeline have been described in detail elsewhere.(5) Due to the vast extent of the human biomedical literature, BioGRID has in part taken a biological processand/or disease-focused approach in order to build curation depth in critical”
Comparative Toxicogenomics Database (CTD): update 2023 (2022, background): “External integration of CTD content with imported annotations from the Gene Ontology (GO) (9), KEGG (10), Reactome (11) and BioGRID (12) produces an additional 13 million inferences.”
Comparative Toxicogenomics Database (CTD): update 2021 (2020, background): “External integration of CTD content with annotations from Gene Ontology (GO) (21), KEGG (22), Reactome (23) and BioGRID (24) produces an additional 12 million inferences.”
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics (2019, methodology): “The target-interacting protein data were collected from BioGrid, which provides experimentally documented human protein physical interactions (62) based on evidence from such experimentalmethods as affinity capture-western blotting, colocalization studies, yeast two-hybrid screens, fluorescence reso”