The BioGRID interaction database: 2019 update

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.

Figure 1.

Increase in data content of BioGRID from March 2010 (release 2.0.62) to September 2018 (release 3.4.164). Left panel shows the increase of annotated protein interactions (red), genetic interactions (green) and total interactions (blue). Right panel shows the number of curated publications that contained protein or genetic interaction data (blue) versus the total number of publications examined by curators (red).

Figure 2.

Example of result summary page for chemical interactions of the E3 ubiquitin ligase VHL. (A) Details for Bivalent_ligand_52, a PROTAC composed of a ligand for VHL and a ligand for the degradation targets EFGR and ERBB2 (68). (B) Additional notes display the BVL name in a standardized format based on details provided in the original paper. (C) Chemical-protein interactions curated by BioGRID also include other small molecule inhibitors of UPS enzymes, in this case VH298 as an inhibitor of VHL. External links to ChemSpider provide additional chemical information.

Figure 3.

Example of screen summary result page in BioGRID ORCS. (A) Annotated screen details. (B) Score distribution graph. (C) Screen search and filter functions. (D) Sort function for screen scores and annotation. Genes scored as significant in the original publication are designated by ‘Yes’ in the hit column.

Figure 4.

S. cerevisiae kinome project page at BioGRID. (A) Description of project with hyperlinks to resources and downloads. (B) Project-level statistics. (C) Searchable project gene list and annotation.