The BioGRID interaction database: 2017 update

Abstract

The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical-protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases.

Figure 1.

Increase in data content of BioGRID. Increments in interaction records and source publications reported in BioGRID from March 2010 (release 2.0.62) to September 2016 (release 3.4.140). Left panel shows the increase of annotated protein interactions (red), genetic interactions (green) and total interactions (blue). Right panel shows the number of publications that actually reported protein or genetic interactions (blue) as a function of the total number of publications examined by BioGRID curators (red).

Figure 2.

New BioGRID network viewer. (A) The network tab in the ‘Switch View’ menu opens a network view for the selected query gene, as shown for human DHFR. (B) Users may export the network view as a figure file in PNG format, set filters that show or hide interactions, set thresholds for experimental evidence, and select from a number of layout formats. Explanatory text is provided under the help menu. (C) Node and edge colour indicates the interaction type and node size is proportional to its connectivity. In this example, green nodes represent chemicals and blue nodes represent proteins. When common names are not available, compounds are abbreviated by the chemical formula. (D) Yellow edges represent protein interactions, green edges represent genetic interactions, blue edges represent chemical interactions and purple edges represent both protein and genetic interactions.

Figure 3.

New BioGRID post-translational modification (PTM) viewer. (A) Users can select the ‘PTM Sites’ tab from the ‘Switch View’ menu to view PTM data when available. (B) The ‘Stats & Options’ box indicates the number of PTM sites and defines the colours assigned to each PTM type. (C) PTM locations are displayed on the protein sequence with modified residues highlighted. (D) Assigned PTM sites are displayed in tabular format with supporting evidence and citations. (E and F) Non-assigned PTMs are displayed at the bottom of the page.