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The BioGRID interaction database: 2013 update - PubMed

The BioGRID interaction database: 2013 update

Andrew Chatr-Aryamontri et al. Nucleic Acids Res. 2013 Jan.

Abstract

The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and the model plant Arabidopsis thaliana. A number of themed curation projects in areas of biomedical importance are also supported. BioGRID has established collaborations and/or shares data records for the annotation of interactions and phenotypes with most major model organism databases, including Saccharomyces Genome Database, PomBase, WormBase, FlyBase and The Arabidopsis Information Resource. BioGRID also actively engages with the text-mining community to benchmark and deploy automated tools to expedite curation workflows. BioGRID data are freely accessible through both a user-defined interactive interface and in batch downloads in a wide variety of formats, including PSI-MI2.5 and tab-delimited files. BioGRID records can also be interrogated and analyzed with a series of new bioinformatics tools, which include a post-translational modification viewer, a graphical viewer, a REST service and a Cytoscape plugin.

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Figures

Figure 1.
Figure 1.

BioGRID curation pipeline. The curation workflow consists of three major steps: (i) triage of the literature of interest by text-mining tools and/or interaction-directed PubMed queries; (ii) curation, annotation and tracking of interaction data through the web-based IMS and (iii) monthly public release of interaction data records.

Figure 2.
Figure 2.

PTM display features. (A) Button to reveal PTM sites. (B) Statistics for different types of PTMs. (C) Pop-up with links to publications that document PTM evidence and relationships. (D) Tabular view of PTM site locations and links to publications. (E) Tabular view of PTM relationships and links to publications. (F) Custom gene tags.

Figure 3.
Figure 3.

The BioGRID viewer. (A) In the example shown the viewer returns all the interactions of the query gene/protein and interactions between the hit genes/protein. Properties of individual interactions are revealed by hovering over the interaction node of interest. (B) Network view can be simplified by several available filters. In this example, all genetic interactions have been filtered out. See text for further details.

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