The BioGRID interaction database: 2013 update

Chatr-aryamontri, Andrew; Breitkreutz, Bobby-Joe; Heinicke, Sven; Boucher, Lorrie; Winter, Andrew; Stark, Chris; Nixon, Julie; Ramage, Lindsay; Kolas, Nadine; O'Donnell, Lara; Reguly, Teresa; Breitkreutz, Ashton; Sellam, Adnane; Chen, Daici; Chang, Christie; Rust, Jennifer; Livstone, Michael; Oughtred, Rose; Dolinski, Kara; Tyers, Mike

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.

Citation

Chatr-aryamontri, A., Breitkreutz, B., Heinicke, S., Boucher, L., Winter, A., Stark, C., …Tyers, M. (2013). The BioGRID interaction database: 2013 update. Nucleic Acids Research, 41(D1), D816-D823. https://doi.org/10.1093/nar/gks1158

• Journal Article Type: Article
• Acceptance Date: Oct 25, 2012
• Online Publication Date: Nov 30, 2012
• Publication Date: Jan 1, 2013
• Deposit Date: Mar 25, 2017
• Publicly Available Date: Mar 26, 2017
• Journal: Nucleic Acids Research
• Print ISSN: 0305-1048
• Electronic ISSN: 1362-4962
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 41
• Issue: D1
• Pages: D816-D823
• DOI: https://doi.org/10.1093/nar/gks1158
• Keywords: phenotype, arabidopsis, benchmarking, genes, genome, mining, plants, protein processing, post-translational, saccharomyces, saccharomyces cerevisiae, saccharomycetales, schizosaccharomyces, yeasts, genetics, collaboration, information resources, community
• Public URL: http://researchrepository.napier.ac.uk/Output/819842