The BioGRID interaction database: 2013 update

By A. Chatr-aryamontri, Bobby-Joe Breitkreutz, Sven Heinicke, Lorrie Boucher, Andrew G. Winter, Chris Stark, Julie Nixon, Lindsay Ramage, Nadine Kolas, Lara O'Donnell and 10 more. 2012

1,354 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases (2013, methodology): “The MENTHA interactome browser (26) will continue to be built on the PSICQUIC web services of IMex databases (6) and BioGRID (27), as before.”
Pathway and Network Analysis of Cancer Genomes (2015, positive): “These methods begin with a list of mutated or otherwise altered genes, and one or more databases of gene or protein interactions, such as those compiled by iRefIndex 35 , BioGRID 36 , IntAct 37 , STRING 38 , or GeneMANIA 39 ( Supplementary Table 2 ).”
Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies (2012, methodology): “To overcome this challenge, protein interaction networks extracted from BioGrid [48] were added.”
A highly conserved program of neuronal microexons is misregulated in autistic brains (2014, background): “, 2013) and BioGrid (Chatr-Aryamontri et al., 2013) databases with the dashed lines representing indirect interactions that are either between proteins found within same protein complex but not interacting directly or predicted interactions based on paralogs (Franceschini et al.”
Understanding multicellular function and disease with human tissue-specific networks (2015, neutral): “This resulted in a tissue-naïve gold standard of 604,038 functionally related gene pairs (positive examples) and 12,425,713 potentially un-related pairs (negative examples).”
HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores (2012, background): “62; release date: March 16, 2010) [4], DIP”
GeneMANIA Prediction Server 2013 Update (2013, methodology): “Our network data come from six main sources: IRefIndex (23) and BioGRID (24) for physical (i.e., protein) interactions and genetic interactions; Gene Expression Omnibus (GEO) for co-expression networks (25); InterPro, via Ensembl, for protein domains (26); I2D for networks of interologs of physical ”
PATRIC, the bacterial bioinformatics database and analysis resource (2013, methodology): “New interactions are retrieved and added every month using automated scripts and the most recent release of the tool includes host–pathogen interactions from BIND, BioGRID (17), DIP, IntAct and MINT.”