The BioGRID Interaction Database: 2008 update

By Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, M. Livstone, Rose Oughtred, D. Lackner, J. Bähler, V. Wood and 2 more. 2007

780 citations recorded by the source corpus.

The Biological General Repository for Interaction Datasets (BioGRID) database (http://www.thebiogrid.org) was developed to house and distribute collections of protein and genetic interactions from major model organism species. BioGRID currently contains over 198 000 interactions from six different species, as derived from both high-throughput studies and conventional focused studies. Through comprehensive curation efforts, BioGRID now includes a virtually complete set of interactions reported to date in the primary literature for both the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management system to coordinate curation across different locations. The BioGRID provides interaction data with monthly updates to Saccharomyces Genome Database, Flybase and Entrez Gene. Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction.

Subfields: Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

PID: the Pathway Interaction Database (2008, neutral): “This reﬂects not a judgment on the quality of high-throughput data, but a recognition that there are databases speciﬁcally designed to provide access to this data (11, 12, 13).”
HSP90 at the hub of protein homeostasis: emerging mechanistic insights (2010, background): “In recent years, however, knowledge of HSP90 clients has grown mainly owing to genome-wide studies in yeast, in which 1,232 unique proteins interact physically or genetically with Hsp90 (Ref”
The mathematics of tanning (2009, positive): “sion intermediates [23], interactome [49], orthology [50], etc.”
Disentangled Graph Convolutional Networks (2019, neutral): “BlogCatalog (Tang & Liu, 2009), PPI (Breitkreutz et al., 2008; Grover & Leskovec, 2016), POS (Grover & Leskovec, 2016) are for multi-label node classiﬁcation.”
STRING 8—a global view on proteins and their functional interactions in 630 organisms (2008, background): “Apart form the resources already included in the previous release [MINT (10), HPRD (9), BIND (12), DIP (11), BioGRID (8), KEGG (13) and Reactome (14)], a number of resources have been newly included [IntAct (7), EcoCyc (15), NCI-Nature Pathway Interaction Database and Gene Ontology (GO) protein comp”
Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory (2016, methodology): “Integrating DEGs data with the BioGrid [38] PPI data yielded a list of binary interactions among DEGs for both up and down groups.”
Pathway Commons, a web resource for biological pathway data (2010, background): “67) Model organisms (20) Cancer Cell Map BioPAX L2 10 Pathways May 2006 Human http://cancer.”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “Experimental data on physical protein–protein interactions are mostly stored in a group of dedicated databases that together form the International Molecular Exchange (IMEx) consortium (14–21).”
Network Representation Learning: A Survey (2017, background): “As a typical biological network, the Protein-Protein Interaction network [90] is a subgraph of the PPI network for Homo Sapiens.”
Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping (2011, methodology): “While there are already several interaction databases implementing the PSICQUIC interface [43-50], Bio::Homology:: InterologWalk currently relies on EBI IntAct [36] as its source of experimental interactions.”
ExoCarta: A compendium of exosomal proteins and RNA (2009, methodology): “Protein–protein interaction data is obtained from BioGRID [16], a leading protein interaction database.”
ConsensusPathDB—a database for integrating human functional interaction networks (2008, background): “org), IntAct (15) (data from small-scale experiments only), DIP (16), MINT (17), HPRD (18), BioGRID (19) and SPIKE (20).”