The BioGRID captures, annotates and distributes comprehensive collections of physical and genetic interactions from model organisms in a standardized format based on a uniform set of experimental evidence codes. BioGRID provides full annotation support for 50 species of biomedical relevance, and currently archives interactions for Homo sapiens, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Drosophila melanogaster, Bacillus subtilis, Bos taurus, Caenorhabditis elegans, Canis familiaris, Danio rerio, Escherichia coli, Gallus gallus, human herpesvirus, Macaca mulatta, Mus musculus, Rattus norvegicus and Xenopus laevis. Annotation resources for all supported species are routinely updated to prevent ambiguous or out-of-date nomenclature. The BioGRID houses over 17 million gene names, aliases, systematic names and external database identifiers to provide relevant search results.
As of 1 August 2010 (version 3.0.67) BioGRID contains 347
005 non-redundant) interactions comprised of 177
683 non-redundant) protein and 170
410 non-redundant) genetic interactions (). Of these curated interactions, ~31% are drawn from 22
653 focused low-throughput (LTP) studies and 69% stem from 113 HTP studies, defined as reporting more than 100 interactions in tabular form. Through monthly updates, complete coverage of the entire literature is maintained for the budding yeast S. cerevisiae
850 interactions) and the fission yeast S. pombe
546 interactions). Comprehensive curation of the primary literature for protein interactions has also been completed for the model plant A. thaliana
(currently 4893 interactions). These collated data sets are available from the BioGRID website for both searches and downloads, and are fully linked from the respective model organism databases Saccharomyces Genome Database (SGD, S. cerevisiae
), GeneDB (GDB, S. pombe
) and The Arabidopsis Information Resource (TAIR, A. thaliana
). BioGRID supports an international user base, as directed from a variety of traffic sources ().
Increase in BioGRID data content since previous update
Distribution of BioGRID users (left) and traffic sources (right).
Literature coverage for animal model species, including humans, is far from complete (see below). Recent curation efforts have focused on human protein interactions, given both the richness of data and the obvious biomedical relevance. A recent BioGRID curation drive has increased the number of annotated human protein interactions to 48
017 non-redundant) as drawn from more than 10
000 publications (). As part of this effort, we have undertaken new cross-species curation initiatives in areas of chromatin remodeling (CR) and the ubiquitin proteasome system (UPS) that have thus far resulted in 12
455 (7529 non-redundant) and 6875 (4881 non-redundant) interactions, respectively. All of the interactions from these ongoing projects are updated monthly and made available on the BioGRID website for download. Analogous curation drives are being coordinated with WormBase for C. elegans
) and the Gene Ontology (GO) Consortium for the 12 GO Reference Genomes (12
Interaction data in the BioGRID is augmented by other associated data types for some species. Protein phosphorylation plays a critical role in controlling the dynamics of cellular interaction networks, and the recent development of mass spectrometric methods for HTP detection has resulted in a deluge of phosphorylation sites. To complement HTP data sets, we developed a resource for budding yeast phosphorylation site data captured from the primary literature, called PhosphoGRID (http://www.phosphogrid.org
). This sister database currently contains 6440 experimentally verified in vivo
phosphorylation sites found on 1770 proteins, as curated from 329 publications (13
). In collaboration with SGD, we have also curated 126
818 phenotypes for genetic interactions in both budding and fission yeast, which are available in search results and as downloads from BioGRID and SGD (8