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The Biogrid Interaction Database Published online 24 November 2018 Nucleic Acids Research, 2019, Vol. 47, Database issue D529–D541 doi: 10.1093/nar/gky1079 The BioGRID interaction database: 2019 update Rose Oughtred1,†, Chris Stark2,†, Bobby-Joe Breitkreutz2,†, Jennifer Rust1, Lorrie Boucher2, Christie Chang1, Nadine Kolas2, Lara O’Donnell2, Genie Leung2, Rochelle McAdam3, Frederick Zhang3, Sonam Dolma3, Andrew Willems2, Jasmin Coulombe-Huntington4, Andrew Chatr-aryamontri4, Kara Dolinski1 and Mike Tyers 2,4,* 1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, 2The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada, 3Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada and 4Institute for Research in Immunology and Cancer, Universitede´ Montreal,´ Montreal,´ Quebec H3C 3J7, Canada Received September 23, 2018; Revised October 15, 2018; Editorial Decision October 18, 2018; Accepted November 22, 2018 ABSTRACT INTRODUCTION The Biological General Repository for Interaction Biological interaction networks, as aggregated from a Datasets (BioGRID: https://thebiogrid.org) is an open plethora of individual protein or genetic interactions, as access database dedicated to the curation and well as interactions of RNA, DNA, membranes, carbohy- archival storage of protein, genetic and chemical in- drates and small molecule metabolites, serve as a framework teractions for all major model organism species and for understanding gene–phenotype relationships and the mechanistic basis for all cellular functions (1,2). The charac- humans. As of September 2018 (build 3.4.164), Bi- terization of molecular and functional interactions between oGRID contains records for 1 598 688 biological in- genes, their products and biomolecules has been instrumen- teractions manually annotated from 55 809 publica- tal in interpreting genetic associations related to cancer and tions for 71 species, as classified by an updated set other diseases in a myriad of different contexts (3–6). These of controlled vocabularies for experimental detec- efforts have been tremendously accelerated by the devel- tion methods. BioGRID also houses records for >700 opment of unbiased high-throughput (HTP) methods for 000 post-translational modification sites. BioGRID the detection of gene–phenotype relationships, protein in- now captures chemical interaction data, including teractions, genetic interactions and chemical interactions. chemical–protein interactions for human drug tar- Such methods have been progressively refined to increase gets drawn from the DrugBank database and man- coverage and resolution, and newer techniques are gener- ually curated bioactive compounds reported in the ating other types of biological data that had not been pre- viously available at such a large scale (7). In particular, re- literature. A new dedicated aspect of BioGRID an- / / cent genome-wide genetic screens based on CRISPR Cas9 notates genome-wide CRISPR Cas9-based screens genome editing technology have enabled the rapid charac- that report gene–phenotype and gene–gene relation- terization of gene–phenotype relationships both in cell lines ships. An extension of the BioGRID resource called derived from a variety of tissue types and in vivo mouse the Open Repository for CRISPR Screens (ORCS) models (8,9). CRISPR/Cas9 approaches have also been de- database (https://orcs.thebiogrid.org) currently con- vised to allow systematic exploration of gene–gene interac- tains over 500 genome-wide screens carried out in tions in human cells (10,11). These comprehensive maps of human or mouse cell lines. All data in BioGRID is gene function promise to further accelerate biomedical re- made freely available without restriction, is directly search and drug discovery (12,13). downloadable in standard formats and can be readily The biological network paradigm has been used to facil- incorporated into existing applications via our web itate drug target selection, interpret drug resistance or off- target effects, and forms the basis for targeted therapies and service platforms. BioGRID data are also freely dis- personalized medicine (14,15). An on-going challenge, how- tributed through partner model organism databases ever, is the unstructured nature of the biomedical literature, and meta-databases. i.e., free form text, that cannot be easily parsed for compu- tationally tractable data elements such as protein or genetic *To whom correspondence should be addressed. Tel: +1 514 343 6668; Email: [email protected] †The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint first authors. C The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] D530 Nucleic Acids Research, 2019, Vol. 47, Database issue interactions. A primary goal of biomedical data curation directly supported by experimental evidence that is catego- is thus to convert text-, figure- and table-based experimen- rized according to a structured set of interaction types that tal information from the biomedical literature into discrete, map to the experimental detection methods in the PSI-MI consistently structured records that can be easily parsed, 2.5 standard (24). BioGRID also currently contains data on combined and computed. To this end, the accurate anno- 726 378 protein PTMs (419 472 non-redundant) from 4742 tation of protein, genetic and other forms of interaction publications, an increase of ∼600 000 PTMs since our pre- data from the literature by a host of databases and meta- vious update, as derived primarily from HTP studies. databases has expedited the formulation of both intuitive In 2018, Google Analytics reported that BioGRID re- and more formal models of cellular functions (16), as well ceived on average 114 151 page views and 12 100 unique as the interpretation of complex genome-wide association visitors per month. We estimate that these page views cor- studies for a wide variety of disease phenotypes (17). respond to perusal of ∼24 million interactions by BioGRID The Biological General Repository for Interaction users in 2018. These statistics do not include the widespread Datasets (BioGRID: https://thebiogrid.org) was first de- dissemination of BioGRID records by various partner veloped as an open-access centralized repository for pro- databases, which include the MODs SGD (19), PomBase tein and genetic interaction data reported in the biomed- (25), Candida Genome Database (CGD) (26), WormBase ical literature (18). Since its inception in 2003, BioGRID (20), FlyBase (27), the Arabidopsis Information Resource has amassed almost 1.6 million biological interactions sup- (TAIR) (28), ZFIN (29) and Mouse Genome Database ported by published experimental data in humans and (MGD) (30) and the meta-database resources NCBI (21), other major model organisms including the bacterium Es- UniProt (22), Pathway Commons (31), STRING (32)and cherichia coli, the budding yeast Saccharomyces cerevisiae, others. In 2018, the BioGRID user base was located pri- the fission yeast Schizosaccharomyces pombe, the plant Ara- marily in the USA (28%), followed by China (13%), India bidopsis thaliana, the nematode worm Caenorhabditis el- (7%), United Kingdom (6%), Germany (5%), Canada (4%), egans, the fruit fly Drosophila melanogaster, the zebrafish Japan (4%), France (3%) and all other countries (30%). Danio rerio, and the mouse Mus musculus, among many others. BioGRID has also grown in scope to include the cu- CURATION STRATEGY AND SPECIFIC PROJECTS ration of post-translational modifications (PTMs) and the annotation of chemical interactions between genes/proteins All curation activity in BioGRID continues to be con- and bioactive small molecules. BioGRID curation is gov- trolled by an internal dedicated database called the Inter- erned by controlled experimental vocabularies and guided action Management System (IMS), which is used to ad- by text mining methods. BioGRID data content is up- minister triaged lists of publications for curation for dif- dated and freely distributed to the biomedical community ferent projects, to standardize all aspects of curation based as monthly releases, as well as through partnerships with on controlled vocabularies for experimental evidence and model organism databases (MODs) such as Saccharomyces gene names, and to track individual curator contributions. Genome Database (SGD) (19) or WormBase (20), vari- BioGRID now contains interaction data for 71 different ous meta-databases for interaction data, and general data model species, an increase of five species from the previ- portals, such as NCBI (21) or UniProt (22). Since the previ- ous update. As BioGRID now maintains annotation sup- ous update (23), a new resource within BioGRID called the port for 350 species, an increase of over 100 species since the Open Repository for CRISPR Screens (ORCS) has been de- previous update, the database is well positioned to rapidly veloped to house and distribute large-scale CRISPR screen incorporate data for additional new species as opportunities
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