The BioGRID interaction database: 2015 update

By A. Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell and 12 more. 2014

895 citations recorded by the source corpus.

The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749 912 interactions as drawn from 43 149 publications that represent 30 model organisms. This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control.

Subfields: Molecular Biology

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Citations in the corpus

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species (2016, methodology): “Monarch has integrated data from a variety of human, model organism, and other biomedical sources such as OMIM (1), Orphanet (3), Clin-Var (2), HPO (30), KEGG (31), CTD (4), MyGene (32), BioGrid (33) and via orthology in PantherDB (34) we also incorporate Fgg gene data from ZFIN (35) and from MGI (3”
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology[OPEN] (2017, background): “…or TAIR (Berardini et al., 2015) for annotation and sequence information, the BAR Arabidopsis InteractionsViewer(Geisler-Leeetal.,2007)orBioGRID(Chatr-Aryamontri et al., 2015) for protein-protein interactions, SUBA3 (Tanz et al., 2013) for subcellular localization information, Phyre2 (Kelley…”
The Comparative Toxicogenomics Database: update 2017 (2016, background): “Finally, integration with external annotations from GO (19), KEGG (20), Reactome (21) and BioGRID (22) yields additional inferred relationships (Table 1).”
The BioGRID interaction database: 2017 update (2016, methodology): “Since our 2015 NAR Database report (33), the number of curated interactions housed in BioGRID has increased by 30%.”
Systematic Functional Annotation and Visualization of Biological Networks (2016, methodology): “A global protein-protein interaction network, containing 5,699 nodes and 78,406 edges, was constructed from all yeast protein pairs sharing a physical interaction type in the BioGRID database (Chatr-Aryamontri et al., 2015) (Experimental Procedures).”
Integrated interactions database: tissue-specific view of the human and model organism interactomes (2015, methodology): “Experimentally detected PPIs were downloaded from seven databases: BioGRID (14 16) 2013-03-26.”
HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks (2016, background): “Several databases exist that collect the knowledge about human and model organism PPIs by manual curation (1,2) and provide the community with invaluable resources on the functional organization of the cell.”
ExoCarta: A web-based compendium of exosomal cargo (2015, neutral): “A nonredundant protein-protein interaction network for all the exosomal proteins catalogued in ExoCarta was generated using HPRD [21] and BioGRID [22] databases.”
Embedding Logical Queries on Knowledge Graphs (2018, methodology): “We used the human proteinprotein interaction (PPI) network compiled by [26] and [10], integrated with additional PPI information from [40], and [38].”
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible (2016, background): “This channel is populated mainly from the primary interaction databases organized in the IMEx consortium, plus BioGRID.”