The BioGRID interaction database: 2015 update

Abstract

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.

Figure 1.

Growth of the BioGRID database. Increments in interaction records and source publications reported in BioGRID from July 2006 (release 2.0.18) to August 2014 (release 3.2.115). Left panel shows the increase of annotated protein interactions (PI, red), genetic interactions (GI, green) and total interactions (blue). Right panel shows the number of publications that report protein or genetic interactions and the total number of curated publications.

Figure 2.

The Interaction Management System. Overview of the new database architecture that allows BioGRID to transition from a pairwise interaction format to an n-way interaction format for representation of complex protein or genetic interaction relationships. The database schema has also been extended to include support for post-translational modification (PTM) and phenotype curation. The central components illustrated (Interactors, Post-translational Modifications, Interactions, and Ontologies) represent the four major sectors of the IMS architecture. Partial representations of the child support tables that link to the main parent tables are shown but precise entity relationships are not indicated. In total, the IMS contains 57 interlinked tables. All controlled vocabularies (experimental systems, modifications and tags) have been converted into formal ontologies in order to remove redundancies present in the previous database architecture.

Figure 3.

Snapshot of the new IMS curation interface. The main functionalities available to BioGRID curators in the new IMS for the annotation of protein and genetic interactions are shown (A–D). The new system is based on ontologies (E) for the annotation of gene function (Gene Ontology), cell type (Cell Type Ontology), tissue (BRENDA Tissue ontology), small molecules (CheBI), human disease (Human Disease Ontology), human phenotypes (Human Phenotype Ontology, Phenotypic Qualities Ontologies) or anatomical structures (Uberon) and accepts annotation of binary and n-way interactions (F).