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BioGRID

A curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. The current version searches over 41,000 publications containing over 720,000 interactions (June 2014) and contributions are welcome. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. It provides interaction data to several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including IMEx compatible PSI MI XML. For developers, BioGRID interactions are also available via a REST based Web Service and Cytoscape plugin.

URL: http://www.thebiogrid.org/

Resource ID: nif-0000-00432     Resource Type: Resource     Version: Latest Version

Keywords

budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics

Funding Information

NIH, BBSRC, Canadian Institutes of Health Research, R01 RR024031

Additional Resource Types

database, software resource, data repository

Used By

NIF Data Federation, Monarch Initiative

Alternate IDs

OMICS_01901

Related To

Resource:Cytoscape, Resource:PSI-MI, Resource:NIH Data Sharing Repositories

Abbreviation

BioGRID

Parent Organization

Related Application

Research

Species

saccharomyces cerevisiae, schizosaccharomyces pombe, arabidopsis thaliana, metazoa, human, mouse, caenorhabditis elegans, drosophila melanogaster, other

Synonyms

Biological General Repository for Interaction Datasets

Comment

Start date: 2003 Type: Disciplinary Deposit: Accepting data for deposit - http://wiki.thebiogrid.org/doku.php/contribute#send_us_your_interaction_data

Listed By

re3data.org, OMICtools, DataCite, NIH Data Sharing Repositories

Availability

Public, Free, Only for research, The community can contribute to this resource

Supercategory

Resource

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 20, 2010

Originated From

SciCrunch

Changes from Previous Version

  • Description was changed
  • Related To was changed
  • Comment was changed
  • Listed By was changed

Version 2

Created 1 month ago by Kristen Jensen

Version 1

Created 5 years ago by Anonymous

The GRID: the General Repository for Interaction Datasets.

  • Breitkreutz BJ
  • Genome Biol.
  • 2003 6

We have developed a relational database, called the General Repository for Interaction Datasets (The GRID) to archive and display physical, genetic and functional interactions. The GRID displays data-rich interaction tables for any protein of interest, combines literature-derived and high-throughput interaction datasets, and is readily accessible via the web. Interactions parsed in The GRID can be viewed in graphical form with a versatile visualization tool called Osprey.

BioGRID: a general repository for interaction datasets.

  • Stark C
  • Nucleic Acids Res.
  • 2006 1

Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org. BioGRID release version 2.0 includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. Over 30 000 interactions have recently been added from 5778 sources through exhaustive curation of the Saccharomyces cerevisiae primary literature. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.

The BioGRID Interaction Database: 2011 update.

  • Stark C
  • Nucleic Acids Res.
  • 2011 23

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347,966 interactions (170,162 genetic, 177,804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48,831 human protein interactions that have been curated from 10,247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions.

The BioGRID interaction database: 2013 update.

  • Chatr-Aryamontri A
  • Nucleic Acids Res.
  • 2013 20

The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and the model plant Arabidopsis thaliana. A number of themed curation projects in areas of biomedical importance are also supported. BioGRID has established collaborations and/or shares data records for the annotation of interactions and phenotypes with most major model organism databases, including Saccharomyces Genome Database, PomBase, WormBase, FlyBase and The Arabidopsis Information Resource. BioGRID also actively engages with the text-mining community to benchmark and deploy automated tools to expedite curation workflows. BioGRID data are freely accessible through both a user-defined interactive interface and in batch downloads in a wide variety of formats, including PSI-MI2.5 and tab-delimited files. BioGRID records can also be interrogated and analyzed with a series of new bioinformatics tools, which include a post-translational modification viewer, a graphical viewer, a REST service and a Cytoscape plugin.