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PMID: 23203989 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The BioGRID interaction database: 2013 update.

Nucleic acids research ·Vol. 41 ·No. Database issue ·2013-01-00 ·Pages D816-23

Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O'Donnell L, Reguly T, Breitkreutz A, Sellam A, Chen D, Chang C, Rust J, Livstone M, Oughtred R, Dolinski K, Tyers M

Abstract

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.

MeSH Terms
Arabidopsis/genetics,metabolism Databases, Genetic Gene Regulatory Networks Humans Internet Protein Interaction Mapping Saccharomyces cerevisiae/genetics,metabolism Schizosaccharomyces/genetics,metabolism User-Computer Interface
Authors & Affiliations
20 authors, click to expand affiliations / ORCID
Chatr-Aryamontri Andrew
Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada H3C 3J7.
Breitkreutz Bobby-Joe
Heinicke Sven
Boucher Lorrie
Winter Andrew
Stark Chris
Nixon Julie
Ramage Lindsay
Kolas Nadine
O'Donnell Lara
Reguly Teresa
Breitkreutz Ashton
Sellam Adnane
Chen Daici
Chang Christie
Rust Jennifer
Livstone Michael
Oughtred Rose
Dolinski Kara
Tyers Mike
References (48)
48 references, click to expand
  1. Cytoscape 2.8: new features for data integration and network visualization.
    Bioinformatics. 2011 Feb 1;27(3):431-2 PMID: 21149340
  2. A census of human soluble protein complexes.
    Cell. 2012 Aug 31;150(5):1068-81 PMID: 22939629
  3. Global landscape of HIV-human protein complexes.
    Nature. 2011 Dec 21;481(7381):365-70 PMID: 22190034
  4. Global gene deletion analysis exploring yeast filamentous growth.
    Science. 2012 Sep 14;337(6100):1353-6 PMID: 22984072
  5. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.
    Nature. 2012 Jul 26;487(7408):491-5 PMID: 22810586
  6. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
    BMC Bioinformatics. 2011 Oct 03;12 Suppl 8:S3 PMID: 22151929
  7. BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID.
    Bioinformatics. 2011 Apr 1;27(7):1043-4 PMID: 21300700
  8. genenames.org: the HGNC resources in 2011.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D514-9 PMID: 20929869
  9. iRefIndex: a consolidated protein interaction database with provenance.
    BMC Bioinformatics. 2008 Sep 30;9:405 PMID: 18823568
  10. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8 PMID: 21045058
  11. Textpresso: an ontology-based information retrieval and extraction system for biological literature.
    PLoS Biol. 2004 Nov;2(11):e309 PMID: 15383839
  12. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25 PMID: 22140104
  13. VectorBase: a data resource for invertebrate vector genomics.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D583-7 PMID: 19028744
  14. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
    BMC Biol. 2007 Oct 09;5:44 PMID: 17925023
  15. GenBank.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7 PMID: 21071399
  16. FlyBase 101--the basics of navigating FlyBase.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D706-14 PMID: 22127867
  17. Boosting signal-to-noise in complex biology: prior knowledge is power.
    Cell. 2011 Mar 18;144(6):860-3 PMID: 21414478
  18. Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases.
    BMC Bioinformatics. 2011 Oct 03;12 Suppl 8:S8 PMID: 22151178
  19. Human Protein Reference Database--2009 update.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72 PMID: 18988627
  20. GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle.
    Database (Oxford). 2010 Dec 11;2010:baq030 PMID: 21149299
  21. How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.
    Database (Oxford). 2012 Mar 21;2012:bas017 PMID: 22438567
  22. Next-generation sequencing to generate interactome datasets.
    Nat Methods. 2011 Jun;8(6):478-80 PMID: 21516116
  23. Saccharomyces Genome Database: the genomics resource of budding yeast.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5 PMID: 22110037
  24. The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D667-74 PMID: 22064862
  25. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
    Nucleic Acids Res. 2010 Jul;38(Web Server issue):W214-20 PMID: 20576703
  26. Pathway Commons, a web resource for biological pathway data.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90 PMID: 21071392
  27. The ubiquitin system, an immense realm.
    Annu Rev Biochem. 2012;81:167-76 PMID: 22663079
  28. PomBase: a comprehensive online resource for fission yeast.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D695-9 PMID: 22039153
  29. ProHits: integrated software for mass spectrometry-based interaction proteomics.
    Nat Biotechnol. 2010 Oct;28(10):1015-7 PMID: 20944583
  30. A global protein kinase and phosphatase interaction network in yeast.
    Science. 2010 May 21;328(5981):1043-6 PMID: 20489023
  31. Big data: The future of biocuration.
    Nature. 2008 Sep 4;455(7209):47-50 PMID: 18769432
  32. Reorganizing the protein space at the Universal Protein Resource (UniProt).
    Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5 PMID: 22102590
  33. BioCreative III interactive task: an overview.
    BMC Bioinformatics. 2011 Oct 03;12 Suppl 8:S4 PMID: 22151968
  34. Text mining for the biocuration workflow.
    Database (Oxford). 2012 Apr 18;2012:bas020 PMID: 22513129
  35. A protein interaction network of the malaria parasite Plasmodium falciparum.
    Nature. 2005 Nov 3;438(7064):103-7 PMID: 16267556
  36. Mass spectrometry-based proteomics and network biology.
    Annu Rev Biochem. 2012;81:379-405 PMID: 22439968
  37. WormBase 2012: more genomes, more data, new website.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D735-41 PMID: 22067452
  38. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.
    Nature. 2012 Sep 27;489(7417):585-9 PMID: 22940862
  39. The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D881-6 PMID: 22075990
  40. DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D736-43 PMID: 21036869
  41. Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D658-62 PMID: 21071397
  42. The BioGRID Interaction Database: 2011 update.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704 PMID: 21071413
  43. Ensembl 2012.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90 PMID: 22086963
  44. DAnCER: disease-annotated chromatin epigenetics resource.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D889-94 PMID: 20876685
  45. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10 PMID: 22140109
  46. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
    Nat Methods. 2012 Apr;9(4):345-50 PMID: 22453911
  47. Osprey: a network visualization system.
    Genome Biol. 2003;4(3):R22 PMID: 12620107
  48. ZFIN: enhancements and updates to the Zebrafish Model Organism Database.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D822-9 PMID: 21036866
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gks1158
Published
2013-01-00
Epub
2012-00-30
Pages
D816-23
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3531226
Subset
IM
Grants
NIH HHS · R01 OD010929 · United States
NCRR NIH HHS · R01RR024031 · United States
NCRR NIH HHS · R24RR032659 · United States
Wellcome Trust · 092076 · United Kingdom
CIHR · FRN 82940 · Canada
NIH HHS · R24 OD011194 · United States
Biotechnology and Biological Sciences Research Council · BB/F010486/1 · United Kingdom
NCRR NIH HHS · R24 RR032659 · United States
External Links
PubMed source DOI: 10.1093/nar/gks1158 PMC Full Text View journal details
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