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BioGRID: a general repository for interaction datasets

C. Stark
2006 Nucleic Acids Research  
BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org.  ...  Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/ protein function and analysis of global network properties.  ...  ACKNOWLEDGEMENTS We thank Jim Woodgett for generous support and advice, Rachel Drysdale and Don Gilbert for assistance in parsing genetic interactions from FlyBase; Kara Dolinski, Michael Cherry and David  ... 
doi:10.1093/nar/gkj109 pmid:16381927 pmcid:PMC1347471 fatcat:p2t7ikft3fap3e2f72vmk7mqim

BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID

Andrew G. Winter, Jan Wildenhain, Mike Tyers
2011 Computer applications in the biosciences : CABIOS  
The Biological General Repository for Interaction Datasets (BioGRID) representational state transfer (REST) service allows full URL-based access to curated protein and genetic interaction data at the BioGRID  ...  Availability and implementation: BioGRID data and applications are completely free for commercial and non-commercial use. http://webservice.thebiogrid.org/resources/interactions (REST Service), http://  ...  ACKNOWLEDGEMENTS We thank Bobby-Joe Breitkreutz and Chris Stark for reading the manuscript and testing.  ... 
doi:10.1093/bioinformatics/btr062 pmid:21300700 pmcid:PMC3065694 fatcat:ocuiea765jbuzfjweetuqcs62i

The BioGRID Interaction Database

Michael Livstone, Michael Livstone, Bobby-Joe Breitkreutz, Chris Stark, Lorrie Boucher, Andrew Chatr-Aryamontri, Rose Oughtred, Julie Nixon, Teresa Reguly, Jennifer Rust, Andrew Winter, Kara Dolinski (+1 others)
2011 Nature Precedings  
Searching BioGRID The number of interactions ("edges" in the The goal of the Biological General Repository for Interaction Datasets (BioGRID) is to archive and freely disseminate collections of genetic  ...  BioGRID currently contains over 355,000 interactions curated from high-throughput datasets and individual focused studies from over 23,000 publications in the primary literature.  ... 
doi:10.1038/npre.2011.5627 fatcat:wmquh5ym2feztipbjitlwlkxva

The BioGRID Interaction Database: 2008 update

B.-J. Breitkreutz, C. Stark, T. Reguly, L. Boucher, A. Breitkreutz, M. Livstone, R. Oughtred, D. H. Lackner, J. Bahler, V. Wood, K. Dolinski, M. Tyers
2007 Nucleic Acids Research  
The Biological General Repository for Interaction Datasets (BioGRID) database (http://www. thebiogrid.org) was developed to house and distribute collections of protein and genetic interactions from major  ...  A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management  ...  Previously, we described a database called 'Biological General Repository for Interaction Datasets' (BioGRID) (www.thebiogrid.org) to archive and distribute comprehensive collections of physical and genetic  ... 
doi:10.1093/nar/gkm1001 pmid:18000002 pmcid:PMC2238873 fatcat:cqmz56s4uje2tmjr5mejrvompy

The BioGRID Interaction Database

Michael Livstone, Michael Livstone, Bobby-Joe Breitkreutz, Chris Stark, Lorrie Boucher, Andrew Chatr-Aryamontri, Rose Oughtred, Julie Nixon, Teresa Reguly, Jennifer Rust, Andrew Winter, Kara Dolinski (+1 others)
2011 Nature Precedings  
Searching BioGRID The number of interactions ("edges" in the The goal of the Biological General Repository for Interaction Datasets (BioGRID) is to archive and freely disseminate collections of genetic  ...  BioGRID currently contains over 355,000 interactions curated from high-throughput datasets and individual focused studies from over 23,000 publications in the primary literature.  ... 
doi:10.1038/npre.2011.5627.1 fatcat:uovsr42ak5eajb2rs2gargrudu

The BioGRID interaction database: 2019 update

Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer Rust, Lorrie Boucher, Christie Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam, Frederick Zhang, Sonam Dolma (+5 others)
2018 Nucleic Acids Research  
The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions  ...  A new dedicated aspect of BioGRID annotates genome-wide CRISPR/Cas9-based screens that report gene-phenotype and gene-gene relationships.  ...  The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) was first developed as an open-access centralized repository for protein and genetic interaction data reported  ... 
doi:10.1093/nar/gky1079 pmid:30476227 pmcid:PMC6324058 fatcat:72ppbdg3vbbhzfeugxmqu7athm

The BioGRID interaction database: 2013 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Sven Heinicke, Lorrie Boucher, Andrew Winter, Chris Stark, Julie Nixon, Lindsay Ramage, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Ashton Breitkreutz (+8 others)
2012 Nucleic Acids Research  
The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions  ...  This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update.  ...  ACKNOWLEDGEMENTS The authors thank Chris Grove, Paul Sternberg and Anastasia Baryshnikova for ongoing collaborative development of the Genetic Interaction Structured Terminology.  ... 
doi:10.1093/nar/gks1158 pmid:23203989 pmcid:PMC3531226 fatcat:nmn2ijk3qje6jfpsgpzgk2p2nm

The BioGRID Interaction Database: 2011 update

C. Stark, B.-J. Breitkreutz, A. Chatr-aryamontri, L. Boucher, R. Oughtred, M. S. Livstone, J. Nixon, K. Van Auken, X. Wang, X. Shi, T. Reguly, J. M. Rust (+3 others)
2010 Nucleic Acids Research  
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  ...  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.  ...  Sternberg, Bill Gelbart, Gary Bader, Quaid Morris, Olga Troyanskaya, David Botstein, Henning Hermjakob, Shoshana Wodak, Ian Donaldson, Anne-Claude Gingras, Val Wood, Jurg Bahler, Lincoln Stein and Judy Blake for  ... 
doi:10.1093/nar/gkq1116 pmid:21071413 pmcid:PMC3013707 fatcat:5e7qa7hecfbnfj7o3dvxiw4yum

The BioGRID interaction database: 2015 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Julie Nixon (+10 others)
2014 Nucleic Acids Research  
The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein in- teractions curated from the primary biomedical  ...  This interaction count represents a 50% increase compared to our previous 2013 BioGRID update.  ...  ACKNOWLEDGEMENTS The authors thank Chris Grove and Paul Sternberg at WormBase for ongoing collaborative development of the Genetic Interaction Ontology. We also thank Mike Cherry  ... 
doi:10.1093/nar/gku1204 pmid:25428363 pmcid:PMC4383984 fatcat:jeok6meldzhmphu3mpxqxpeoiy

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions

Rose Oughtred, Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Christie S. Chang, Jennifer M. Rust, Chandra L. Theesfeld, Sven Heinicke, Ashton Breitkreutz, Daici Chen, Jodi Hirschman, Nadine Kolas, Michael S. Livstone (+10 others)
2016 Cold Spring Harbor Protocols  
The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and the yeast Candida  ...  viewer, and how to download data files for either selected interactions or the entire BioGRID interaction data set.  ...  ACKNOWLEDGMENTS The authors thank Chris Grove and Paul Sternberg at WormBase for ongoing collaborative development of the Genetic Interaction Ontology.  ... 
doi:10.1101/pdb.prot088880 pmid:26729909 pmcid:PMC5975959 fatcat:ublifsrndreuhomte4g7527r2e

GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction

Fiona Browne, Haiying Wang, Huiru Zheng, Francisco Azuaje
2009 Source Code for Biology and Medicine  
Both positive and negative cases for a reference dataset can be extracted, organised and downloaded by the user.  ...  Although, the automatic construction of reference datasets for classification is a useful resource for researchers no public resource currently exists to perform this task.  ...  Acknowledgements We wish to thank Anyela Camargo for her help and expertise with the hosting of GRIP on a Linux server.  ... 
doi:10.1186/1751-0473-4-2 pmid:19171033 pmcid:PMC2636808 fatcat:r5dshd57eze5bcw7i7a74kbhkq

Towards Evaluation of Inferred Gene Network

S. Zainudin, S. Deris
2007 2007 International Conference on Computational Science and its Applications (ICCSA 2007)  
Gene network is a representation for gene interactions. A gene collaborates with other genes in order to function.  ...  Gene expression microarray data represent different levels of gene expressions for organisms during biological activity such as cell cycle.  ...  Introduction to Biogrid Biogrid is a freely accessible repository of protein and genetic interactions.  ... 
doi:10.1109/iccsa.2007.29 dblp:conf/iccsa/ZainudinD07 fatcat:dfuovkd4vbd4bclfcdtqp47lza

Inter-Tools: a toolkit for interactome analysis [article]

Hannah Beth Catabia, Caren Smith, Jose Ordovas
2017 bioRxiv   pre-print
Inter-Tools allows users to search databases in the PSI-MITAB standard format for interactions meeting specified criteria, then combine them into a single, species-specific interactome dataset.  ...  However, protein interaction data is scattered among different sources, and researchers must often sift through several large repositories before beginning a project.  ...  There are currently several different repositories that catalog protein-protein interactions (PPIs) in the standard PSI-MITAB [1] format: BioGRID [2] , IntAct [3] , the Database of Interacting Proteins  ... 
doi:10.1101/150706 fatcat:q3vsja76dfbgtohrg7ate4fcri

Open Data for Differential Network Analysis in Glioma

Claire Jean-Quartier, Fleur Jeanquartier, Andreas Holzinger
2020 International Journal of Molecular Sciences  
networks as a basis for signaling.  ...  The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only.  ...  Acknowledgments: We thank the PCAWG project as well as tool providers such as EMBL-EBI with its Expression Atlas, the STRING consortium and cBioPortal's maintainers and its collaborators for providing  ... 
doi:10.3390/ijms21020547 pmid:31952211 pmcid:PMC7013918 fatcat:5a5wbq4t75bp5jkkucrsemxgp4

Recurated protein interaction datasets

Lukasz Salwinski, Luana Licata, Andrew Winter, David Thorneycroft, Jyoti Khadake, Arnaud Ceol, Andrew Chatr Aryamontri, Rose Oughtred, Michael Livstone, Lorrie Boucher, David Botstein, Kara Dolinski (+6 others)
2009 Nature Methods  
) 5 and the Biological General Repository for Interaction Datasets (BioGRID) 6 critiqued by Cusick et al. 1 is to collect and organize experiments supporting protein-protein interactions into a comprehensive  ...  These databases allow the biological community facile and searchable access to a vast repository of biological interactions for many purposes ranging from individual hypothesis generation to functional  ... 
doi:10.1038/nmeth1209-860 pmid:19935838 fatcat:yevtbhfilzf2tpuwu3dxp7o6ba
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