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BioGRID: a general repository for interaction datasets
2006
Nucleic Acids Research
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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
2011
Computer applications in the biosciences : CABIOS
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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
2011
Nature Precedings
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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
2007
Nucleic Acids Research
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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
2011
Nature Precedings
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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
2018
Nucleic Acids Research
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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
2012
Nucleic Acids Research
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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
2010
Nucleic Acids Research
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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
2014
Nucleic Acids Research
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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
2016
Cold Spring Harbor Protocols
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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
2009
Source Code for Biology and Medicine
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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
2007
2007 International Conference on Computational Science and its Applications (ICCSA 2007)
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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]
2017
bioRxiv
pre-print
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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
2020
International Journal of Molecular Sciences
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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
2009
Nature Methods
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) 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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