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The BioGRID interaction database: 2015 update
2014
Nucleic Acids Research
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This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. ...
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 ...
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
The BioGRID interaction database: 2013 update
2012
Nucleic Acids Research
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This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. ...
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 ...
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: 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 ...
BioGRID now captures chemical interaction data, including chemical-protein interactions for human drug targets drawn from the DrugBank database and manually curated bioactive compounds reported in the ...
ACKNOWLEDGEMENTS The authors thank John Aitchison, Brenda Andrews, Gary Bader, Anastasia Baryshnikova ...
doi:10.1093/nar/gky1079
pmid:30476227
pmcid:PMC6324058
fatcat:72ppbdg3vbbhzfeugxmqu7athm
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
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015
2014
Nucleic Acids Research
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Ten years ago, the Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) was developed out of a need to formalize, harmonize and centralize the information on numerous genes and proteins responding ...
The prototype database originally described in our first report has transformed into a sophisticated resource used actively today to help scientists develop and test hypotheses about the etiologies of ...
ACKNOWLEDGEMENTS We thank Roy McMorran for CTD system/database administration. ...
doi:10.1093/nar/gku935
pmid:25326323
pmcid:PMC4384013
fatcat:7frs7rcwlfdmzmqlm5eagcfkva
HitPredict version 4: comprehensive reliability scoring of physical protein–protein interactions from more than 100 species
2015
Database: The Journal of Biological Databases and Curation
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The combined interaction score performs better than either of the individual scores in HitPredict as well as the reliability score of another similar database. ...
Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of physical, genetic and predicted ...
Supplementary Data Supplementary data are available at Database Online. Figure 1 . 1 HitPredict database content in all updates from 2005 to 2015. ...
doi:10.1093/database/bav117
pmid:26708988
pmcid:PMC4691340
fatcat:7jy6xrtonvbxxg7camvpmf7tuq
Measuring pathway database coverage of the phosphoproteome
2021
PeerJ
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We first determined the global coverage of each database at both the protein and phosphosite level. ...
Finally, we looked in detail at the coverage of each database over six experimental datasets. ...
ACKNOWLEDGEMENTS The authors thank Daniel Esposito, Samuel Lee and Dharmesh Bhuva for technical support.
ADDITIONAL INFORMATION AND DECLARATIONS ...
doi:10.7717/peerj.11298
pmid:34113485
pmcid:PMC8162239
fatcat:yx4zibz3cvcm7h344ie3g2ge5u
Database of RNA binding protein expression and disease dynamics (READ DB)
2015
Database: The Journal of Biological Databases and Curation
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Database URL: READ DB is freely available on the web at http://darwin.soic.iupui.edu/ with all major browsers supported. ...
RNA Binding Protein (RBP) Expression and Disease Dynamics database (READ DB) is a non-redundant, curated database of human RBPs. ...
(G) Protein-Protein Interactions Protein interactions for RBPs are retrieved from BioGRID database (8) . ...
doi:10.1093/database/bav072
pmid:26210853
pmcid:PMC4515031
fatcat:hm6xi7b7bzat3laoxvgr5yzske
GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes
2015
Database: The Journal of Biological Databases and Curation
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available databases, as a summary story. ...
The most challenging part during the development of the GeneStoryTeller was to keep balance between storing data locally within the app and obtaining the updated content dynamically via a network connection ...
/) (6) and (iii) PathWayCommons (www.pathwaycom-mons.org/) (7), (iv) the protein-protein interaction repository Biogrid (http://thebiogrid.org/) (8), (v) the Drug-Gene Interaction database DGIdb (http: ...
doi:10.1093/database/bav048
pmid:26055097
pmcid:PMC4460399
fatcat:j2iyqpovhbcsfk3egknh4xryhu
HPIDB 2.0: a curated database for host–pathogen interactions
2016
Database: The Journal of Biological Databases and Curation
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All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. ...
Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. ...
Acknowledgements The authors thank the IntAct biocurators for training, support and access to the IntAct curation system. ...
doi:10.1093/database/baw103
pmid:27374121
pmcid:PMC4930832
fatcat:4jnd4gtbcnfwtn2e6eei2mlqse
Integrated web visualizations for protein-protein interaction databases
2015
BMC Bioinformatics
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The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. ...
There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. ...
The research work was later on improved and narrowed down by the authors. ...
doi:10.1186/s12859-015-0615-z
pmid:26077899
pmcid:PMC4466863
fatcat:zgaaf7hwnbap5ayondw3eqqhgu
The human DEPhOsphorylation Database DEPOD: 2019 update
2019
Database: The Journal of Biological Databases and Curation
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We report here an update to DEPOD by integrating and/or linking to annotations from 69 other open access databases including disease associations, phosphorylating kinases, protein interactions, and also ...
The human Dephosphorylation Database (DEPOD) is a manually curated resource that harbors human phosphatases, their protein and non-protein substrates, dephosphorylation sites and the associated signaling ...
The authors would like to thank the users of DEPOD and colleagues for their feedback (see also the acknowledgments section online). ...
doi:10.1093/database/baz133
pmid:31836896
pmcid:PMC6911163
fatcat:gkmqr3epm5bfvb3zxkn3kp26ee
FR database 1.0: a resource focused on fruit development and ripening
2015
Database: The Journal of Biological Databases and Curation
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Furthermore, protein-protein interaction analysis by integrating information from FR database presents the possible function network that affects fleshy fruit size formation. ...
Collectively, FR database will be a valuable platform for comprehensive understanding and future experiments in fruit biology. Database URL: http://www.fruitech.org/ V C The Author(s) ...
Acknowledgements The authors thank earnestly Dr. Yuanwei Zhang for his generous help. ...
doi:10.1093/database/bav002
pmid:25725058
pmcid:PMC4343184
fatcat:xu4ewjt2e5aijblh5jjbp5ohpy
YCRD: Yeast Combinatorial Regulation Database
2016
PLoS ONE
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Because there is no such kind of databases in the public domain, this prompts us to construct a database, called Yeast Combinatorial Regulation Database (YCRD), which deposits 434,197 regulatory associations ...
TF1-TF2) are defined as the common target genes of TF1 and TF2, where a TF's experimentally validated target genes were downloaded from YEASTRACT database. ...
Acknowledgments The physical/genetic interaction data and a TF's experimentally validated target genes were retrieved from BioGRID and YEASTRACT in March 2016, respectively. ...
doi:10.1371/journal.pone.0159213
pmid:27392072
pmcid:PMC4938206
fatcat:ms2wntabaff77b7ynqsspyvapa
The Comparative Toxicogenomics Database: update 2017
2016
Nucleic Acids Research
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The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between chemicals and gene products, and their relationships to diseases. ...
In this update, we report a 33% increase in our core data content since 2015, describe our new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduce ...
This represents a 33% increase in chemical-gene-disease interactions since our last update (4) . ...
doi:10.1093/nar/gkw838
pmid:27651457
pmcid:PMC5210612
fatcat:povogyqyofcebnljc3jnl4fnoq
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