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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  
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

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  
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

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  ...  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

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

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015

Allan Peter Davis, Cynthia J. Grondin, Kelley Lennon-Hopkins, Cynthia Saraceni-Richards, Daniela Sciaky, Benjamin L. King, Thomas C. Wiegers, Carolyn J. Mattingly
2014 Nucleic Acids Research  
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

Yosvany López, Kenta Nakai, Ashwini Patil
2015 Database: The Journal of Biological Databases and Curation  
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

Hannah Huckstep, Liam G. Fearnley, Melissa J. Davis
2021 PeerJ  
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)

Seyedsasan Hashemikhabir, Yaseswini Neelamraju, Sarath Chandra Janga
2015 Database: The Journal of Biological Databases and Curation  
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

Stergiani V. Eleftheriou, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou
2015 Database: The Journal of Biological Databases and Curation  
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

Mais G. Ammari, Cathy R. Gresham, Fiona M. McCarthy, Bindu Nanduri
2016 Database: The Journal of Biological Databases and Curation  
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

Fleur Jeanquartier, Claire Jean-Quartier, Andreas Holzinger
2015 BMC Bioinformatics  
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  
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

J. Yue, X. Ma, R. Ban, Q. Huang, W. Wang, J. Liu, Y. Liu
2015 Database: The Journal of Biological Databases and Curation  
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

Wei-Sheng Wu, Yen-Chen Hsieh, Fu-Jou Lai, Robertus A M de Bruin
2016 PLoS ONE  
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

Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Benjamin L. King, Roy McMorran, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly
2016 Nucleic Acids Research  
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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