DGIdb 2.0: mining clinically relevant drug–gene interactions

By A. Wagner, Adam C. Coffman, Benjamin J. Ainscough, N. Spies, Zachary L. Skidmore, Katie M. Campbell, K. Krysiak, Deng Pan, Joshua F. McMichael, James M. Eldred and 5 more. Nucleic Acids Res., 2015

394 citations recorded by the source corpus.

The Drug–Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that consolidates disparate data sources describing drug–gene interactions and gene druggability. It provides an intuitive graphical user interface and a documented application programming interface (API) for querying these data. DGIdb was assembled through an extensive manual curation effort, reflecting the combined information of twenty-seven sources. For DGIdb 2.0, substantial updates have been made to increase content and improve its usefulness as a resource for mining clinically actionable drug targets. Specifically, nine new sources of drug–gene interactions have been added, including seven resources specifically focused on interactions linked to clinical trials. These additions have more than doubled the overall count of drug–gene interactions. The total number of druggable gene claims has also increased by 30%. Importantly, a majority of the unrestricted, publicly-accessible sources used in DGIdb are now automatically updated on a weekly basis, providing the most current information for these sources. Finally, a new web view and API have been developed to allow searching for interactions by drug identifiers to complement existing gene-based search functionality. With these updates, DGIdb represents a comprehensive and user friendly tool for mining the druggable genome for precision medicine hypothesis generation.

Subfields: Computational Theory and Mathematics, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/f23500ac9594a102f90da506368935bc8a769399

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Citations in the corpus

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer (2017, background): “The goals of this group are to (1) harmonize global efforts for clinical interpretation of”
DGIdb 3.0: a redesign and expansion of the drug–gene interaction database (2017, neutral): “DGIdb 2.0 was released in 2016 and featured substantial content updates, a more intuitive user interface, and the inclusion of an API (2).”
Human Ageing Genomic Resources: new and updated databases (2017, methodology): “DrugAge is also integrated with other HAGR databases using drug-gene interaction data from DGIdb (42).”
Machine learning approaches and databases for prediction of drug–target interaction: a survey paper (2020, background): “The first release (in 2013) of DGIdb integrated 13 data sources that cover information in disease-related human genes, drugs, drug interactions and potential druggability [263,264].”