DGIdb 5.0: rebuilding the drug-gene interaction database for precision medicineãnd drug discovery platforms

Matthew Cannon, James Stevenson, Kathryn Stahl, Rohit Basu, Adam Coffman, Susanna Kiwala, Joshua F. McMichael, Kori Kuzma, Dorian Morrissey, Kelsy Cotto, Elaine R. Mardis, Obi L. Griffith, Malachi Griffith, Alex H. Wagner

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

The Drug-Gene Interaction Database (DGIdb, https://dgidb.org ) isã publiclyãccessible resource thatãggregates genes or gene products, drugsãnd drug-gene interaction records to drive hypothesis generationãnd discovery for cliniciansãnd researchers. DGIdb 5.0 is the latest releaseãnd includes substantialãrchitecturalãnd functional updates to support integration into clinicalãnd drug disco v ery pipelines. T he DGIdb serviceãrchitecture has been split into separate clientãnd serverãpplications, enabling consistent dataãccess for users of both theãpplication pro- gramming interface (API)ãnd web interface. The new interface was developed in ReactJS,ãnd includes dynamic visualizationsãnd consistency in the display of user interface elements. A GraphQL API has beenãdded to support customizable queries forãll drugs, genes,ãnnotationsãndãssociated data. Updated documentation provides users with example queriesãnd detailed usage instructions for these new features. Inãddition, six sources ha v e beenãddedãnd man y e xisting sources ha v e been updated. Newlyãdded sources include ChemIDplus, HemOnc, NCIt (National Cancer Institute Thesaurus), Drugs@FDA, HGNC (HUGO Gene Nomenclature Committee)ãnd RxNorm. T hese ne w sources ha v e been incorporated into DGIdb to provideãdditional recordsãnd enhanceãnnotations of regulatoryãppro vãl status for therapeutics. Methods for grouping drugsãnd genes have been expanded uponãnd developedãs independent modular normalizers during import. The updates to these sourcesãnd grouping methods ha v e resulted inãn impro v ement in FAIR (findabilit y,ãccessibilit y, interoperabilit yãnd reusabilit y) datã representation in DGIdb.

Original languageEnglish
Pages (from-to)D1227-D1235
JournalNucleic acids research
Volume52
Issue numberD1
DOIs
StatePublished - Jan 5 2024

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