TY - JOUR
T1 - DGIdb 5.0
T2 - rebuilding the drug-gene interaction database for precision medicineãnd drug discovery platforms
AU - Cannon, Matthew
AU - Stevenson, James
AU - Stahl, Kathryn
AU - Basu, Rohit
AU - Coffman, Adam
AU - Kiwala, Susanna
AU - McMichael, Joshua F.
AU - Kuzma, Kori
AU - Morrissey, Dorian
AU - Cotto, Kelsy
AU - Mardis, Elaine R.
AU - Griffith, Obi L.
AU - Griffith, Malachi
AU - Wagner, Alex H.
N1 - Publisher Copyright:
© The Author(s) 2023.
PY - 2024/1/5
Y1 - 2024/1/5
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85181760552&partnerID=8YFLogxK
U2 - 10.1093/nar/gkad1040
DO - 10.1093/nar/gkad1040
M3 - Article
C2 - 37953380
AN - SCOPUS:85181760552
SN - 0305-1048
VL - 52
SP - D1227-D1235
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -