a-r-j / DrugTranslatoR

R package for translating between drug identifiers using the Chemical Translation Service (CTS)

DrugTranslatoR

R package for translating between drug identifiers using the Chemical Translation Service (CTS)

Details

Simple R wrapper to send HTTP requests to the CTS server.

Installation

# install devtools if required
if (!requireNamespace("devtools")) install.packages("devtools")
# then install DrugTranslatoR
devtools::install_github("a-r-j/DrugTranslatoR")

Usage

translateDrugID(from, to, query) - Translate between different drug/chemical identifiers
sourceIDs() - Fetch list of valid identifies that can be translated from
targetIDs() - Fetch list of valid identifiers that can be translated to
expandChemicalFormula(formula) - Expands a compact chemical formula
InChIKey2MolDef(inchikey) - Converts InChIKey to molecule definition (MDL/SDF)
countBiologicalIDs(inchikey) - Counts biological IDs for InChIKey
scoredInChiKeys(from, query, algorithm) - Gets a list of scored InChIKeys

Reference:

The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports. Gert Wohlgemuth, Pradeep Kumar Haldiya, Egon Willighagen, Tobias Kind, Oliver Fiehn. Bioinformatics, Volume 26, Issue 20, 15 October 2010, Pages 2647–2648, https://doi.org/10.1093/bioinformatics/btq476