In DrugComb/TidyComb: Preparing drug combination data for DrugComb

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(TidyComb)

1. PubChem

1. Get CID from PubChem

GetCid queries PubChem database via PUG REST to search matched CIDs of drugs according to other identifiers. Available identifiers are: name, SMILES, InChIKey.

GetCid(c("aspirin", "blebbistatin"), type = "name")
GetCid("RDHQFKQIGNGIED-UHFFFAOYSA-N", type = "inchikey")
GetCid("CC1(CCCN1)C2=NC3=C(C=CC=C3N2)C(=O)N.Cl.Cl", type = "smiles")

2. Get drug name or synonyms

Drug name and synonyms from CID

GetPubNames(c(2244, 1))

Drug name and synonyms from Name

names <- c("Aspirin", "5-FU")
synonyms <- GetPubSynonymFromName(names)

3. Get drug property from CID

Drug properties

GetPubchemPro(c(2244, 1))

Max clinital trial phase: `GetPubPhase

GetPubPhase(c(2244, 1))

1. ChEMBL

Check the database version information of ChEMBL

ChemblVersion()

Get ChEMBL ID and max clinical trial with InChI Key

GetChembl("PMATZTZNYRCHOR-CGLBZJNRSA-N")

1. UniChem

Get DrugBank ID, KEGG compound ID, and ChEMBL ID with InChI Key from UniChem

GetIds(inchikey = "BSYNRYMUTXBXSQ-UHFFFAOYSA-N")

DrugComb/TidyComb documentation built on June 22, 2022, 2:49 a.m.