R interface to the [Chemical Translation Service (CTS)] (http://cts.fiehnlab.ucdavis.edu/)
#library(devtools) # install.packages("devtools") if missing
#install_github(repo = "CTSgetR", username = "dgrapov",ref="simple")
library(CTSgetR)help(CTSgetR)trans<-unlist(CTS.options())
head(trans,10)## [1] "BioCyc" "CAS"
## [3] "ChEBI" "Chemical Name"
## [5] "Human Metabolome Database" "InChI Code"
## [7] "InChIKey" "KEGG"
## [9] "LMSD" "LipidMAPS"
want<-'zinc'
fuzzy<-1 # larger more fuzzy matching
trans[agrepl(want,trans,ignore.case=TRUE,max.distance=fuzzy)]## [1] "InChI Code" "InChIKey"
## [3] "ZINC" "Tetrahedron Scientific Inc"
## [5] "AK Scientific, Inc. (AKSCI)" "Ark Pharm, Inc."
## [7] "Zancheng Functional Chemicals"
library(CTSgetR)
#translate from chemical name to InchiKey
id<-"alanine"
from<-"Chemical Name"
to<-"InChIKey"
CTSgetR(id,from,to,progress=FALSE)## fromIdentifier searchTerm toIdentifier value
## 1 Chemical Name alanine InChIKey QNAYBMKLOCPYGJ-REOHCLBHSA-N
#translate from one to many identifiers
id<-c("DMULVCHRPCFFGV-UHFFFAOYSA-N","ZPUCINDJVBIVPJ-LJISPDSOSA-N","ZAGRKAFMISFKIO-QMTHXVAHSA-N")
from<-"InChIKey"
to<- c("Chemical Name", "PubChem CID", "KEGG","Human Metabolome Database")
CTSgetR(id,from,to,progress=FALSE,limit.values = FALSE)## fromIdentifier searchTerm toIdentifier
## 1 InChIKey DMULVCHRPCFFGV-UHFFFAOYSA-N Chemical Name
## 2 InChIKey DMULVCHRPCFFGV-UHFFFAOYSA-N Chemical Name
## 3 InChIKey ZPUCINDJVBIVPJ-LJISPDSOSA-N Chemical Name
## 4 InChIKey ZPUCINDJVBIVPJ-LJISPDSOSA-N Chemical Name
## 5 InChIKey ZAGRKAFMISFKIO-QMTHXVAHSA-N Chemical Name
## 6 InChIKey ZAGRKAFMISFKIO-QMTHXVAHSA-N Chemical Name
## 7 InChIKey DMULVCHRPCFFGV-UHFFFAOYSA-N PubChem CID
## 8 InChIKey ZPUCINDJVBIVPJ-LJISPDSOSA-N PubChem CID
## 9 InChIKey ZAGRKAFMISFKIO-QMTHXVAHSA-N PubChem CID
## 10 InChIKey ZAGRKAFMISFKIO-QMTHXVAHSA-N PubChem CID
## 11 InChIKey DMULVCHRPCFFGV-UHFFFAOYSA-N KEGG
## 12 InChIKey ZPUCINDJVBIVPJ-LJISPDSOSA-N KEGG
## 13 InChIKey ZAGRKAFMISFKIO-QMTHXVAHSA-N KEGG
## 14 InChIKey DMULVCHRPCFFGV-UHFFFAOYSA-N Human Metabolome Database
## 15 InChIKey ZPUCINDJVBIVPJ-LJISPDSOSA-N Human Metabolome Database
## 16 InChIKey ZAGRKAFMISFKIO-QMTHXVAHSA-N Human Metabolome Database
## value
## 1 2-(1H-Indol-3-yl)-N,N-dimethylethanamine
## 2 1H-Indole-3-ethanamine, N,N-dimethyl-
## 3 8-Azabicyclo[3.2.1]octane-2-carboxylic acid, 3-(benzoyloxy)-8-methyl-, methyl ester, (1R,2R,3S,5S)-
## 4 Methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate
## 5 (8beta)-6-Methyl-9,10-didehydroergoline-8-carboxylic acid
## 6 Ergoline-8-carboxylic acid, 9,10-didehydro-6-methyl-, (8beta)-
## 7 6089
## 8 446220
## 9 11861108
## 10 6717
## 11 C08302
## 12 C01416
## 13
## 14 HMDB05973
## 15
## 16
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