search the Human Metabolome Database from the R Console
devtools::install_github("wilsontom/hmdbR")
library(hmdbR)
results <- search_hmdb("anserine")
dim(results)
[1] 3 7
results[,"name"]
[1] "Anserine" "Homoanserine" "Mianserin"
results[,c("name", "smiles", "accession_id")]
name smiles accession_id
126 Anserine CN1C=NC=C1C[C@H](NC(=O)CCN)C(O)=O HMDB00194
2541 Homoanserine CN1C=NC=C1C[C@H](NC(=O)CCCN)C(O)=O HMDB05767
9876 Mianserin CN1CCN2C(C1)C1=CC=CC=C1CC1=CC=CC=C21 HMDB15620
Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35 (Database issue):D521-6. 17202168
Wishart DS, Knox C, Guo AC, et al., HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 37(Database issue):D603-610. 18953024
Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0 — The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7. 23161693
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