HMDB_ID_from_name: Query Human Metabolome Database by metabolite name

In venkmurthy/vmtools: Venk Murthy's Handy Tools

Query Human Metabolome Database by metabolite name

Description

This function searches the HMDB to find the canonical HMDB ID for a given metabolite name. It does look through the synonym list as well. Importantly, it takes the *first* match among the names returned by the HMDB search engine and if none, the first match among the synonyms.

Usage

HMDB_ID_from_name(met.names, max.depth = 25, max.tries = 5)

Arguments

max.depth	number indicating how many entries to be checked (may be slightly more than this, depending on entries per page)
max.tries	number of times to retry loading a page
met.name	string containing metabolite name

Value

string with canonical HMDB ID

Examples

HMDB_ID_from_one_name("valine")
HMDB_ID_from_one_name("ectoine")

test.list <- c("valine-d8","phenylalanine-d8","glycine","alanine","serine","threonine","methionine","glutamate",
"asparagine","glutamine","histidine","arginine","lysine","valine","leucine","isoleucine","phenylalanine",
"tyrosine","tryptophan","proline","hydroxyproline","ornithine","citrulline","taurine","GABA",
"dimethylglycine","ADMA","SDMA","NMMA","2-aminoisobutyric acid","kynurenic acid","1-methylhistamine",
"N-carbamoyl-beta-alanine","thiamine","niacinamide","betaine","PE(P-36:4)/PE(O-36:5)","PE(P-36:2)/PE(O-36:3)",
"PE(P-38:6)/PE(O-38:7)","PE(P-38:4)/PE(O-38:5)","PE(P-40:6)/PE(O-40:7)")

t0 <- Sys.time()
HMDB_ID_from_name(test.list)
Sys.time() -t0

HMDB_ID_from_name("C5 carnitine")

venkmurthy/vmtools documentation built on Oct. 16, 2024, 10:48 a.m.