getSuspectIdentifiers: Get PubChem CID, ChemSpider ID and CAS from InChIKey via...

In schymane/RChemMass: Various Cheminformatic, Curation and Mass Spectrometry Functions

Description

A wrapper function to obtain identifiers from an InChIKey using various webservices. PubChem CIDs are obtained with getPcId from PubChem direct (https://pubchem.ncbi.nlm.nih.gov/), ChemSpider IDs directly from ChemSpider (http://www.chemspider.com/) with getCSID. CAS numbers are retrieved using getCactus from Cactus (https://cactus.nci.nih.gov/chemical/structure); if this fails the Chemical Translation Service (CTS, http://cts.fiehnlab.ucdavis.edu/ is queried. Options are given to return all CAS numbers, the "smallest" CAS number or the first entry.

Usage

getSuspectIdentifiers(InChIKey, allCAS=FALSE, sep=",", minCAS=TRUE)

Arguments

InChIKey	Valid InChIKey used to retrieve information.
allCAS	Default FALSE will result in only one CAS number. If TRUE, all CAS are returned in one string, separated by sep. This overrides minCAS.
sep	Determines the separator used with allCAS, default ",".
minCAS	Default TRUE returns the smallest CAS number (shortest string) if allCAS=FALSE. If FALSE, returns the first CAS number in the list.

Value

Returns a list with the resulting identifiers, with NA if the query failed.

Author(s)

Emma Schymanski <[e-mail]>

See Also

getCactus, getPcId, getCSID , getCtsRecord, getSuspectInChIKey.

Examples

benz_key <- "UHOVQNZJYSORNB-UHFFFAOYSA-N"
getSuspectIdentifiers(benz_key)
getSuspectIdentifiers(benz_key,allCAS=TRUE)
getSuspectIdentifiers(benz_key,allCAS=FALSE,minCAS=TRUE)
getSuspectIdentifiers(benz_key,allCAS=FALSE,minCAS=FALSE)

schymane/RChemMass documentation built on Jan. 25, 2021, 5:45 a.m.