ChemSpider SOAP APIs are now retired

[sharped-rsc]

The ChemSpider SOAP APIs are now retired, which means that the look-up based upon ChemSpider can no-longer be used. There is a new replacement API which is described at https://developer.rsc.org, which could be used to provide the same functionality.

[yufree]

Thanks for your reminder! I think the new API totally changed chspider.batch.annotation.child.R

If @kuppal2 plan to re-write this function, I could update when the svn repo is updated. Otherwise I might add warnings when someone use this function. The 1000 compounds per day of free API plan might not be enough for metabolomics studies while enough for targeted analysis.

[sharped-rsc]

Thanks for your response. The 1000 calls per day is only a restriction on the default account. Higher usage allowances are available upon request - at no charge for non-commercial users.

[sharped-rsc]

Hi @yufree, have you heard anything from @kuppal2. If not I would be willing to help with updating the code to use the new APIs but I'm not that familiar with R so I would need to work with you on that.

[yufree]

I add you and @kuppal2 as collaborators of this repo and you could directly modify the code now. I could help to explain the R code. The major function is chspider.batch.annotation.child.R. The former function pastes the request via SOAP and now you use REST. Here is the related code

xMSannotator/R/chspider.batch.annotation.child.R

Lines 71 to 240 in cf9e599

	# csids<-o@functions$SearchByMass2(mass=mz,range=delta_ppm)
	# csids<-o@functions$SearchByMassAsync(mass=mz,range=delta_ppm,dbs='KEGG',token=tokenstr)
	# csids<-o@functions$SearchByMassAsync(mass=mz,range=delta_ppm,dbs=c('PubChem','MassBank',
	# 'EPA DSSTox','EPA Toxcast','NIST Chemistry
	# WebBook','KEGG',
	#'Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common Names','SMPDB Small Molecule Pathway Database',
	#'MeSH','LipidMAPS','ChemBank','BioCyc'),token=tokenstr)
	# ttest_res=try(t.test(x,y,paired=TRUE),silent=TRUE)
	csids <- try(o@functions$SearchByMassAsync(mass = mz,
	range = delta_ppm, dbs = datasources, token = tokenstr),
	silent = TRUE)
	if (is(csids, "try-error")) {
	annotres <- c(mz.val, rep("NC", 50))
	write.table(mz.val, file = "chemspider_bad_mzs.txt",
	sep = "\t", append = TRUE, row.names = FALSE)
	} else {
	csids <- try(o2@functions$GetAsyncSearchResult(rid = csids,
	token = tokenstr), silent = TRUE)
	if (is(csids, "try-error")) {
	annotres <- c(mz.val, rep("NC", 50))
	write.table(mz.val, file = "chemspider_bad_mzs.txt",
	sep = "\t", append = TRUE, row.names = FALSE)
	} else {
	# WikiPathways, DrugBank, Comparative Toxicogenomics
	# Database, ACToR: Aggregated Computational Toxicology
	# Resource
	external_sources <- c("PubChem", "MassBank",
	"EPA DSSTox", "EPA Toxcast", "NIST Chemistry WebBook",
	"KEGG", "Human Metabolome Database", "ChEMBL",
	"ChEBI", "NIAID", "Pesticide Common Names",
	"SMPDB Small Molecule Pathway Database",
	"MeSH", "LipidMAPS", "ChemBank", "BioCyc",
	"WikiPathways", "DrugBank", "Comparative Toxicogenomics Database",
	"ACToR: Aggregated Computational Toxicology Resource")
	write.table(mz.val, file = "mzval.txt", sep = "\t",
	row.names = FALSE)
	if (length(csids) > 0) {
	countid <- 0
	if (length(csids) < maxhits) {
	maxhits = length(csids)
	}
	for (id_ind in 1:maxhits) {
	Sys.sleep(syssleep)
	csid <- csids[id_ind]
	csid1 <- o2@functions$CSID2ExtRefs(CSID = as.integer(csid),
	datasources = external_sources, token = tokenstr)
	info <- o@functions$GetExtendedCompoundInfo(CSID = csid,
	token = tokenstr)
	urllink1 <- paste("www.chemspider.com/Chemical-Structure.",
	csid, ".html", sep = "")
	urllink2 <- paste("<a href=http://www.chemspider.com/Chemical-Structure.",
	csid, ".html>", csid, "</a>", sep = "")
	CommonName = "-"
	MF = "-"
	SMILES = "-"
	InChI = "-"
	InChIKey = "-"
	AverageMass = "-"
	MolecularWeight = "-"
	MonoisotopicMass = "-"
	NominalMass = "-"
	ALogP = "-"
	XLogP = "-"
	slotnames <- slotNames(class(info))
	for (i in slotnames) {
	if (i == "CommonName") {
	if (length(info@CommonName) > 0) {
	CommonName = info@CommonName
	}
	} else {
	if (i == "MF") {
	if (length(info@MF) > 0) {
	MF = info@MF
	}
	} else {
	if (i == "SMILES") {
	if (length(info@SMILES) > 0) {
	SMILES = info@SMILES
	}
	} else {
	if (i == "InChI") {
	if (length(info@InChI) > 0) {
	InChI = info@InChI
	}
	} else {
	if (i == "InChIKey") {
	if (length(info@InChIKey) >
	0) {
	InChIKey = info@InChIKey
	}
	} else {
	if (i == "AverageMass") {
	if (length(info@AverageMass) >
	0) {
	AverageMass = info@AverageMass
	}
	} else {
	if (i == "MolecularWeight") {
	if (length(info@MolecularWeight) >
	0) {
	MolecularWeight = info@MolecularWeight
	}
	} else {
	if (i == "MonoisotopicMass") {
	if (length(info@MonoisotopicMass) >
	0) {
	MonoisotopicMass = info@MonoisotopicMass
	}
	} else {
	if (i == "NominalMass") {
	if (length(info@NominalMass) >
	0) {
	NominalMass = info@NominalMass
	}
	} else {
	if (i == "ALogP") {
	if (length(info@ALogP) >
	0) {
	ALogP = info@ALogP
	}
	} else {
	if (i == "XLogP") {
	if (length(info@XLogP) >
	0) {
	XLogP = info@XLogP
	}
	}
	}
	}
	}
	}
	}
	}
	}
	}
	}
	}
	}
	csid1NAME <- o2@functions$GetCompoundThumbnail(id = csid,
	token = tokenstr)
	dec <- base64Decode(csid1NAME, "raw")
	pngoutloc <- "pngfiles"
	dir.create(pngoutloc)
	png_image <- readPNG(dec)
	fname <- paste(pngoutloc, "/", csid, ".png",
	sep = "")