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CTS retrieving non-live CIDs #225

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schymane opened this issue Dec 13, 2019 · 6 comments
Open

CTS retrieving non-live CIDs #225

schymane opened this issue Dec 13, 2019 · 6 comments
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bug enhancement

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@schymane
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@schymane schymane commented Dec 13, 2019

We should make our default source of CIDs PubChem, and not CTS. There are too many discrepancies/error cropping up.
@meier-rene we may have to check the "status" of CIDs during validation, to catch and fix.

Example from freshly-created infolist:
https://pubchem.ncbi.nlm.nih.gov/compound/4644
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@tsufz tsufz commented Dec 13, 2019

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@schymane schymane commented Apr 16, 2020

getPcId will also return non-live CIDs for non-standard tautomeric forms. We can fix this using a function in RChemMass, but we should make sure we upgrade the getPcId function to automatically do this. On the "todo" list ...

> getPcId("NPZTUJOABDZTLV-UHFFFAOYSA-N")
[1] 2759291
> getPCIDs.CIDtype(getPcId("NPZTUJOABDZTLV-UHFFFAOYSA-N"),type="preferred")
[1] 135399369
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@schymane schymane commented Apr 17, 2020

@meowcat I will need to upgrade getPcId to make sure it returns "live" CIDs, this is fine - but where can I check whether we grab PubChem CIDs from PubChem vs CTS? If we already use getPcId (not CTS), then all I will need to do is fix that function, then this issue is solved. Thanks.
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@meowcat meowcat commented Apr 17, 2020

So:
https://github.com/MassBank/RMassBank/createMassBank.R
Line 577 is where we call gatherPubChem to get data off PubChem.

RMassBank/R/createMassBank.R

Line 577 in 611b785

PcInfo <- gatherPubChem(inchikey_split)

Lines 602..608 is where we get CTS data. To do: what do we still need from CTS at this point?

RMassBank/R/createMassBank.R

Lines 602 to 608 in 611b785

##Use CTS to retrieve information
CTSinfo <- getCtsRecord(inchikey_split)
if((CTSinfo[1] == "Sorry, we couldn't find any matching results") || is.null(CTSinfo[1]))
{
CTSinfo <- NA
}

Lines 775-786 is where we decide which PubChem ID to use. I guess you want to drop CTS completely as an option?

RMassBank/R/createMassBank.R

Lines 775 to 786 in 611b785

# PubChem CID
if(is.na(PcInfo$PcID[1])){
if(!is.na(CTSinfo[1])){
if("PubChem CID" %in% CTS.externalIdTypes(CTSinfo))
{
pc <- CTS.externalIdSubset(CTSinfo,"PubChem CID")
link[["PUBCHEM"]] <- paste0(min(pc))
}
}
} else{
link[["PUBCHEM"]] <- PcInfo$PcID[1]
}

Then the actual data retrieval from PubChem is in gatherPubChem, where getPcId is called:

RMassBank/R/createMassBank.R

Lines 454 to 466 in 611b785

gatherPubChem <- function(key){
PubChemData <- list()
##Trycatches are there because pubchem has connection issues 1 in 50 times.
##Write NA into the respective fields if something goes wrong with the conenction or the data.
##Retrieve Pubchem CID
tryCatch(
PubChemData$PcID <- getPcId(key),
error=function(e){
PubChemData$PcID <<- NA
})

getPcId is then the function in webAccess,R:

RMassBank/R/webAccess.R

Lines 109 to 144 in 611b785

getPcId <- function(query, from = "inchikey")
{
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "description", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
data <- getURL(URLencode(url),timeout=5),
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
# This happens if the InChI key is not found:
r <- fromJSON(data)
if(!is.null(r$Fault))
return(NA)
titleEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Title))))
titleEntry <- titleEntry[which.min(sapply(titleEntry, function(x)r$InformationList$Information[[x]]$CID))]
PcID <- r$InformationList$Information[[titleEntry]]$CID
if(is.null(PcID)){
return(NA)
} else{
return(PcID)
}
}

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@schymane schymane commented Apr 18, 2020

@meowcat I've created a new branch:
https://github.com/MassBank/RMassBank/tree/preferredPCIDs

I've added getPCIDs.CIDtype, adjusted getPcId and createMassBank.R (and updated my old email address). I'm stuck on the documentation - see emails.
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@schymane schymane commented Apr 20, 2020

Just pushed 445b432 thanks to @MaliRemorker for docs tips.
@meowcat pls let me know if I should do a pull request (this results in a lot of changes), or if you want me to change anything?
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