Nothing
R/webAccess.R
In RMassBank: Workflow to process tandem MS files and build MassBank records
Defines functions
getPcSDF
getPcInchiKey
getCSID
getCompTox
getPcCHEBI
.pubChemOnline
CTS.externalIdTypes
CTS.externalIdSubset
getCtsKey
getCtsRecord
getPcId
getCactus
retrieveDataWithRetry
Documented in
CTS.externalIdSubset
CTS.externalIdTypes
getCactus
getCompTox
getCSID
getCtsKey
getCtsRecord
getPcId
#' @import XML RCurl rjson httr
NULL
## library(XML)
## library(httr)
## library(jsonlite)
retrieveDataWithRetry <- function(url, timeout, maximumNumberOfRetries = 5, retryDelayInSeconds = 3){
#data <- getURL(URLencode(url), timeout=8)
data <- NULL
queryIsSuccessful <- FALSE
numberOfRetries <- 0
while(!queryIsSuccessful & numberOfRetries < maximumNumberOfRetries){
data <- tryCatch(
expr = {
#data <- getURL(url = url, timeout = timeout)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
queryIsSuccessful <- TRUE
data
},
warning=function(w){
numberOfRetries <<- numberOfRetries + 1
if(RMassBank.env$verbose.output)
cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of warning '", w, "'\n", sep = ""))
if(numberOfRetries < maximumNumberOfRetries)
Sys.sleep(time = retryDelayInSeconds)
},
error=function(e){
numberOfRetries <<- numberOfRetries + 1
if(RMassBank.env$verbose.output)
cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of error '", e, "'\n", sep = ""))
if(numberOfRetries < maximumNumberOfRetries)
Sys.sleep(time = retryDelayInSeconds)
}
)
}
return(data)
}
#' Retrieve information from Cactus
#'
#' Retrieves information from the Cactus Chemical Identifier Resolver
#' (PubChem).
#'
#' It is not necessary to specify in which format the \code{identifier} is.
#' Somehow, cactus does this automatically.
#'
#' @usage getCactus(identifier, representation)
#' @param identifier Any identifier interpreted by the resolver, e.g. an InChI
#' key or a SMILES code.
#' @param representation The desired representation, as required from the
#' resolver. e.g. \code{stdinchikey}, \code{chemspider_id}, \code{formula}...
#' Refer to the webpage for details.
#' @return The result of the query, in plain text. Can be NA, or one or
#' multiple lines (character array) of results.
#' @note Note that the InChI key is retrieved with a prefix (\code{InChIkey=}),
#' which must be removed for most database searches in other databases (e.g.
#' CTS).
#' @author Michael Stravs
#' @seealso \code{\link{getCtsRecord}}, \code{\link{getPcId}}
#' @references cactus Chemical Identifier Resolver:
#' \url{http://cactus.nci.nih.gov/chemical/structure}
#' @examples
#'
#' # Benzene:
#' getCactus("C1=CC=CC=C1", "cas")
#' getCactus("C1=CC=CC=C1", "stdinchikey")
#' getCactus("C1=CC=CC=C1", "chemspider_id")
#'
#' @export
#'
#'
getCactus <- function(identifier,representation){
identifier <- gsub('#', '%23', identifier)
ret <- tryCatch(httr::GET(paste("https://cactus.nci.nih.gov/chemical/structure/",
URLencode(identifier), "/", representation, sep = "")),
error = function(e) NA)
if (all(is.na(ret)))
return(NA)
if (ret["status_code"] == 404)
return(NA)
ret <- httr::content(ret)
return(unlist(strsplit(ret, "\n")))
}
#' Search Pubchem CID
#'
#' Retrieves PubChem CIDs for a search term.
#'
#' Only the first result is returned currently. \bold{The function should be
#' regarded as experimental and has not thoroughly been tested.}
#'
#' @usage getPcId(query, from = "inchikey")
#' @param query ID to be converted
#' @param from Type of input ID
#' @return The PubChem CID (in string type).
#' @author Michael Stravs, Erik Mueller
#' @seealso \code{\link{getCtsRecord}}, \code{\link{getCactus}}
#' @references PubChem search: \url{http://pubchem.ncbi.nlm.nih.gov/}
#'
#' Pubchem REST:
#' \url{https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html}
#' @examples
#' getPcId("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
#'
#' @export
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=8),
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
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]]$CID
if(is.null(PcID)){
return(NA)
} else{
return(PcID)
}
}
# The following function is unfinished.
# getPcRecord <- function(pcid)
# {
# baseUrl <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
# term <- paste(baseUrl, "esummary.fcgi?db=pccompound&id=", URLencode(as.character(pcid)),
#
# sep='')
# ret <- getURL(term)
# xml <- xmlParseDoc(ret,asText=TRUE)
# browser()
# }
# Note: some of the CHEBI codes returned are erroneous. (When the entry in
# CTS starts with "CHEBI:" instead of just the number, the XML output)
# Also, there is no ChemSpider ID in the XML output, unfortunately.
#' Retrieve information from CTS
#'
#' Retrieves a complete CTS record from the InChI key.
#'
#' @usage getCtsRecord(key)
#'
#' @param key The InChI key.
#' @return Returns a list with all information from CTS: \code{inchikey,
#' inchicode, formula, exactmass} contain single values. \code{synonyms} contains
#' an unordered list of scored synonyms (\code{type, name, score}, where \code{type}
#' indicates either a normal name or a specific IUPAC name, see below).
#' \code{externalIds} contains an unordered list of identifiers of the compound in
#' various databases (\code{name, value}, where \code{name} is the database name and
#' \code{value} the identifier in that database.)
#'
#' @note Currently, the CTS results are still incomplete; the name scores are all 0,
#' formula and exact mass return zero.
#' @references Chemical Translation Service:
#' \url{https://cts.fiehnlab.ucdavis.edu}
#'
#' @examples
#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' # show all synonym "types"
#' types <- unique(unlist(lapply(data$synonyms, function(i) i$type)))
#' \dontrun{print(types)}
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
getCtsRecord <- function(key)
{
baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/compound/"
errorvar <- 0
currEnvir <- environment()
##tryCatch a CTS timeout
##
tryCatch(
{
#data <- getURL(paste0(baseURL,key), timeout=10)
url <- paste0(baseURL,key)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
}
)
if(errorvar){
warning("CTS seems to be currently unavailable or incapable of interpreting your request")
return(NULL)
}
r <- fromJSON(data)
if(length(r) == 1)
if(r == "You entered an invalid InChIKey")
return(list())
return(r)
}
#' Convert a single ID to another using CTS.
#'
#' @usage getCtsKey(query, from = "Chemical Name", to = "InChIKey")
#' @param query ID to be converted
#' @param from Type of input ID
#' @param to Desired output ID
#' @return An unordered array with the resulting converted key(s).
#'
#' @examples
#' k <- getCtsKey("benzene", "Chemical Name", "InChIKey")
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
getCtsKey <- function(query, from = "Chemical Name", to = "InChIKey")
{
baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/convert"
url <- paste(baseURL, from, to, query, sep='/')
errorvar <- 0
currEnvir <- environment()
##tryCatch a CTS timeout
##
tryCatch(
{
#data <- getURL(URLencode(url), timeout=10)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
}
)
if(errorvar){
warning("CTS seems to be currently unavailable or incapable of interpreting your request")
return(NULL)
}
if(res$status_code != 200){
warning(paste("CTS has return code", res$status_code))
return(NULL)
}
r <- fromJSON(data)
if(length(r) == 0)
return(NULL)
else
{
# read out the results in simplest form:
results <- unlist(lapply(r, function(row) row$result))
return(results)
}
}
#' Select a subset of external IDs from a CTS record.
#'
#' @usage CTS.externalIdSubset(data, database)
#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}.
#' @param database The database for which keys should be returned.
#' @return Returns an array of all external identifiers stored in the record for the
#' given database.
#'
#' @examples
#'
#' \dontrun{
#' # Return all CAS registry numbers stored for benzene.
#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' cas <- CTS.externalIdSubset(data, "CAS")
#' }
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
CTS.externalIdSubset <- function(data, database)
{
select <- which(unlist(lapply(data$externalIds, function(id)
{
id[["name"]] == database
})))
keyEntries <- data$externalIds[select]
keys <- unlist(lapply(keyEntries, function(e) e[["value"]]))
}
#' Find all available databases for a CTS record
#'
#' @usage CTS.externalIdTypes(data)
#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}.
#' @return Returns an array of all database names for which there are external
#' identifiers stored in the record.
#'
#' @examples
#'
#' \dontrun{
#' # Return all databases for which the benzene entry has
#' # links in the CTS record.
#'
#' data <- getCTS("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' databases <- CTS.externalIdTypes(data)
#' }
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
CTS.externalIdTypes <- function(data)
{
unique(unlist(lapply(data$externalIds, function(id)
{
id[["name"]]
})))
}
.pubChemOnline <- function(){
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, "inchikey", "QEIXBXXKTUNWDK-UHFFFAOYSA-N", "description", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#ret <- getURL(URLencode(url), timeout=8),
res <- GET(URLencode(url))
ret <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
warning("Pubchem is currently offline")
return(FALSE)
} else{
return(TRUE)
}
}
getPcCHEBI <- function(query, from = "inchikey")
{
# Get the JSON-Data from Pubchem
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "synonyms", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8),
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the entries which contain Chebi-links
synonymEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Synonym))))
synonymList <- r$InformationList$Information[[synonymEntry]]$Synonym
matchChebi <- which(grepl("CHEBI:", synonymList, fixed=TRUE))
# It doesn't matter if the db is down or if chebi isn't found, so return NA also
if(length(matchChebi) == 0){
return (NA)
} else {
return (sapply(matchChebi, function(x) synonymList[[x]]))
}
}
#' Retrieves DTXSID (if it exists) from EPA Comptox Dashboard
#'
#' @usage getCompTox(query)
#' @param query The InChIKey of the compound.
#' @return Returns the DTXSID.
#'
#'
#' @examples
#'
#' \dontrun{
#' # getCompTox("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
#' }
#'
#' @author Adelene Lai <adelene.lai@uni.lu>
#' @export
getCompTox <- function(query)
{
baseURL <- "https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve.json?identifier="
url <- paste0(baseURL,query)
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url), timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1 #TRUE?
}
)
if(errorvar){ #if TRUE?
warning("EPA web service is currently offline")
return(NA)
}
r <- fromJSON(data) #returns list
return(r$DataRow$dtxsid)
}
#' Retrieve the Chemspider ID for a given compound
#'
#' Given an InChIKey, this function queries the chemspider web API to retrieve
#' the Chemspider ID of he compound with that InChIkey.
#'
#' @usage getCSID(query)
#'
#' @param query The InChIKey of the compound
#' @return Returns the chemspide
#'
#' @examples
#'
#' \dontrun{
#' # Return all CAS registry numbers stored for benzene.
#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' cas <- CTS.externalIdSubset(data, "CAS")
#' }
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @author Erik Mueller, UFZ <erik.mueller@@ufz.de>
#' @export
getCSID <- function(query)
{
baseURL <- "http://www.chemspider.com/InChI.asmx/InChIKeyToCSID?inchi_key="
url <- paste0(baseURL, query)
#errorvar <- 0
#currEnvir <- environment()
#
#tryCatch(
# data <- getURL(URLencode(url), timeout=8),
# error=function(e){
# currEnvir$errorvar <- 1
#})
#
#if(errorvar){
# warning("Chemspider is currently offline")
# return(NA)
#}
data <- retrieveDataWithRetry(url = URLencode(url), timeout=8)
if(is.null(data)){
warning("Chemspider is currently offline")
return(NA)
}
xml <- xmlParseDoc(data,asText=TRUE)
# the returned XML document contains only the root node called "string" which contains the correct CSID
idNodes <- getNodeSet(xml, "/")
id <- xmlValue(idNodes[[1]])
return(id)
}
##This function returns a sensible name for the compound
getPcSynonym <- function (query, from = "inchikey")
{
# Get the JSON-Data from Pubchem
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=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the synonym
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))]
title <- r$InformationList$Information[[titleEntry]]$Title
if(is.null(title)){
return(NA)
} else{
return(title)
}
}
##A function to retrieve a IUPAC Name from Pubchem
getPcIUPAC <- function (query, from = "inchikey")
{
# Get the JSON-Data from Pubchem
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "record", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the IUPAC-Names
if(!is.null(r$PC_Compounds[[1]]$props)){
IUPACIndex <- which(unlist(lapply(r$PC_Compounds[[1]]$props, function(i) (i$urn$label == "IUPAC Name"))))
if(length(IUPACIndex) > 0){
# Retrieve all IUPAC-Names
IUPACEntries <- lapply(IUPACIndex, function(x) r$PC_Compounds[[1]]$props[[x]])
if(!is.null(IUPACEntries)){
# Is there a preferred IUPAC-Name? If yes, retrieve that
PrefIUPAC <- which(unlist(lapply(IUPACEntries, function(x) x$urn$name == "Preferred")))
} else{return(NA)}
} else{return(NA)}
} else{return(NA)}
if(length(PrefIUPAC) == 1){
return(IUPACEntries[[PrefIUPAC]]$value$sval)
} else{
# Else it doesn't matter which
return(IUPACEntries[[1]]$value$sval)
}
}
getPcInchiKey <- function(query, from = "smiles"){
# Get the JSON-Data from Pubchem
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "record", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the entries which contain Chebi-links
if(!is.null(r$PC_Compounds[[1]]$props)){
INKEYindex <- which(sapply(r$PC_Compounds[[1]]$props, function(x) x$urn$label) == "InChIKey")
if(length(INKEYindex) > 0){
return(r$PC_Compounds[[1]]$props[[INKEYindex]]$value$sval)
} else{return(NA)}
} else{return(NA)}
}
getPcSDF <- function(query, from = "smiles"){
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "sdf", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
molEnd <- regexpr(data,pattern="M END",fixed=TRUE)+5
data <- c(strsplit(substring(data,1,molEnd),"\n")[[1]],"$$$$")
return(data)
}
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Defines functions getPcSDF getPcInchiKey getCSID getCompTox getPcCHEBI .pubChemOnline CTS.externalIdTypes CTS.externalIdSubset getCtsKey getCtsRecord getPcId getCactus retrieveDataWithRetry
Documented in CTS.externalIdSubset CTS.externalIdTypes getCactus getCompTox getCSID getCtsKey getCtsRecord getPcId
#' @import XML RCurl rjson httr
NULL
## library(XML)
## library(httr)
## library(jsonlite)
retrieveDataWithRetry <- function(url, timeout, maximumNumberOfRetries = 5, retryDelayInSeconds = 3){
#data <- getURL(URLencode(url), timeout=8)
data <- NULL
queryIsSuccessful <- FALSE
numberOfRetries <- 0
while(!queryIsSuccessful & numberOfRetries < maximumNumberOfRetries){
data <- tryCatch(
expr = {
#data <- getURL(url = url, timeout = timeout)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
queryIsSuccessful <- TRUE
data
},
warning=function(w){
numberOfRetries <<- numberOfRetries + 1
if(RMassBank.env$verbose.output)
cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of warning '", w, "'\n", sep = ""))
if(numberOfRetries < maximumNumberOfRetries)
Sys.sleep(time = retryDelayInSeconds)
},
error=function(e){
numberOfRetries <<- numberOfRetries + 1
if(RMassBank.env$verbose.output)
cat(paste("### Warning ### Web query failed (", numberOfRetries, " / ", maximumNumberOfRetries, ") for url '", url, "' because of error '", e, "'\n", sep = ""))
if(numberOfRetries < maximumNumberOfRetries)
Sys.sleep(time = retryDelayInSeconds)
}
)
}
return(data)
}
#' Retrieve information from Cactus
#'
#' Retrieves information from the Cactus Chemical Identifier Resolver
#' (PubChem).
#'
#' It is not necessary to specify in which format the \code{identifier} is.
#' Somehow, cactus does this automatically.
#'
#' @usage getCactus(identifier, representation)
#' @param identifier Any identifier interpreted by the resolver, e.g. an InChI
#' key or a SMILES code.
#' @param representation The desired representation, as required from the
#' resolver. e.g. \code{stdinchikey}, \code{chemspider_id}, \code{formula}...
#' Refer to the webpage for details.
#' @return The result of the query, in plain text. Can be NA, or one or
#' multiple lines (character array) of results.
#' @note Note that the InChI key is retrieved with a prefix (\code{InChIkey=}),
#' which must be removed for most database searches in other databases (e.g.
#' CTS).
#' @author Michael Stravs
#' @seealso \code{\link{getCtsRecord}}, \code{\link{getPcId}}
#' @references cactus Chemical Identifier Resolver:
#' \url{http://cactus.nci.nih.gov/chemical/structure}
#' @examples
#'
#' # Benzene:
#' getCactus("C1=CC=CC=C1", "cas")
#' getCactus("C1=CC=CC=C1", "stdinchikey")
#' getCactus("C1=CC=CC=C1", "chemspider_id")
#'
#' @export
#'
#'
getCactus <- function(identifier,representation){
identifier <- gsub('#', '%23', identifier)
ret <- tryCatch(httr::GET(paste("https://cactus.nci.nih.gov/chemical/structure/",
URLencode(identifier), "/", representation, sep = "")),
error = function(e) NA)
if (all(is.na(ret)))
return(NA)
if (ret["status_code"] == 404)
return(NA)
ret <- httr::content(ret)
return(unlist(strsplit(ret, "\n")))
}
#' Search Pubchem CID
#'
#' Retrieves PubChem CIDs for a search term.
#'
#' Only the first result is returned currently. \bold{The function should be
#' regarded as experimental and has not thoroughly been tested.}
#'
#' @usage getPcId(query, from = "inchikey")
#' @param query ID to be converted
#' @param from Type of input ID
#' @return The PubChem CID (in string type).
#' @author Michael Stravs, Erik Mueller
#' @seealso \code{\link{getCtsRecord}}, \code{\link{getCactus}}
#' @references PubChem search: \url{http://pubchem.ncbi.nlm.nih.gov/}
#'
#' Pubchem REST:
#' \url{https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html}
#' @examples
#' getPcId("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
#'
#' @export
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=8),
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
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)
}
}
# The following function is unfinished.
# getPcRecord <- function(pcid)
# {
# baseUrl <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
# term <- paste(baseUrl, "esummary.fcgi?db=pccompound&id=", URLencode(as.character(pcid)),
#
# sep='')
# ret <- getURL(term)
# xml <- xmlParseDoc(ret,asText=TRUE)
# browser()
# }
# Note: some of the CHEBI codes returned are erroneous. (When the entry in
# CTS starts with "CHEBI:" instead of just the number, the XML output)
# Also, there is no ChemSpider ID in the XML output, unfortunately.
#' Retrieve information from CTS
#'
#' Retrieves a complete CTS record from the InChI key.
#'
#' @usage getCtsRecord(key)
#'
#' @param key The InChI key.
#' @return Returns a list with all information from CTS: \code{inchikey,
#' inchicode, formula, exactmass} contain single values. \code{synonyms} contains
#' an unordered list of scored synonyms (\code{type, name, score}, where \code{type}
#' indicates either a normal name or a specific IUPAC name, see below).
#' \code{externalIds} contains an unordered list of identifiers of the compound in
#' various databases (\code{name, value}, where \code{name} is the database name and
#' \code{value} the identifier in that database.)
#'
#' @note Currently, the CTS results are still incomplete; the name scores are all 0,
#' formula and exact mass return zero.
#' @references Chemical Translation Service:
#' \url{https://cts.fiehnlab.ucdavis.edu}
#'
#' @examples
#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' # show all synonym "types"
#' types <- unique(unlist(lapply(data$synonyms, function(i) i$type)))
#' \dontrun{print(types)}
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
getCtsRecord <- function(key)
{
baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/compound/"
errorvar <- 0
currEnvir <- environment()
##tryCatch a CTS timeout
##
tryCatch(
{
#data <- getURL(paste0(baseURL,key), timeout=10)
url <- paste0(baseURL,key)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
}
)
if(errorvar){
warning("CTS seems to be currently unavailable or incapable of interpreting your request")
return(NULL)
}
r <- fromJSON(data)
if(length(r) == 1)
if(r == "You entered an invalid InChIKey")
return(list())
return(r)
}
#' Convert a single ID to another using CTS.
#'
#' @usage getCtsKey(query, from = "Chemical Name", to = "InChIKey")
#' @param query ID to be converted
#' @param from Type of input ID
#' @param to Desired output ID
#' @return An unordered array with the resulting converted key(s).
#'
#' @examples
#' k <- getCtsKey("benzene", "Chemical Name", "InChIKey")
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
getCtsKey <- function(query, from = "Chemical Name", to = "InChIKey")
{
baseURL <- "https://cts.fiehnlab.ucdavis.edu/service/convert"
url <- paste(baseURL, from, to, query, sep='/')
errorvar <- 0
currEnvir <- environment()
##tryCatch a CTS timeout
##
tryCatch(
{
#data <- getURL(URLencode(url), timeout=10)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
}
)
if(errorvar){
warning("CTS seems to be currently unavailable or incapable of interpreting your request")
return(NULL)
}
if(res$status_code != 200){
warning(paste("CTS has return code", res$status_code))
return(NULL)
}
r <- fromJSON(data)
if(length(r) == 0)
return(NULL)
else
{
# read out the results in simplest form:
results <- unlist(lapply(r, function(row) row$result))
return(results)
}
}
#' Select a subset of external IDs from a CTS record.
#'
#' @usage CTS.externalIdSubset(data, database)
#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}.
#' @param database The database for which keys should be returned.
#' @return Returns an array of all external identifiers stored in the record for the
#' given database.
#'
#' @examples
#'
#' \dontrun{
#' # Return all CAS registry numbers stored for benzene.
#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' cas <- CTS.externalIdSubset(data, "CAS")
#' }
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
CTS.externalIdSubset <- function(data, database)
{
select <- which(unlist(lapply(data$externalIds, function(id)
{
id[["name"]] == database
})))
keyEntries <- data$externalIds[select]
keys <- unlist(lapply(keyEntries, function(e) e[["value"]]))
}
#' Find all available databases for a CTS record
#'
#' @usage CTS.externalIdTypes(data)
#' @param data The complete CTS record as retrieved by \code{\link{getCtsRecord}}.
#' @return Returns an array of all database names for which there are external
#' identifiers stored in the record.
#'
#' @examples
#'
#' \dontrun{
#' # Return all databases for which the benzene entry has
#' # links in the CTS record.
#'
#' data <- getCTS("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' databases <- CTS.externalIdTypes(data)
#' }
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @export
CTS.externalIdTypes <- function(data)
{
unique(unlist(lapply(data$externalIds, function(id)
{
id[["name"]]
})))
}
.pubChemOnline <- function(){
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, "inchikey", "QEIXBXXKTUNWDK-UHFFFAOYSA-N", "description", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#ret <- getURL(URLencode(url), timeout=8),
res <- GET(URLencode(url))
ret <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
warning("Pubchem is currently offline")
return(FALSE)
} else{
return(TRUE)
}
}
getPcCHEBI <- function(query, from = "inchikey")
{
# Get the JSON-Data from Pubchem
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "synonyms", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8),
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the entries which contain Chebi-links
synonymEntry <- which(unlist(lapply(r$InformationList$Information, function(i) !is.null(i$Synonym))))
synonymList <- r$InformationList$Information[[synonymEntry]]$Synonym
matchChebi <- which(grepl("CHEBI:", synonymList, fixed=TRUE))
# It doesn't matter if the db is down or if chebi isn't found, so return NA also
if(length(matchChebi) == 0){
return (NA)
} else {
return (sapply(matchChebi, function(x) synonymList[[x]]))
}
}
#' Retrieves DTXSID (if it exists) from EPA Comptox Dashboard
#'
#' @usage getCompTox(query)
#' @param query The InChIKey of the compound.
#' @return Returns the DTXSID.
#'
#'
#' @examples
#'
#' \dontrun{
#' # getCompTox("MKXZASYAUGDDCJ-NJAFHUGGSA-N")
#' }
#'
#' @author Adelene Lai <adelene.lai@uni.lu>
#' @export
getCompTox <- function(query)
{
baseURL <- "https://actorws.epa.gov/actorws/chemIdentifier/v01/resolve.json?identifier="
url <- paste0(baseURL,query)
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url), timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1 #TRUE?
}
)
if(errorvar){ #if TRUE?
warning("EPA web service is currently offline")
return(NA)
}
r <- fromJSON(data) #returns list
return(r$DataRow$dtxsid)
}
#' Retrieve the Chemspider ID for a given compound
#'
#' Given an InChIKey, this function queries the chemspider web API to retrieve
#' the Chemspider ID of he compound with that InChIkey.
#'
#' @usage getCSID(query)
#'
#' @param query The InChIKey of the compound
#' @return Returns the chemspide
#'
#' @examples
#'
#' \dontrun{
#' # Return all CAS registry numbers stored for benzene.
#' data <- getCtsRecord("UHOVQNZJYSORNB-UHFFFAOYSA-N")
#' cas <- CTS.externalIdSubset(data, "CAS")
#' }
#'
#' @author Michele Stravs, Eawag <stravsmi@@eawag.ch>
#' @author Erik Mueller, UFZ <erik.mueller@@ufz.de>
#' @export
getCSID <- function(query)
{
baseURL <- "http://www.chemspider.com/InChI.asmx/InChIKeyToCSID?inchi_key="
url <- paste0(baseURL, query)
#errorvar <- 0
#currEnvir <- environment()
#
#tryCatch(
# data <- getURL(URLencode(url), timeout=8),
# error=function(e){
# currEnvir$errorvar <- 1
#})
#
#if(errorvar){
# warning("Chemspider is currently offline")
# return(NA)
#}
data <- retrieveDataWithRetry(url = URLencode(url), timeout=8)
if(is.null(data)){
warning("Chemspider is currently offline")
return(NA)
}
xml <- xmlParseDoc(data,asText=TRUE)
# the returned XML document contains only the root node called "string" which contains the correct CSID
idNodes <- getNodeSet(xml, "/")
id <- xmlValue(idNodes[[1]])
return(id)
}
##This function returns a sensible name for the compound
getPcSynonym <- function (query, from = "inchikey")
{
# Get the JSON-Data from Pubchem
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=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the synonym
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))]
title <- r$InformationList$Information[[titleEntry]]$Title
if(is.null(title)){
return(NA)
} else{
return(title)
}
}
##A function to retrieve a IUPAC Name from Pubchem
getPcIUPAC <- function (query, from = "inchikey")
{
# Get the JSON-Data from Pubchem
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "record", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the IUPAC-Names
if(!is.null(r$PC_Compounds[[1]]$props)){
IUPACIndex <- which(unlist(lapply(r$PC_Compounds[[1]]$props, function(i) (i$urn$label == "IUPAC Name"))))
if(length(IUPACIndex) > 0){
# Retrieve all IUPAC-Names
IUPACEntries <- lapply(IUPACIndex, function(x) r$PC_Compounds[[1]]$props[[x]])
if(!is.null(IUPACEntries)){
# Is there a preferred IUPAC-Name? If yes, retrieve that
PrefIUPAC <- which(unlist(lapply(IUPACEntries, function(x) x$urn$name == "Preferred")))
} else{return(NA)}
} else{return(NA)}
} else{return(NA)}
if(length(PrefIUPAC) == 1){
return(IUPACEntries[[PrefIUPAC]]$value$sval)
} else{
# Else it doesn't matter which
return(IUPACEntries[[1]]$value$sval)
}
}
getPcInchiKey <- function(query, from = "smiles"){
# Get the JSON-Data from Pubchem
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "record", "json", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
r <- fromJSON(data)
# This happens if the InChI key is not found:
if(!is.null(r$Fault))
return(NA)
# Find the entries which contain Chebi-links
if(!is.null(r$PC_Compounds[[1]]$props)){
INKEYindex <- which(sapply(r$PC_Compounds[[1]]$props, function(x) x$urn$label) == "InChIKey")
if(length(INKEYindex) > 0){
return(r$PC_Compounds[[1]]$props[[INKEYindex]]$value$sval)
} else{return(NA)}
} else{return(NA)}
}
getPcSDF <- function(query, from = "smiles"){
baseURL <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound"
url <- paste(baseURL, from, query, "sdf", sep="/")
errorvar <- 0
currEnvir <- environment()
tryCatch(
{#data <- getURL(URLencode(url),timeout=8)
res <- GET(URLencode(url))
data <- httr::content(res, type="text", encoding="UTF-8")
},
error=function(e){
currEnvir$errorvar <- 1
})
if(errorvar){
return(NA)
}
molEnd <- regexpr(data,pattern="M END",fixed=TRUE)+5
data <- c(strsplit(substring(data,1,molEnd),"\n")[[1]],"$$$$")
return(data)
}
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