R/rUniChembl.r
In abhik1368/rUniChEMBL: Accessing the ChEMBL and Unichem data.
library(RCurl)
library(jsonlite)
#' get.scid.sid
#' @title Get the source compound ids from another source compound id
#' @description a list of all src_compound_ids from all sources which are
#' CURRENTLY assigned to the same structure as a currently assigned
#' query src_compound_id.
#' The output will include query src_compound_id if it is a valid src_compound_id
#' with a current assignment.
#' @name get.scid.sid
#' @docType package
#' @param x : Input string Source compound id
#' @param y : Input integer Source id
#' @export
#' @examples
#' \donttest{
#' # Get source compound ids and source information
#' # Using ChEMBL ID and source
#' get.scid.sid("CHEMBL12",1)
#' # Using drugbank id and source
#' get.scid.sid("DB00789",2)
#' }
get.scid.sid <- function(x,y) {
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id/%s/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
} else {
return(NULL)
}
}
#' get.sAll.sid
#' @title Get the all source compound ids from another source compound id
#' @description Obtain a list of all src_compound_ids from all sources
#' (including BOTH current AND obsolete assignments) to the same structure
#' as a currently assigned query
#' src_compound_id.
#' @name get.sAll.sid
#' @docType package
#' @param x : Input chemblid
#' @param y : Input integer source id
#' @export
#' @examples
#' \donttest{
#' # Get all source ids using ChEMBL id and source
#' get.sAll.sid("CHEMBL12",1)
#' # Using drugbank id and source
#' get.sAll.sid("DB00789",2)
#' }
get.sAll.sid <- function(x,y) {
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id_all/%s/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
}else {
return(NULL)
}
}
#' get.mapping.full
#' @title Get full mapping between two sources.
#' @description Obtain a full mapping between two sources. Uses only currently
#' assigned src_compound_ids from both sources.
#' @name get.mapping.full
#' @docType package
#' @param x : Input integer source id
#' @param y : Input integer source id
#' @export
#' @examples
#' \donttest{
#' # Get full mapping of PDBe and ChEMBL
#' get.mapping.full(3,1)
#' # Get full mapping of ZINC and ChEMBL
#' get.mapping.full(9,1)
#' }
get.mapping.full <-function(x,y) {
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/mapping/%d/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.src_id.InCHIKey
#' @title Get source compound ids
#' @description Obtain a list of src_compound_ids (from all sources) which
#' are CURRENTLY assigned to a query InChI Key. Returns a list of data from
#' Unichem and ChEMBL databases.
#' @name get.src_id.InCHIKey
#' @docType package
#' @param x : Input string InCHI Key
#' @export
#' @examples
#' \donttest{
#' # Get source compound ids from InCHIKey
#' get.sid.InCHIKey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
#'
#' data<-get.sid.InCHIKey("BSYNRYMUTXBXSQ-UHFFFAOYSA-N")
#' # to get chembl data
#' data$Chem
#' to get Unichem data
#' data$Uni
#' }
get.sid.InCHIKey<-function(x){
url_uni <- sprintf("https://www.ebi.ac.uk/unichem/rest/inchikey/%s",x)
url_chem<-sprintf("https://www.ebi.ac.uk/chemblws/compounds/stdinchikey/%s.json",x)
h <- getCurlHandle()
d <- getURL(url_uni, curl=h)
c<-getURL(url_chem, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
cf<-do.call(rbind, lapply(fromJSON(c), data.frame))
return(list(uni=df,Chem=cf))
} else {
return(NULL)
}
}
#' get.sAll.InCHIKey
#' @title Get all src_compound_ids.
#' @description Get a list of all src_compound_ids (from all sources) which
#' have current AND obsolete assignments to a query InChIKey
#' @name get.sAll.InCHIKey
#' @docType package
#' @param x : Input string InCHI Key
#' @export
#' @examples
#' \donttest{
#' # Get all the IDs using InCHIKey
#' get.sAll.InCHIKey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
#' }
get.sAll.InCHIKey<-function(x){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/inchikey_all/%s",x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
}else {
return(NULL)
}
}
#' get.structure
#' @title Get structure
#' @description Get structure(s) currently assigned to a query src_compound_id.
#' @name get.structure
#' @docType package
#' @param x : Input string chemblid
#' @param s : Input integer source id (default is 1)
#' @export
#' @examples
#' \donttest{
#' # Get Standard inhci and InCHIKey from drugbank compound and source
#' get.structure("DB00321",2)
#' # Using ChEMBL compound and source id
#' get.structure("CHEMBL1231",1)
#' }
get.structure<-function(x,s=1){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/structure/%s/%d",x,s)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.struc.all
#' @title Get Structures for source compound id
#' @description Get the standard InCHI and standard InCHI Key for the source
#' compound id
#' @name get.struc.all
#' @docType package
#' @param x : Input string chemblid
#' @param s : Input integer source id (default is 1)
#' @export
#' @examples
#' \donttest{
#' # Get all the structure information using ChEMBL id and source.
#' get.struc.all("CHEMBL1231",1)
#' #using drugbank id and source
#' get.structure("DB00321",2)
#' }
get.struc.all<-function(x,s=1){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/structure_all/%s/%d",x,s)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.url.sid
#' @title Get url for the query compound
#' @description Get a list of URLs for all src_compound_ids, from a specified
#' source .
#' @name get.url.sid
#' @docType package
#' @param x : Input string source compound id
#' @param y : Input integer source id
#' @param z : Input integer to source id
#' @export
#' @examples
#' \donttest{
#' # get urls of compounds using source compound id, source id
#' # get drugbank url from ChEMBL source id and ChEMBL source
#' get.url.sid("ChEMBL490",1,2)
#'
#' # get chembl url from drugbank id and source
#' get.url.sid("DB00715",2,1)
#' }
get.url.sid<-function(x,y,z){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id_url/%s/%d/%d",x,y,z)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.sAll.obs
#' @title Get source compound id from obsolete source compound id
#' @description Get a list of all src_compound_ids from all sources with BOTH
#' current AND obsolete to the same structure with an obsolete assignment to the #' query src_compound_id.
#' @name get.SrcAll.obs
#' @docType package
#' @param x : Input string source compound id
#' @param y : Input integer to source id
#' @export
#' @examples
#' \donttest{
#' #get for drugbank compound and source
#' get.sAll.obs("DB07699",2)
#' #get for chembl compound and source
#' get.sAll.obs("CHEMBL12",1)
#' }
get.sAll.obs<-function(x,y){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id_all_obsolete/%s/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
} else {
return(NULL)
}
}
#' get.verbose.InCHIkey
#' @title Get all src_compound_ids to a query InChIKey
#' @description Returns a dataframe containing src_id (the src_id for this source),
#' src_url (the main home page of the source), name (the unique name for the source in
#' UniChem, always lower case), name_long (the full name of the source, as defined by the
#' source),name_label (A name for the source
#' suitable for use as a 'label' for the source within a web-page. Correct case setting
#' for source, and always less than 30 characters), description (a description of the
#' content of the source), base_id_url_available (an flag indicating whether this source
#' provides a valid base_id_url for creating cpd-specific links [1=yes, 0=no]),base_id_url
#' (the base url for constructing hyperlinks to this source [append an identifier from
#' this source to the end of this url to create a valid url to a specific page for this
#' cpd], unless aux_for_url=1), aux_for_url (A flag to indicate whether the aux_src field
#' should be used to create hyperlinks instead of the src_compound_id [1=yes, 0=no] ,
#' src_compound_id (a list of src_compound_ids from this source which are currently
#' assigned to the query InChIKey, aux_src (a list of src-compound_id keys mapping to
#' corresponding auxiliary data (url_id:value), for creating links if aux_for_url=1. Only
#' shown if aux_for_url=1).
#' @name get.verbose.InCHIkey
#' @docType package
#' @param x : Input string InCHI Key
#' @export
#' @examples
#' \donttest{
#' # get for InCHIkey
#' get.verbose.InCHIkey("GZUITABIAKMVPG-UHFFFAOYSA-N")
#'
#' get.verbose.InCHIkey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
#' }
get.verbose.InCHIkey<-function(x){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/verbose_inchikey/%s",x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.cmp.inf
#' @title Get compound information from ChEMBL
#' @description These functions allow one to retrieve compounds information from ChEMBL
#' compounds are identified either by a ChEMBL ID or by a standard InChI key.
#' @name get.cmp.inf
#' @docType package
#' @param x : String representing chemblid or standard InCHI key for the molecule.
#' @param type : For \code{get.compound}, one of \code{chemblid} or
#' \code{stdinchi} to indicate the nature of the molecule id.
#' @export
#' @examples
#' \donttest{
#' #get information for chembl compound id
#' get.compound("CHEMBL12")
#'
#' #get information for standard inchi
#' get.compound("QFFGVLORLPOAEC-SNVBAGLBSA-N",type='stdinchi')
#' }
get.cmp.inf <- function(x, type='chemblid') {
types <- c('chemblid', 'stdinchi')
type <- pmatch(type, types)
if (is.na(type)) stop("Invalid type given")
url <- switch(type,
url = 'https://www.ebi.ac.uk/chemblws/compounds/',
url = 'https://www.ebi.ac.uk/chemblws/compounds/stdinchikey/')
url <- sprintf('%s%s.json', url, id)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.cmp.sim
#' @title Retrive similar compounds from ChEMBL database.
#' @description This function retrieves a dataframe of similar compounds
#' from ChEMBL database given a smiles string as query and also given a similarity score above 70.
#' @name get.cmp.sim
#' @docType package
#' @param mol : String representing smiles of the moelcule
#' @param sim : Integer representing for percentage of similarity
#' for the query compound and the database molecules. Values ranges
#' from 70 to 100.
#' @export
get.cmp.sim <- function(mol,sim=70) {
url <- 'https://www.ebi.ac.uk/chemblws/compounds/similarity/'
url <- sprintf('%s%s/%d.json', url,mol,sim)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d)[[1]])
} else {
return(NULL)
}
}
#' get.cmp.substruct
#' @title Get compound information from substructure query smiles.
#' @description This function retrieves a dataframe of all compounds from ChEMBL database
#' containing the substructure represented by the given Canonical SMILES and their
#' chemical properties.
#' @name get.compound.substruct
#' @docType package
#' @param mol : String representing smiles of the moelcule
#' @export
#' @examples
#' \donttest{
#' #get compounds by substructure
#' get.cmp.subsruct("CN(CCCN)c1cccc2ccccc12")
#' }
get.cmp.substruct<-function(mol){
url <- sprintf('https://www.ebi.ac.uk/chemblws/compounds/substructure/%s.json',mol)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<-fromJSON(d)
return(data$compounds)
} else {
return(NULL)
}
}
#' get.appDrugs
#' @title Get approved drugs for target.
#' @description This function retrieves a dataframe of all approved drug compounds from
#' ChEMBL database given a string of ChEMBL target ID.
#' @name get.appDrugs
#' @docType package
#' @param x : string ChEMBL target ID.
#' @export
#' @examples
#' \donttest{
#' #get chembl ids of approved drugs
#' get.appDrugs("CHEMBL1824")
#' }
get.appDrugs<-function(x){
url<-sprintf('https://www.ebi.ac.uk/chemblws/targets/%s/approvedDrug.json',x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))[[1]]
} else {
return(NULL)
}
}
#' get.bioactivity.
#' @title Get Bioactivity Information for Compounds, Targets or Assays.
#' @description This method retrieves bioactivity information for a compound
#' across multiple targets/assays or else for a target across multiple compounds.
#' The function can also be used to retrieve all activities within a given assay.
#' In all cases, ChEMBL identifiers must be used.
#' @name get.bioactivity
#' @docType package
#' @param x : Input string chemblid
#' @param type : Input string \code{'compound'},\code{'target'},\code{'assay'}. Default is
#' \code{'compound'}.
#' @export
#' @examples
#' \donttest{
#' # get bioactivities of compounds
#' get.bioactivity("CHEMBL12",type='compound')
#'
#' # get compound bioactivities for targets
#' get.bioactivity("CHEMBL240",type="target")
#'
#' # get bioactivities by assay
#' get.bioactivity("CHEMBL1217643",type='assay')
#' }
get.bioactivity <- function(x, type='compound') {
types <- c('compound', 'target', 'assay')
type <- pmatch(type, types)
if (is.na(type)) stop("Invalid type given")
url <- switch(type,
url = 'https://www.ebi.ac.uk/chemblws/compounds/%s/bioactivities.json',
url = 'https://www.ebi.ac.uk/chemblws/targets/%s/bioactivities.json',
url = 'https://www.ebi.ac.uk/chemblws/assays/%s/bioactivities.json')
url <- sprintf(url,x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<-do.call(rbind, lapply(fromJSON(d), data.frame))
return(data)
} else {
return(NULL)
}
}
#' get.moa
#' @title Get mechanism of action
#' @description This function retrieves a data frame of compounds and its
#' mode of action for a compound (where compound is a drug) and drug targets.
#' @name get.moa
#' @docType package
#' @param x : Input string chemblid
#' @export
#' @examples
#' \donttest{
#' # get moa of drug
#' get.moa("CHEMBL1642")
#' }
get.moa<-function(x){
url <- 'https://www.ebi.ac.uk/chemblws/compounds/'
url<-sprintf('%s%s/drugMechanism.json',url,x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<- do.call(rbind, lapply(fromJSON(d), data.frame))
return(data)
} else {
return(NULL)
}
}
#' get.targets
#' @title Get target information.
#' @description This function retrieves the target information by chembl id and
#' uniprot id and also retrieves all the names of targets by organisms. When
#' \code{org="Homo sapiens"} subsets the data frame by organism homo sapiens and retrieves
#' all the Homo sapiens taregts
#' @name get.targets
#' @docType package
#' @param x : Input string chemblid
#' @param type : Input string 'chemblid' or 'uniprot'
#' @param org : Input string species name like "Homo sapiens","Plasmodium falciparum" and etc.
#' @export
#' @examples
#' \donttest{
#' #get target information by chembl ids
#' get.targets("CHEMBL1862",type='chemblid')
#'
#' #get target information by uniprot ids
#' get.targets("Q13936",type='uniprot')
#'
#' #get all the target information using organism name
#' get.targets(org="Homo Sapiens")
#' }
get.targets <- function(x,type='chemblid',org=NULL){
types <- c('chemblid', 'uniprot')
type <- pmatch(type, types)
if (is.na(type)) stop("Invalid type given")
if(is.null(org)){
url<-switch(type,'https://www.ebi.ac.uk/chemblws/targets/%s.json',
'https://www.ebi.ac.uk/chemblws/targets/uniprot/%s.json')
url <- sprintf(url,x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<- do.call(rbind, lapply(fromJSON(d), data.frame))
return(data)
} else {
return(NULL)
}
}else{
url<-'https://www.ebi.ac.uk/chemblws/targets.json'
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
df <- do.call(rbind, lapply(fromJSON(d), data.frame))
data<-df[ which(df$organism==org)]
return (data)
} else {
return(NULL)
}
}
}
abhik1368/rUniChEMBL documentation built on May 10, 2019, 4:10 a.m.
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library(RCurl)
library(jsonlite)
#' get.scid.sid
#' @title Get the source compound ids from another source compound id
#' @description a list of all src_compound_ids from all sources which are
#' CURRENTLY assigned to the same structure as a currently assigned
#' query src_compound_id.
#' The output will include query src_compound_id if it is a valid src_compound_id
#' with a current assignment.
#' @name get.scid.sid
#' @docType package
#' @param x : Input string Source compound id
#' @param y : Input integer Source id
#' @export
#' @examples
#' \donttest{
#' # Get source compound ids and source information
#' # Using ChEMBL ID and source
#' get.scid.sid("CHEMBL12",1)
#' # Using drugbank id and source
#' get.scid.sid("DB00789",2)
#' }
get.scid.sid <- function(x,y) {
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id/%s/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
} else {
return(NULL)
}
}
#' get.sAll.sid
#' @title Get the all source compound ids from another source compound id
#' @description Obtain a list of all src_compound_ids from all sources
#' (including BOTH current AND obsolete assignments) to the same structure
#' as a currently assigned query
#' src_compound_id.
#' @name get.sAll.sid
#' @docType package
#' @param x : Input chemblid
#' @param y : Input integer source id
#' @export
#' @examples
#' \donttest{
#' # Get all source ids using ChEMBL id and source
#' get.sAll.sid("CHEMBL12",1)
#' # Using drugbank id and source
#' get.sAll.sid("DB00789",2)
#' }
get.sAll.sid <- function(x,y) {
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id_all/%s/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
}else {
return(NULL)
}
}
#' get.mapping.full
#' @title Get full mapping between two sources.
#' @description Obtain a full mapping between two sources. Uses only currently
#' assigned src_compound_ids from both sources.
#' @name get.mapping.full
#' @docType package
#' @param x : Input integer source id
#' @param y : Input integer source id
#' @export
#' @examples
#' \donttest{
#' # Get full mapping of PDBe and ChEMBL
#' get.mapping.full(3,1)
#' # Get full mapping of ZINC and ChEMBL
#' get.mapping.full(9,1)
#' }
get.mapping.full <-function(x,y) {
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/mapping/%d/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.src_id.InCHIKey
#' @title Get source compound ids
#' @description Obtain a list of src_compound_ids (from all sources) which
#' are CURRENTLY assigned to a query InChI Key. Returns a list of data from
#' Unichem and ChEMBL databases.
#' @name get.src_id.InCHIKey
#' @docType package
#' @param x : Input string InCHI Key
#' @export
#' @examples
#' \donttest{
#' # Get source compound ids from InCHIKey
#' get.sid.InCHIKey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
#'
#' data<-get.sid.InCHIKey("BSYNRYMUTXBXSQ-UHFFFAOYSA-N")
#' # to get chembl data
#' data$Chem
#' to get Unichem data
#' data$Uni
#' }
get.sid.InCHIKey<-function(x){
url_uni <- sprintf("https://www.ebi.ac.uk/unichem/rest/inchikey/%s",x)
url_chem<-sprintf("https://www.ebi.ac.uk/chemblws/compounds/stdinchikey/%s.json",x)
h <- getCurlHandle()
d <- getURL(url_uni, curl=h)
c<-getURL(url_chem, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
cf<-do.call(rbind, lapply(fromJSON(c), data.frame))
return(list(uni=df,Chem=cf))
} else {
return(NULL)
}
}
#' get.sAll.InCHIKey
#' @title Get all src_compound_ids.
#' @description Get a list of all src_compound_ids (from all sources) which
#' have current AND obsolete assignments to a query InChIKey
#' @name get.sAll.InCHIKey
#' @docType package
#' @param x : Input string InCHI Key
#' @export
#' @examples
#' \donttest{
#' # Get all the IDs using InCHIKey
#' get.sAll.InCHIKey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
#' }
get.sAll.InCHIKey<-function(x){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/inchikey_all/%s",x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
}else {
return(NULL)
}
}
#' get.structure
#' @title Get structure
#' @description Get structure(s) currently assigned to a query src_compound_id.
#' @name get.structure
#' @docType package
#' @param x : Input string chemblid
#' @param s : Input integer source id (default is 1)
#' @export
#' @examples
#' \donttest{
#' # Get Standard inhci and InCHIKey from drugbank compound and source
#' get.structure("DB00321",2)
#' # Using ChEMBL compound and source id
#' get.structure("CHEMBL1231",1)
#' }
get.structure<-function(x,s=1){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/structure/%s/%d",x,s)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.struc.all
#' @title Get Structures for source compound id
#' @description Get the standard InCHI and standard InCHI Key for the source
#' compound id
#' @name get.struc.all
#' @docType package
#' @param x : Input string chemblid
#' @param s : Input integer source id (default is 1)
#' @export
#' @examples
#' \donttest{
#' # Get all the structure information using ChEMBL id and source.
#' get.struc.all("CHEMBL1231",1)
#' #using drugbank id and source
#' get.structure("DB00321",2)
#' }
get.struc.all<-function(x,s=1){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/structure_all/%s/%d",x,s)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.url.sid
#' @title Get url for the query compound
#' @description Get a list of URLs for all src_compound_ids, from a specified
#' source .
#' @name get.url.sid
#' @docType package
#' @param x : Input string source compound id
#' @param y : Input integer source id
#' @param z : Input integer to source id
#' @export
#' @examples
#' \donttest{
#' # get urls of compounds using source compound id, source id
#' # get drugbank url from ChEMBL source id and ChEMBL source
#' get.url.sid("ChEMBL490",1,2)
#'
#' # get chembl url from drugbank id and source
#' get.url.sid("DB00715",2,1)
#' }
get.url.sid<-function(x,y,z){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id_url/%s/%d/%d",x,y,z)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.sAll.obs
#' @title Get source compound id from obsolete source compound id
#' @description Get a list of all src_compound_ids from all sources with BOTH
#' current AND obsolete to the same structure with an obsolete assignment to the #' query src_compound_id.
#' @name get.SrcAll.obs
#' @docType package
#' @param x : Input string source compound id
#' @param y : Input integer to source id
#' @export
#' @examples
#' \donttest{
#' #get for drugbank compound and source
#' get.sAll.obs("DB07699",2)
#' #get for chembl compound and source
#' get.sAll.obs("CHEMBL12",1)
#' }
get.sAll.obs<-function(x,y){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/src_compound_id_all_obsolete/%s/%d",x,y)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data(SourceNames)
sn<-SourceNames
data<-fromJSON(d)
df<-merge(data,sn,by.x="src_id",by.y="src_id")
return(df)
} else {
return(NULL)
}
}
#' get.verbose.InCHIkey
#' @title Get all src_compound_ids to a query InChIKey
#' @description Returns a dataframe containing src_id (the src_id for this source),
#' src_url (the main home page of the source), name (the unique name for the source in
#' UniChem, always lower case), name_long (the full name of the source, as defined by the
#' source),name_label (A name for the source
#' suitable for use as a 'label' for the source within a web-page. Correct case setting
#' for source, and always less than 30 characters), description (a description of the
#' content of the source), base_id_url_available (an flag indicating whether this source
#' provides a valid base_id_url for creating cpd-specific links [1=yes, 0=no]),base_id_url
#' (the base url for constructing hyperlinks to this source [append an identifier from
#' this source to the end of this url to create a valid url to a specific page for this
#' cpd], unless aux_for_url=1), aux_for_url (A flag to indicate whether the aux_src field
#' should be used to create hyperlinks instead of the src_compound_id [1=yes, 0=no] ,
#' src_compound_id (a list of src_compound_ids from this source which are currently
#' assigned to the query InChIKey, aux_src (a list of src-compound_id keys mapping to
#' corresponding auxiliary data (url_id:value), for creating links if aux_for_url=1. Only
#' shown if aux_for_url=1).
#' @name get.verbose.InCHIkey
#' @docType package
#' @param x : Input string InCHI Key
#' @export
#' @examples
#' \donttest{
#' # get for InCHIkey
#' get.verbose.InCHIkey("GZUITABIAKMVPG-UHFFFAOYSA-N")
#'
#' get.verbose.InCHIkey("AAOVKJBEBIDNHE-UHFFFAOYSA-N")
#' }
get.verbose.InCHIkey<-function(x){
url <- sprintf("https://www.ebi.ac.uk/unichem/rest/verbose_inchikey/%s",x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.cmp.inf
#' @title Get compound information from ChEMBL
#' @description These functions allow one to retrieve compounds information from ChEMBL
#' compounds are identified either by a ChEMBL ID or by a standard InChI key.
#' @name get.cmp.inf
#' @docType package
#' @param x : String representing chemblid or standard InCHI key for the molecule.
#' @param type : For \code{get.compound}, one of \code{chemblid} or
#' \code{stdinchi} to indicate the nature of the molecule id.
#' @export
#' @examples
#' \donttest{
#' #get information for chembl compound id
#' get.compound("CHEMBL12")
#'
#' #get information for standard inchi
#' get.compound("QFFGVLORLPOAEC-SNVBAGLBSA-N",type='stdinchi')
#' }
get.cmp.inf <- function(x, type='chemblid') {
types <- c('chemblid', 'stdinchi')
type <- pmatch(type, types)
if (is.na(type)) stop("Invalid type given")
url <- switch(type,
url = 'https://www.ebi.ac.uk/chemblws/compounds/',
url = 'https://www.ebi.ac.uk/chemblws/compounds/stdinchikey/')
url <- sprintf('%s%s.json', url, id)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))
} else {
return(NULL)
}
}
#' get.cmp.sim
#' @title Retrive similar compounds from ChEMBL database.
#' @description This function retrieves a dataframe of similar compounds
#' from ChEMBL database given a smiles string as query and also given a similarity score above 70.
#' @name get.cmp.sim
#' @docType package
#' @param mol : String representing smiles of the moelcule
#' @param sim : Integer representing for percentage of similarity
#' for the query compound and the database molecules. Values ranges
#' from 70 to 100.
#' @export
get.cmp.sim <- function(mol,sim=70) {
url <- 'https://www.ebi.ac.uk/chemblws/compounds/similarity/'
url <- sprintf('%s%s/%d.json', url,mol,sim)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d)[[1]])
} else {
return(NULL)
}
}
#' get.cmp.substruct
#' @title Get compound information from substructure query smiles.
#' @description This function retrieves a dataframe of all compounds from ChEMBL database
#' containing the substructure represented by the given Canonical SMILES and their
#' chemical properties.
#' @name get.compound.substruct
#' @docType package
#' @param mol : String representing smiles of the moelcule
#' @export
#' @examples
#' \donttest{
#' #get compounds by substructure
#' get.cmp.subsruct("CN(CCCN)c1cccc2ccccc12")
#' }
get.cmp.substruct<-function(mol){
url <- sprintf('https://www.ebi.ac.uk/chemblws/compounds/substructure/%s.json',mol)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<-fromJSON(d)
return(data$compounds)
} else {
return(NULL)
}
}
#' get.appDrugs
#' @title Get approved drugs for target.
#' @description This function retrieves a dataframe of all approved drug compounds from
#' ChEMBL database given a string of ChEMBL target ID.
#' @name get.appDrugs
#' @docType package
#' @param x : string ChEMBL target ID.
#' @export
#' @examples
#' \donttest{
#' #get chembl ids of approved drugs
#' get.appDrugs("CHEMBL1824")
#' }
get.appDrugs<-function(x){
url<-sprintf('https://www.ebi.ac.uk/chemblws/targets/%s/approvedDrug.json',x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
return(fromJSON(d))[[1]]
} else {
return(NULL)
}
}
#' get.bioactivity.
#' @title Get Bioactivity Information for Compounds, Targets or Assays.
#' @description This method retrieves bioactivity information for a compound
#' across multiple targets/assays or else for a target across multiple compounds.
#' The function can also be used to retrieve all activities within a given assay.
#' In all cases, ChEMBL identifiers must be used.
#' @name get.bioactivity
#' @docType package
#' @param x : Input string chemblid
#' @param type : Input string \code{'compound'},\code{'target'},\code{'assay'}. Default is
#' \code{'compound'}.
#' @export
#' @examples
#' \donttest{
#' # get bioactivities of compounds
#' get.bioactivity("CHEMBL12",type='compound')
#'
#' # get compound bioactivities for targets
#' get.bioactivity("CHEMBL240",type="target")
#'
#' # get bioactivities by assay
#' get.bioactivity("CHEMBL1217643",type='assay')
#' }
get.bioactivity <- function(x, type='compound') {
types <- c('compound', 'target', 'assay')
type <- pmatch(type, types)
if (is.na(type)) stop("Invalid type given")
url <- switch(type,
url = 'https://www.ebi.ac.uk/chemblws/compounds/%s/bioactivities.json',
url = 'https://www.ebi.ac.uk/chemblws/targets/%s/bioactivities.json',
url = 'https://www.ebi.ac.uk/chemblws/assays/%s/bioactivities.json')
url <- sprintf(url,x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<-do.call(rbind, lapply(fromJSON(d), data.frame))
return(data)
} else {
return(NULL)
}
}
#' get.moa
#' @title Get mechanism of action
#' @description This function retrieves a data frame of compounds and its
#' mode of action for a compound (where compound is a drug) and drug targets.
#' @name get.moa
#' @docType package
#' @param x : Input string chemblid
#' @export
#' @examples
#' \donttest{
#' # get moa of drug
#' get.moa("CHEMBL1642")
#' }
get.moa<-function(x){
url <- 'https://www.ebi.ac.uk/chemblws/compounds/'
url<-sprintf('%s%s/drugMechanism.json',url,x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<- do.call(rbind, lapply(fromJSON(d), data.frame))
return(data)
} else {
return(NULL)
}
}
#' get.targets
#' @title Get target information.
#' @description This function retrieves the target information by chembl id and
#' uniprot id and also retrieves all the names of targets by organisms. When
#' \code{org="Homo sapiens"} subsets the data frame by organism homo sapiens and retrieves
#' all the Homo sapiens taregts
#' @name get.targets
#' @docType package
#' @param x : Input string chemblid
#' @param type : Input string 'chemblid' or 'uniprot'
#' @param org : Input string species name like "Homo sapiens","Plasmodium falciparum" and etc.
#' @export
#' @examples
#' \donttest{
#' #get target information by chembl ids
#' get.targets("CHEMBL1862",type='chemblid')
#'
#' #get target information by uniprot ids
#' get.targets("Q13936",type='uniprot')
#'
#' #get all the target information using organism name
#' get.targets(org="Homo Sapiens")
#' }
get.targets <- function(x,type='chemblid',org=NULL){
types <- c('chemblid', 'uniprot')
type <- pmatch(type, types)
if (is.na(type)) stop("Invalid type given")
if(is.null(org)){
url<-switch(type,'https://www.ebi.ac.uk/chemblws/targets/%s.json',
'https://www.ebi.ac.uk/chemblws/targets/uniprot/%s.json')
url <- sprintf(url,x)
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
data<- do.call(rbind, lapply(fromJSON(d), data.frame))
return(data)
} else {
return(NULL)
}
}else{
url<-'https://www.ebi.ac.uk/chemblws/targets.json'
h <- getCurlHandle()
d <- getURL(url, curl=h)
status <- getCurlInfo(h)$response.code
rm(h)
if (status == 200) {
df <- do.call(rbind, lapply(fromJSON(d), data.frame))
data<-df[ which(df$organism==org)]
return (data)
} else {
return(NULL)
}
}
}
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