R/downloadChEBI.R
In dosorio/minval: MINimal VALidation for Stoichiometric Reactions
Defines functions
downloadChEBI
Documented in
downloadChEBI
#' @export downloadChEBI
#' @importFrom stats complete.cases setNames
#' @importFrom utils download.file read.delim2 read.table
#' @author Daniel Camilo Osorio <dcosorioh@tamu.edu>
# Bioinformatics and Systems Biology Lab | Universidad Nacional de Colombia
# Experimental and Computational Biochemistry | Pontificia Universidad Javeriana
#' @title Download the ChEBI database
#' @description This function downloads the compounds, formulas, masses and charges from the selected release of the ChEBI database.
#' The ChEBI database (Chemical Entities of Biological Interest), is a database and ontology of molecular entities focused on 'small' chemical compounds.
#' @param release A character string with the release number of the ChEBI database version to be downloaded, by default the \code{'latest'} release is downloaded.
#' @param woAssociations A logical value \code{'TRUE'} or \code{'FALSE'} if a light version of the ChEBI database without associations should be returned.
#' @return A data.frame with the following data associated to the ChEBI compounds: \itemize{
#' \item \code{'ID'}: The unique identifer
#' \item \code{'ChEBI'}: The name recommended for use in biological databases
#' \item \code{'KEGG'}: The associated name(s) in the KEGG database
#' \item \code{'IUPAC'}: The name(s) generated according to recommendations of IUPAC
#' \item \code{'MetaCyc'}: The associated name(s) in the MetaCyc database
#' \item \code{'ChEMBL'}: The associated name(s) in the ChEMBL database
#' \item \code{'FORMULA'}: The molecular formula
#' \item \code{'MASS'}: The molecular mass
#' \item \code{'MONOISOTOPIC'}: The molecular monoisotopic mass
#' \item \code{'CHARGE'}: The molecular net charge
#' }
#' If woAssociations is \code{'TRUE'} a A data.frame with the following data is returned: \itemize{
#' \item \code{'NAME'}: The name(s) associated in several biological databases
#' \item \code{'FORMULA'}: The molecular formula
#' \item \code{'MASS'}: The molecular mass
#' \item \code{'MONOISOTOPIC'}: The molecular monoisotopic mass
#' \item \code{'CHARGE'}: The molecular net charge
#' }
#' @examples
#' \dontrun{
#' # Download ChEBI database with associations
#' ChEBI <- downloadChEBI(release = '142')
#'
#' # Download ChEBI database without associations
#' ChEBI <- downloadChEBI(release = '142', woAssociations = TRUE)
#' }
#' @seealso The ChEBI database webpage: https://www.ebi.ac.uk/chebi/
downloadChEBI <- function(release = "latest",
woAssociations = FALSE) {
# Download folder
chebi_download <- tempdir()
# Download releases
download.file(
"ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/",
paste0(chebi_download, "releases.txt"),
quiet = TRUE, method = "libcurl"
)
releases <-
gsub("rel", "", read.table(
paste0(chebi_download, "releases.txt"),
quote = "\"",
comment.char = ""
)[, 9])
message("Validating ChEBI release number ... ", appendLF = FALSE)
# Match release
if (release == "latest") {
release <- max(releases)
} else {
release <- releases[match(release, releases)]
}
message("OK")
# Download files
ftp <-
paste0(
"ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel",
release,
"/Flat_file_tab_delimited/"
)
message("Downloading compounds ... ", appendLF = FALSE)
download.file(paste0(ftp, "compounds.tsv.gz"),
paste0(chebi_download, "compounds.tsv"),
quiet = TRUE, method = "libcurl")
compounds <- suppressWarnings(
as.data.frame.array(read.delim2(paste0(chebi_download, "compounds.tsv"))))
message("DONE", appendLF = TRUE)
message("Downloading synonyms ... ", appendLF = FALSE)
download.file(paste0(ftp, "names.tsv.gz"),
paste0(chebi_download, "names.tsv"),
quiet = TRUE, method = "libcurl")
names <-
suppressWarnings(as.data.frame.array(read.delim2(paste0(
chebi_download, "names.tsv"
))))
message("DONE", appendLF = TRUE)
message("Downloading formulas ... ", appendLF = FALSE)
download.file(paste0(ftp, "chemical_data.tsv"),
paste0(chebi_download, "formulas.tsv"),
quiet = TRUE, method = "libcurl")
formulas <-
suppressWarnings(as.data.frame.array(read.delim2(
paste0(chebi_download, "formulas.tsv")
)))
message("DONE", appendLF = TRUE)
# Building database
message("Building ChEBI ... ", appendLF = TRUE)
compounds <- compounds[compounds[, "STAR"] >= 3, ]
latest <- compounds[, c("ID", "NAME")]
old <- compounds[, c("ID", "PARENT_ID")]
old <- merge(
x = old,
y = latest,
by.x = "PARENT_ID",
by.y = "ID"
)
compounds <- rbind(latest, old[, c("ID", "NAME")])
if(any(sapply(compounds[, "NAME"] == "null", isTRUE))){
compounds[compounds[, "NAME"] == "null", "NAME"] <- NA
}
compounds <- compounds[complete.cases(compounds), ]
DB <-
suppressWarnings((
merge(
compounds[, c("ID", "NAME")],
names[, c("COMPOUND_ID", "SOURCE", "NAME")],
by.x = "ID",
by.y = "COMPOUND_ID",
all.x = TRUE
)
))
# Associations
## CHEBI
ChEBI <- unique(DB[, c("ID", "NAME.x")])
colnames(ChEBI) <- c("ID", "ChEBI")
## KEGG
message(" KEGG Associations ... ", appendLF = FALSE)
KEGG <-
unique(DB[DB[, "SOURCE"] == "KEGG COMPOUND", c("ID", "NAME.y")])
KEGG <- KEGG[complete.cases(KEGG), ]
colnames(KEGG) <- c("ID", "KEGG")
message("DONE", appendLF = TRUE)
## IUPAC
message(" IUPAC Associations ... ", appendLF = FALSE)
IUPAC <- unique(DB[DB[, "SOURCE"] == "IUPAC", c("ID", "NAME.y")])
IUPAC <- IUPAC[complete.cases(IUPAC), ]
colnames(IUPAC) <- c("ID", "IUPAC")
message("DONE", appendLF = TRUE)
## METACYC
message(" MetaCyc Associations ... ", appendLF = FALSE)
MetaCyc <- unique(DB[DB[, "SOURCE"] == "MetaCyc", c("ID", "NAME.y")])
MetaCyc <- MetaCyc[complete.cases(MetaCyc), ]
colnames(MetaCyc) <- c("ID", "MetaCyc")
message("DONE", appendLF = TRUE)
## CHEMBL
message(" ChEMBL Associations ... ", appendLF = FALSE)
ChEMBL <- unique(DB[DB[, "SOURCE"] == "ChEMBL", c("ID", "NAME.y")])
ChEMBL <- ChEMBL[complete.cases(ChEMBL), ]
colnames(ChEMBL) <- c("ID", "ChEMBL")
message("DONE", appendLF = TRUE)
DB <- unique(merge(DB["ID"], ChEBI, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, KEGG, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, IUPAC, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, MetaCyc, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, ChEMBL, by = "ID", all.x = TRUE))
rm(ChEBI,
ChEMBL,
compounds,
IUPAC,
KEGG,
latest,
MetaCyc,
names,
old)
## FORMULA
if ("FORMULA" %in% unique(formulas[, "TYPE"])) {
message(" Formula Associations ... ", appendLF = FALSE)
formula <-
formulas[formulas[, "TYPE"] == "FORMULA", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(formula) <- c("ID", "FORMULA")
DB <- merge(DB, formula, by = "ID", all.x = TRUE)
DB <-
merge(DB, DB[, c("ChEBI", "FORMULA")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "FORMULA.x"]), "FORMULA.x"] <- "null"
DB[is.na(DB[, "FORMULA.y"]), "FORMULA.y"] <- "null"
DB[DB[, "FORMULA.x"] != "null" &
DB[, "FORMULA.y"] == "null", "FORMULA.y"] <-
DB[DB[, "FORMULA.x"] != "null" &
DB[, "FORMULA.y"] == "null", "FORMULA.x"]
DB[DB[, "FORMULA.y"] != "null" &
DB[, "FORMULA.x"] == "null", "FORMULA.x"] <-
DB[DB[, "FORMULA.y"] != "null" &
DB[, "FORMULA.x"] == "null", "FORMULA.y"]
DB <-
unique(DB[DB[, "FORMULA.x"] != "null" &
DB[, "FORMULA.y"] != "null", c("ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x")])
rm(formula)
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
## MASS
message("Downloading molecular weights ... ", appendLF = FALSE)
if ("MASS" %in% unique(formulas[, "TYPE"])) {
mass <-
formulas[formulas[, "TYPE"] == "MASS", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(mass) <- c("ID", "MASS")
DB <- merge(DB, mass, by = "ID", all.x = TRUE)
DB <- merge(DB, DB[, c("ChEBI", "MASS")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "MASS.x"]), "MASS.x"] <- "null"
DB[is.na(DB[, "MASS.y"]), "MASS.y"] <- "null"
DB[DB[, "MASS.x"] != "null" &
DB[, "MASS.y"] == "null", "MASS.y"] <-
DB[DB[, "MASS.x"] != "null" & DB[, "MASS.y"] == "null", "MASS.x"]
DB[DB[, "MASS.y"] != "null" &
DB[, "MASS.x"] == "null", "MASS.x"] <-
DB[DB[, "MASS.y"] != "null" & DB[, "MASS.x"] == "null", "MASS.y"]
DB <-
unique(DB[, c("ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x",
"MASS.x")])
rm(mass)
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
message("Downloading monoisotopic molecular weights ... ", appendLF = FALSE)
## MMASS
if ("MONOISOTOPIC MASS" %in% unique(formulas[, "TYPE"])) {
mmass <-
formulas[formulas[, "TYPE"] == "MONOISOTOPIC MASS", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(mmass) <- c("ID", "MONOISOTOPIC")
DB <- merge(DB, mmass, by = "ID", all.x = TRUE)
DB <-
merge(DB, DB[, c("ChEBI", "MONOISOTOPIC")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "MONOISOTOPIC.x"]), "MONOISOTOPIC.x"] <- "null"
DB[is.na(DB[, "MONOISOTOPIC.y"]), "MONOISOTOPIC.y"] <- "null"
DB[DB[, "MONOISOTOPIC.x"] != "null" &
DB[, "MONOISOTOPIC.y"] == "null", "MONOISOTOPIC.y"] <-
DB[DB[, "MONOISOTOPIC.x"] != "null" &
DB[, "MONOISOTOPIC.y"] == "null", "MONOISOTOPIC.x"]
DB[DB[, "MONOISOTOPIC.y"] != "null" &
DB[, "MONOISOTOPIC.x"] == "null", "MONOISOTOPIC.x"] <-
DB[DB[, "MONOISOTOPIC.y"] != "null" &
DB[, "MONOISOTOPIC.x"] == "null", "MONOISOTOPIC.y"]
DB <-
unique(DB[, c(
"ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x",
"MASS.x",
"MONOISOTOPIC.x"
)])
rm(mmass)
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
message("Downloading molecular charges ... ", appendLF = FALSE)
## CHARGE
if ("CHARGE" %in% unique(formulas[, "TYPE"])) {
charge <-
formulas[formulas[, "TYPE"] == "CHARGE", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(charge) <- c("ID", "CHARGE")
DB <- merge(DB, charge, by = "ID", all.x = TRUE)
DB <- merge(DB, DB[, c("ChEBI", "CHARGE")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "CHARGE.x"]), "CHARGE.x"] <- "null"
DB[is.na(DB[, "CHARGE.y"]), "CHARGE.y"] <- "null"
DB[DB[, "CHARGE.x"] != "null" &
DB[, "CHARGE.y"] == "null", "CHARGE.y"] <-
DB[DB[, "CHARGE.x"] != "null" & DB[, "CHARGE.y"] == "null", "CHARGE.x"]
DB[DB[, "CHARGE.y"] != "null" &
DB[, "CHARGE.x"] == "null", "CHARGE.x"] <-
DB[DB[, "CHARGE.y"] != "null" & DB[, "CHARGE.x"] == "null", "CHARGE.y"]
DB <-
unique(DB[, c(
"ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x",
"MASS.x",
"MONOISOTOPIC.x",
"CHARGE.x"
)])
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
DB[DB == "null"] <- NA
DB <-
unique(DB[complete.cases(DB[, c("ID",
"ChEBI",
"FORMULA.x",
"MASS.x",
"MONOISOTOPIC.x",
"CHARGE.x")]), ])
colnames(DB) <-
c(
"ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA",
"MASS",
"MONOISOTOPIC",
"CHARGE"
)
if (woAssociations == TRUE) {
compounds <-
unique(rbind(
setNames(DB[, c("ChEBI", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("KEGG", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("IUPAC", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("MetaCyc", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("ChEMBL", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
))
))
compounds <- compounds[complete.cases(compounds), ]
return(compounds)
} else {
return(DB)
}
}
dosorio/minval documentation built on May 24, 2022, 7:42 p.m.
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Defines functions downloadChEBI
Documented in downloadChEBI
#' @export downloadChEBI
#' @importFrom stats complete.cases setNames
#' @importFrom utils download.file read.delim2 read.table
#' @author Daniel Camilo Osorio <dcosorioh@tamu.edu>
# Bioinformatics and Systems Biology Lab | Universidad Nacional de Colombia
# Experimental and Computational Biochemistry | Pontificia Universidad Javeriana
#' @title Download the ChEBI database
#' @description This function downloads the compounds, formulas, masses and charges from the selected release of the ChEBI database.
#' The ChEBI database (Chemical Entities of Biological Interest), is a database and ontology of molecular entities focused on 'small' chemical compounds.
#' @param release A character string with the release number of the ChEBI database version to be downloaded, by default the \code{'latest'} release is downloaded.
#' @param woAssociations A logical value \code{'TRUE'} or \code{'FALSE'} if a light version of the ChEBI database without associations should be returned.
#' @return A data.frame with the following data associated to the ChEBI compounds: \itemize{
#' \item \code{'ID'}: The unique identifer
#' \item \code{'ChEBI'}: The name recommended for use in biological databases
#' \item \code{'KEGG'}: The associated name(s) in the KEGG database
#' \item \code{'IUPAC'}: The name(s) generated according to recommendations of IUPAC
#' \item \code{'MetaCyc'}: The associated name(s) in the MetaCyc database
#' \item \code{'ChEMBL'}: The associated name(s) in the ChEMBL database
#' \item \code{'FORMULA'}: The molecular formula
#' \item \code{'MASS'}: The molecular mass
#' \item \code{'MONOISOTOPIC'}: The molecular monoisotopic mass
#' \item \code{'CHARGE'}: The molecular net charge
#' }
#' If woAssociations is \code{'TRUE'} a A data.frame with the following data is returned: \itemize{
#' \item \code{'NAME'}: The name(s) associated in several biological databases
#' \item \code{'FORMULA'}: The molecular formula
#' \item \code{'MASS'}: The molecular mass
#' \item \code{'MONOISOTOPIC'}: The molecular monoisotopic mass
#' \item \code{'CHARGE'}: The molecular net charge
#' }
#' @examples
#' \dontrun{
#' # Download ChEBI database with associations
#' ChEBI <- downloadChEBI(release = '142')
#'
#' # Download ChEBI database without associations
#' ChEBI <- downloadChEBI(release = '142', woAssociations = TRUE)
#' }
#' @seealso The ChEBI database webpage: https://www.ebi.ac.uk/chebi/
downloadChEBI <- function(release = "latest",
woAssociations = FALSE) {
# Download folder
chebi_download <- tempdir()
# Download releases
download.file(
"ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/",
paste0(chebi_download, "releases.txt"),
quiet = TRUE, method = "libcurl"
)
releases <-
gsub("rel", "", read.table(
paste0(chebi_download, "releases.txt"),
quote = "\"",
comment.char = ""
)[, 9])
message("Validating ChEBI release number ... ", appendLF = FALSE)
# Match release
if (release == "latest") {
release <- max(releases)
} else {
release <- releases[match(release, releases)]
}
message("OK")
# Download files
ftp <-
paste0(
"ftp://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel",
release,
"/Flat_file_tab_delimited/"
)
message("Downloading compounds ... ", appendLF = FALSE)
download.file(paste0(ftp, "compounds.tsv.gz"),
paste0(chebi_download, "compounds.tsv"),
quiet = TRUE, method = "libcurl")
compounds <- suppressWarnings(
as.data.frame.array(read.delim2(paste0(chebi_download, "compounds.tsv"))))
message("DONE", appendLF = TRUE)
message("Downloading synonyms ... ", appendLF = FALSE)
download.file(paste0(ftp, "names.tsv.gz"),
paste0(chebi_download, "names.tsv"),
quiet = TRUE, method = "libcurl")
names <-
suppressWarnings(as.data.frame.array(read.delim2(paste0(
chebi_download, "names.tsv"
))))
message("DONE", appendLF = TRUE)
message("Downloading formulas ... ", appendLF = FALSE)
download.file(paste0(ftp, "chemical_data.tsv"),
paste0(chebi_download, "formulas.tsv"),
quiet = TRUE, method = "libcurl")
formulas <-
suppressWarnings(as.data.frame.array(read.delim2(
paste0(chebi_download, "formulas.tsv")
)))
message("DONE", appendLF = TRUE)
# Building database
message("Building ChEBI ... ", appendLF = TRUE)
compounds <- compounds[compounds[, "STAR"] >= 3, ]
latest <- compounds[, c("ID", "NAME")]
old <- compounds[, c("ID", "PARENT_ID")]
old <- merge(
x = old,
y = latest,
by.x = "PARENT_ID",
by.y = "ID"
)
compounds <- rbind(latest, old[, c("ID", "NAME")])
if(any(sapply(compounds[, "NAME"] == "null", isTRUE))){
compounds[compounds[, "NAME"] == "null", "NAME"] <- NA
}
compounds <- compounds[complete.cases(compounds), ]
DB <-
suppressWarnings((
merge(
compounds[, c("ID", "NAME")],
names[, c("COMPOUND_ID", "SOURCE", "NAME")],
by.x = "ID",
by.y = "COMPOUND_ID",
all.x = TRUE
)
))
# Associations
## CHEBI
ChEBI <- unique(DB[, c("ID", "NAME.x")])
colnames(ChEBI) <- c("ID", "ChEBI")
## KEGG
message(" KEGG Associations ... ", appendLF = FALSE)
KEGG <-
unique(DB[DB[, "SOURCE"] == "KEGG COMPOUND", c("ID", "NAME.y")])
KEGG <- KEGG[complete.cases(KEGG), ]
colnames(KEGG) <- c("ID", "KEGG")
message("DONE", appendLF = TRUE)
## IUPAC
message(" IUPAC Associations ... ", appendLF = FALSE)
IUPAC <- unique(DB[DB[, "SOURCE"] == "IUPAC", c("ID", "NAME.y")])
IUPAC <- IUPAC[complete.cases(IUPAC), ]
colnames(IUPAC) <- c("ID", "IUPAC")
message("DONE", appendLF = TRUE)
## METACYC
message(" MetaCyc Associations ... ", appendLF = FALSE)
MetaCyc <- unique(DB[DB[, "SOURCE"] == "MetaCyc", c("ID", "NAME.y")])
MetaCyc <- MetaCyc[complete.cases(MetaCyc), ]
colnames(MetaCyc) <- c("ID", "MetaCyc")
message("DONE", appendLF = TRUE)
## CHEMBL
message(" ChEMBL Associations ... ", appendLF = FALSE)
ChEMBL <- unique(DB[DB[, "SOURCE"] == "ChEMBL", c("ID", "NAME.y")])
ChEMBL <- ChEMBL[complete.cases(ChEMBL), ]
colnames(ChEMBL) <- c("ID", "ChEMBL")
message("DONE", appendLF = TRUE)
DB <- unique(merge(DB["ID"], ChEBI, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, KEGG, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, IUPAC, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, MetaCyc, by = "ID", all.x = TRUE))
DB <- unique(merge(DB, ChEMBL, by = "ID", all.x = TRUE))
rm(ChEBI,
ChEMBL,
compounds,
IUPAC,
KEGG,
latest,
MetaCyc,
names,
old)
## FORMULA
if ("FORMULA" %in% unique(formulas[, "TYPE"])) {
message(" Formula Associations ... ", appendLF = FALSE)
formula <-
formulas[formulas[, "TYPE"] == "FORMULA", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(formula) <- c("ID", "FORMULA")
DB <- merge(DB, formula, by = "ID", all.x = TRUE)
DB <-
merge(DB, DB[, c("ChEBI", "FORMULA")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "FORMULA.x"]), "FORMULA.x"] <- "null"
DB[is.na(DB[, "FORMULA.y"]), "FORMULA.y"] <- "null"
DB[DB[, "FORMULA.x"] != "null" &
DB[, "FORMULA.y"] == "null", "FORMULA.y"] <-
DB[DB[, "FORMULA.x"] != "null" &
DB[, "FORMULA.y"] == "null", "FORMULA.x"]
DB[DB[, "FORMULA.y"] != "null" &
DB[, "FORMULA.x"] == "null", "FORMULA.x"] <-
DB[DB[, "FORMULA.y"] != "null" &
DB[, "FORMULA.x"] == "null", "FORMULA.y"]
DB <-
unique(DB[DB[, "FORMULA.x"] != "null" &
DB[, "FORMULA.y"] != "null", c("ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x")])
rm(formula)
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
## MASS
message("Downloading molecular weights ... ", appendLF = FALSE)
if ("MASS" %in% unique(formulas[, "TYPE"])) {
mass <-
formulas[formulas[, "TYPE"] == "MASS", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(mass) <- c("ID", "MASS")
DB <- merge(DB, mass, by = "ID", all.x = TRUE)
DB <- merge(DB, DB[, c("ChEBI", "MASS")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "MASS.x"]), "MASS.x"] <- "null"
DB[is.na(DB[, "MASS.y"]), "MASS.y"] <- "null"
DB[DB[, "MASS.x"] != "null" &
DB[, "MASS.y"] == "null", "MASS.y"] <-
DB[DB[, "MASS.x"] != "null" & DB[, "MASS.y"] == "null", "MASS.x"]
DB[DB[, "MASS.y"] != "null" &
DB[, "MASS.x"] == "null", "MASS.x"] <-
DB[DB[, "MASS.y"] != "null" & DB[, "MASS.x"] == "null", "MASS.y"]
DB <-
unique(DB[, c("ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x",
"MASS.x")])
rm(mass)
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
message("Downloading monoisotopic molecular weights ... ", appendLF = FALSE)
## MMASS
if ("MONOISOTOPIC MASS" %in% unique(formulas[, "TYPE"])) {
mmass <-
formulas[formulas[, "TYPE"] == "MONOISOTOPIC MASS", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(mmass) <- c("ID", "MONOISOTOPIC")
DB <- merge(DB, mmass, by = "ID", all.x = TRUE)
DB <-
merge(DB, DB[, c("ChEBI", "MONOISOTOPIC")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "MONOISOTOPIC.x"]), "MONOISOTOPIC.x"] <- "null"
DB[is.na(DB[, "MONOISOTOPIC.y"]), "MONOISOTOPIC.y"] <- "null"
DB[DB[, "MONOISOTOPIC.x"] != "null" &
DB[, "MONOISOTOPIC.y"] == "null", "MONOISOTOPIC.y"] <-
DB[DB[, "MONOISOTOPIC.x"] != "null" &
DB[, "MONOISOTOPIC.y"] == "null", "MONOISOTOPIC.x"]
DB[DB[, "MONOISOTOPIC.y"] != "null" &
DB[, "MONOISOTOPIC.x"] == "null", "MONOISOTOPIC.x"] <-
DB[DB[, "MONOISOTOPIC.y"] != "null" &
DB[, "MONOISOTOPIC.x"] == "null", "MONOISOTOPIC.y"]
DB <-
unique(DB[, c(
"ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x",
"MASS.x",
"MONOISOTOPIC.x"
)])
rm(mmass)
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
message("Downloading molecular charges ... ", appendLF = FALSE)
## CHARGE
if ("CHARGE" %in% unique(formulas[, "TYPE"])) {
charge <-
formulas[formulas[, "TYPE"] == "CHARGE", c("COMPOUND_ID", "CHEMICAL_DATA")]
colnames(charge) <- c("ID", "CHARGE")
DB <- merge(DB, charge, by = "ID", all.x = TRUE)
DB <- merge(DB, DB[, c("ChEBI", "CHARGE")], by = "ChEBI", all.x = TRUE)
DB[is.na(DB[, "CHARGE.x"]), "CHARGE.x"] <- "null"
DB[is.na(DB[, "CHARGE.y"]), "CHARGE.y"] <- "null"
DB[DB[, "CHARGE.x"] != "null" &
DB[, "CHARGE.y"] == "null", "CHARGE.y"] <-
DB[DB[, "CHARGE.x"] != "null" & DB[, "CHARGE.y"] == "null", "CHARGE.x"]
DB[DB[, "CHARGE.y"] != "null" &
DB[, "CHARGE.x"] == "null", "CHARGE.x"] <-
DB[DB[, "CHARGE.y"] != "null" & DB[, "CHARGE.x"] == "null", "CHARGE.y"]
DB <-
unique(DB[, c(
"ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA.x",
"MASS.x",
"MONOISOTOPIC.x",
"CHARGE.x"
)])
message("DONE", appendLF = TRUE)
} else {
message("NOT AVAILABLE FOR THIS RELEASE")
}
DB[DB == "null"] <- NA
DB <-
unique(DB[complete.cases(DB[, c("ID",
"ChEBI",
"FORMULA.x",
"MASS.x",
"MONOISOTOPIC.x",
"CHARGE.x")]), ])
colnames(DB) <-
c(
"ID",
"ChEBI",
"KEGG",
"IUPAC",
"MetaCyc",
"ChEMBL",
"FORMULA",
"MASS",
"MONOISOTOPIC",
"CHARGE"
)
if (woAssociations == TRUE) {
compounds <-
unique(rbind(
setNames(DB[, c("ChEBI", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("KEGG", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("IUPAC", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("MetaCyc", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
)),
setNames(DB[, c("ChEMBL", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE")], c(
"NAME", "FORMULA", "MASS", "MONOISOTOPIC", "CHARGE"
))
))
compounds <- compounds[complete.cases(compounds), ]
return(compounds)
} else {
return(DB)
}
}
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