## Extend readLines() for parsing a remote .gz format file.
#' @keywords internal
readLines_gzfile <- function(url, ...) {
gzf <- tempfile(fileext = ".gz")
download.file(url, gzf)
con <- gzfile(gzf)
on.exit(close(con))
content <- readLines(con, ...)
return(content)
}
## PubChem Resource Description Framework Api
#' @importFrom yulab.utils yread
#' @keywords internal
pubchem_rest <- function(rest_url) {
message("Reading PubChem RDF online: \"", rest_url, "\"...")
content <- yread(rest_url, reader = readLines_gzfile)
content <- content[grep("^[^@]", content)]
content <- content |>
strsplit("\t") |>
do.call(rbind, args = _)
res <- data.frame(from = content[, 1], linktype = content[, 2],
to = content[, 3])
return(res)
}
## Download PubChem annotation of the latest version of PubChem pathway and
## stored in a 'GSON' object.
#' @param rm.protein remove protein nodes in PubChem pathway, defualt TRUE.
#' @keywords internal
gson_PubChemPathway <- function(rm.protein = TRUE) {
url <- "https://ftp.ncbi.nlm.nih.gov/pubchem/RDF/pathway/pc_pathway.ttl.gz"
pc_pw <- pubchem_rest(url)
gsid2name <- pc_pw[pc_pw$linktype == "dcterms:title", c("from", "to")]
gsid2name <- setNames(gsid2name, c("gsid", "name"))
gsid2name$gsid <- sub("pathway:", "", gsid2name$gsid)
gsid2name$name <- gsub("\"| \\.$", "", gsid2name$name)
if (rm.protein) {
patt <- "compound:"
} else {
patt <- "compound:|protein:"
}
gsid2gene <- pc_pw[grep(patt, pc_pw$to), c("from", "to")]
gsid2gene <- setNames(gsid2gene, c("gsid", "gene"))
i <- which(gsid2gene$gsid != "")
times <- diff(c(i, nrow(gsid2gene) + 1))
gsid2gene$gsid <- rep(gsid2gene$gsid[i], times)
gsid2gene$gsid <- sub("pathway:", "", gsid2gene$gsid)
gsid2gene$gene <- gsub("[compound:|protein:| \\.| ,]", "", gsid2gene$gene)
raw_html <- readLines("https://ftp.ncbi.nlm.nih.gov/pubchem/RDF/pathway/")
raw_html <- raw_html[grep("pc_pathway.ttl.gz", raw_html)]
version <- sub("^.+(\\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}).+$", "\\1", raw_html)
version <- paste0("Release ", version)
keytype <- "PubChem Compound ID (CID)"
if (!rm.protein) {
keytype <- paste0(keytype, " or Protein Accession Number")
}
gson_pc_pw <- gson(gsid2gene = gsid2gene,
gsid2name = gsid2name,
species = "Homo sapiens",
gsname = "PubChem Pathway",
version = version,
keytype = keytype,
accessed_date = as.character(Sys.Date()))
return(gson_pc_pw)
}
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