bch441-work-abc-units/RPR-eUtils_XML.R

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# tocID <- "RPR-eUtils_XML.R"
#
# Purpose: A Bioinformatics Course:
# R code accompanying the RPR-Scripting_data_downloads unit.
#
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# Version: 1.2
#
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# Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
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# 1.2 2020 Updates
# 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout
# 1.0 First ABC units version
# 0.1 First code copied from 2016 material.
#
#
# TODO:
#
#
# == DO NOT SIMPLY source() THIS FILE! =======================================
#
# If there are portions you don't understand, use R's help system, Google for an
# answer, or ask your instructor. Don't continue if you don't understand what's
# going on. That's not how it works ...
#
# ==============================================================================
#TOC> ==========================================================================
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#TOC>
#TOC> Section Title Line
#TOC> -----------------------------------------------------------
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#TOC> 1 Working with NCBI eUtils 42
#TOC> 1.1 Task - fetchNCBItaxData() function 144
#TOC> 2 Task solutions 151
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#TOC>
#TOC> ==========================================================================
# = 1 Working with NCBI eUtils ============================================
# To begin, we load the xml2 package that contains functions
# we need to receive and parse html data. NCBI's eUtils send information in
# XML format so we need to be able to parse XML.
if (! requireNamespace("xml2", quietly=TRUE)) {
install.packages("xml2")
}
# Package information:
# library(help = xml2) # basic information
# browseVignettes("xml2") # available vignettes
# data(package = "xml2") # available datasets
# We will walk through the process with the refSeqID
# of yeast Mbp1
refSeqID <- "NP_010227"
# First we build a query URL...
eUtilsBase <- "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
# Then we assemble an URL that will search for get the
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# unique, NCBI internal identifier,
# for our refSeqID...
URL <- paste(eUtilsBase,
"esearch.fcgi?", # ...using the esearch program
# that finds an entry in an
# NCBI database
"db=protein",
"&term=", refSeqID,
sep="")
# Copy the URL and paste it into your browser to see
# what the response should look like.
URL
# To fetch a response in R, we use the function read_xml()
# with our URL as its argument.
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( myXML <- xml2::read_xml(URL) )
# This is XML. We can take the response apart into
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# its individual components with the as_list() function.
xml2::as_list(myXML)
# Note how the XML "tree" is represented as a list of
# lists of lists ...
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# If we know exactly what element we are looking for,
# we can extract it from this structure:
xml2::as_list(myXML)[["eSearchResult"]][["IdList"]][["Id"]][[1]]
# But this is not very robust, it would break with the
# slightest change that the NCBI makes to their data format -
# and the NCBI changes things A LOT!
# Somewhat more robust is to specify the type of element
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# we want - its the text contained in an <Id>...</Id>
# element, and use the XPath XML parsing language to
# retrieve it.
xml2::xml_find_all(myXML, "//Id") # returns a "node set"
xml2::xml_text(xml2::xml_find_all(myXML, "//Id")) # returns the contents
# of the node set
# We will need to do this more than once, so we write a function
# for it...
node2text <- function(doc, tag) {
# an extractor function for the contents of elements
# between given tags in an XML response.
# Contents of all matching elements is returned in
# a vector of strings.
path <- paste0("//", tag)
nodes <- xml2::xml_find_all(doc, path)
return(xml2::xml_text(nodes))
}
# using node2text() ...
(GID <- node2text(myXML, "Id"))
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# The GI is the pivot for data requests at the
# NCBI.
# Let's first get the associated data for this GI
URL <- paste0(eUtilsBase,
"esummary.fcgi?",
"db=protein",
"&id=",
GID,
"&version=2.0")
(myXML <- xml2::read_xml(URL))
(taxID <- node2text(myXML, "TaxId"))
(organism <- node2text(myXML, "Organism"))
# This forms the base of a function that gets taxonomy data
# from an Entrez result. You can write this!
# == 1.1 Task - fetchNCBItaxData() function ================================
# Task: write a function that takes as input a RefSeq ID, fetches the taxonomy
# information, returns a list with taxID and organism, if the operation is
# successful, or a list of length 0 if there is an error.
# = 2 Task solutions ======================================================
# I have placed such a function into the dbUtilities script: look it up by
# clicking on dbFetchNCBItaxData() in the Environment pane.
# Test:
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dbFetchNCBItaxData("XP_001837394")
# [END]