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Asked: 2026-05-15T17:42:20+00:00

I am new to programming so bear with me. I have many XML documents

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I am new to programming so bear with me. I have many XML documents that look like this:

File name: PRIDE_Exp_Complete_Ac_10094.xml.gz

<ExperimentCollection version="2.1">
<Experiment>
    <ExperimentAccession>1015</ExperimentAccession>
    <Title>Protein complexes in Saccharomyces cerevisiae (GPM06600002310)</Title>
    <ShortLabel>GPM06600002310</ShortLabel>
    <Protocol>
        <ProtocolName>None</ProtocolName>
    </Protocol>
    <mzData version="1.05" accessionNumber="1015">
        <cvLookup cvLabel="RESID" fullName="RESID Database of Protein Modifications" version="0.0" address="http://www.ebi.ac.uk/RESID/" />
        <cvLookup cvLabel="UNIMOD" fullName="UNIMOD Protein Modifications for Mass Spectrometry" version="0.0" address="http://www.unimod.org/" />
        <description>
            <admin>
                <sampleName>GPM06600002310</sampleName>
                <sampleDescription comment="Ho, Y., et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002 Jan 10;415(6868):180-3.">
                    <cvParam cvLabel="NEWT" accession="4932" name="Saccharomyces cerevisiae (Baker's yeast)" value="Saccharomyces cerevisiae" />
                </sampleDescription>
                            </admin>
        </description>
        <spectrumList count="0" />
    </mzData>
        </Experiment>

I want to take out the text in between “Title”, “ProtocolName”, and “SampleName” and save into a text file that has the same name as the .xml.gz. I have the following code so far (based on posts I saw on this site), but it seems not to work:

require 'rubygems'
require 'nokogiri'
doc = Nokogiri::XML(File.open("PRIDE_Exp_Complete_Ac_10094.xml.gz"))
@ExperimentCollection = doc.css("ExperimentCollection Title").map {|node| node.children.text }

Can someone help me?

Thanks

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1 Answer

  1. Editorial Team

    IF you are happy with REXML, AND there’s only one <Experiment> per file, then something like the following should help … (by the way, above text is invalid XML since no closing <ExperimentCollection> tag)

    require "rexml/document"
include REXML
xml=<<EOD
<Experiment>
    <ExperimentAccession>1015</ExperimentAccession>
    <Title>Protein complexes in Saccharomyces cerevisiae (GPM06600002310)</Title>
    <ShortLabel>GPM06600002310</ShortLabel>
    <Protocol>
        <ProtocolName>None</ProtocolName>
    </Protocol>
    <mzData version="1.05" accessionNumber="1015">
        <cvLookup cvLabel="RESID" fullName="RESID Database of Protein Modifications" version="0.0" address="http://www.ebi.ac.uk/RESID/" />
        <cvLookup cvLabel="UNIMOD" fullName="UNIMOD Protein Modifications for Mass Spectrometry" version="0.0" address="http://www.unimod.org/" />
        <description>
            <admin>
                <sampleName>GPM06600002310</sampleName>
                <sampleDescription comment="Ho, Y., et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002 Jan 10;415(6868):180-3.">
                    <cvParam cvLabel="NEWT" accession="4932" name="Saccharomyces cerevisiae (Baker's yeast)" value="Saccharomyces cerevisiae" />
                </sampleDescription>
                            </admin>
        </description>
        <spectrumList count="0" />
    </mzData>
        </Experiment>
EOD

doc = Document.new xml
doc.elements["Experiment/Title"].text
doc.elements["Experiment/Protocol/ProtocolName"].text
doc.elements["Experiment/mzData/description/admin/sampleName"].text
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