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Improved XML for SourceData #1350

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Improved XML for SourceData #1350

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96 changes: 21 additions & 75 deletions data/figure-package/figure.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,15 +35,6 @@
<caption id="fig1a-caption">
<title>First panel</title>
<p id="fig1a-caption-p1">First panel caption. </p>
<p id="fig1a-caption-p2">The dataset <xref id="xref-1" ref-type="bibr" rid="r1">[1]</xref> has been analysed to generate the following projection:</p>
<p specific-use="display-element-wrapper">
<supplementary-material id="source-data-1" mimetype="text" mime-sub-type="csv" xlink:href="fig1a-source-data.csv">
<caption>
<title>Orthogroup clustering analysis</title>
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec convallis augue ut orci finibus laoreet.</p>
</caption>
</supplementary-material>
</p>
</caption>
<kwd-group kwd-group-type="exp-system">
<label>Exp. System</label>
Expand All @@ -56,6 +47,7 @@
<kwd>confocal microscopy</kwd>
</kwd-group>
<graphic id="fig1a-graphic" mime-subtype="jpeg" mimetype="image" xlink:href="fig1a.jpg" />
<xref id="xref-1" ref-type="bibr" rid="file-1"/>
</fig>
<fig id="fig1b">
<label>Figure 1B</label>
Expand All @@ -65,78 +57,32 @@
<p id="fig1a-caption-p2"><xref id="xref-1" ref-type="bibr" rid="r2">Source data 1</xref> has been used to generate this figure.</p>
</caption>
<graphic id="fig1b-graphic" mime-subtype="jpeg" mimetype="image" xlink:href="fig1b.jpg" />
<xref id="xref-2" ref-type="bibr" rid="file-1"/>
<xref id="xref-3" ref-type="bibr" rid="file-2"/>
</fig>
<!-- Title of the figure and additional information (=figure footer) -->
<caption>
<title>The title of figure one</title>
<p id="fig1-additional-info">Values are expressed as mean ± SEM. *P < 0.05; **P < 0.01; ***P < 0.001.</p>
</caption>
</fig-group>
<sec>
<title>Supplementary Files</title>
<supplementary-material id="source-data-2" mimetype="text" mime-sub-type="csv" xlink:href="fig1a-source-data.csv">
</body>
<back>
<!-- A dedicated managed section for all files -->
<sec id="files">
<title>Files</title>
<supplementary-material id="file-1" mimetype="text" mime-sub-type="csv" xlink:href="clustering-1.csv">
<caption>
<title>Orthogroup clustering analysis</title>
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec convallis augue ut orci finibus laoreet.</p>
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit.</p>
</caption>
</supplementary-material>
<supplementary-material id="file-2" mimetype="text" mime-sub-type="csv" xlink:href="clustering-2.csv">
<caption>
<title>Orthogroup clustering analysis 2</title>
<p>Donec convallis augue ut orci finibus laoreet.</p>
</caption>
</supplementary-material>
</sec>
</body>
<back>
<ref-list>
<ref id="r1">
<element-citation publication-type="data">
<year>2016</year>
<pub-id pub-id-type="accession">GSE69545</pub-id>
<source>NCBI Gene Expression Omnibus</source>
<data-title>Affinity and Dose of TCR Engagement Yield Proportional Enhancer and Gene Activity in CD4+ T Cells</data-title>
<uri>http://www.michaeleisen.org/blog/?p=1894</uri>
</element-citation>
</ref>
<ref id="r2">
<element-citation publication-type="article">
<year>2017</year>
<pub-id pub-id-type="doi">10.1101/102392</pub-id>
<person-group person-group-type="author">
<name>
<surname>Alasoo</surname>
<given-names>K</given-names>
</name>
<name>
<surname>Rodrigues</surname>
<given-names>J</given-names>
</name>
<name>
<surname>Mukhopadhyay</surname>
<given-names>S</given-names>
</name>
<name>
<surname>Knights</surname>
<given-names>AJ</given-names>
</name>
<name>
<surname>Mann</surname>
<given-names>AL</given-names>
</name>
<name>
<surname>Kundu</surname>
<given-names>K</given-names>
</name>
<collab>
<named-content content-type="name">HIPSCI Consortium</named-content>
</collab>
<name>
<surname>Hale</surname>
<given-names>C</given-names>
</name>
<name>
<surname>Dougan</surname>
<given-names>G</given-names>
</name>
<name>
<surname>Gaffney</surname>
<given-names>DJ</given-names>
</name>
</person-group>
<source>bioRxiv</source>
<article-title>Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune response</article-title>
</element-citation>
</ref>
</ref-list>
</back>
</article>