From 0be4eacc5e308b7e3401062a2a57a080804a1cb4 Mon Sep 17 00:00:00 2001
From: Michael Aufreiter <michael@michael.local>
Date: Mon, 2 Sep 2019 13:33:30 +0200
Subject: [PATCH] Improved XML for files.

---
 data/figure-package/figure.xml | 96 ++++++++--------------------------
 1 file changed, 21 insertions(+), 75 deletions(-)

diff --git a/data/figure-package/figure.xml b/data/figure-package/figure.xml
index 9cf5e8a93..a40b07f39 100644
--- a/data/figure-package/figure.xml
+++ b/data/figure-package/figure.xml
@@ -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>
@@ -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>
@@ -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>
\ No newline at end of file