Graphs encoded in GraphML

  • e.g. to pass them to CytoscapeWeb
  • TODO: detailed description of the graph (what are these keys? subgraphs etc)
  • see also GraphML
  • TODO: how to configure CytoscapeWeb? (javascripts etc)
  • TODO: demo
  • example Graph:
<graphml>
   <key attr.name="name" attr.type="string" for="node" id="name"/>
   <key attr.name="node set" attr.type="string" for="node" id="ns">
         <default>species</default>
   </key>
   <key attr.name="version" attr.type="int" for="all" id="vers">
         <default>0</default>
   </key>
   <key attr.name="modifier" attr.type="string" for="edge" id="mod">
         <default>none</default>
   </key>
   <graph edgedefault="directed" id="G">
      <node id="c1">
         <data key="vers">0</data>
         <data key="name">compartment</data>
         <graph edgedefault="directed" id="G1">
            <node id="s2">
               <data key="ns">species</data>
               <data key="vers">0</data>
               <data key="name">sigb</data>
            </node>
            <node id="s1">
               <data key="ns">species</data>
               <data key="vers">0</data>
               <data key="name">lacz</data>
            </node>
            <node id="r3">
               <data key="ns">reaction</data>
               <data key="vers">2</data>
               <data key="name">sigb degr</data>
            </node>
            <!-- more nodes -->
         </graph>
      </node>
      <edge source="s2" target="r3">
         <data key="mod">none</data>
         <data key="vers">0</data>
      </edge>
      <edge source="s4" target="r3">
         <data key="mod">stimulator</data>
         <data key="vers">-1</data>
      </edge>
      <!-- more edges -->
   </graph>
</graphml>
Last modified 3 years ago Last modified on Feb 7, 2014, 3:05:08 PM
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