.xgmml

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XGMML is a file format written in XML to store network information. Excellent information can be found on Cobweb's tutorial page.

A first line describes the XML Version.

The next line is a <graph> element, which contains all options for defining the network, the most important being the embedded <node> and <edge> elements (see below).

Example

Taken from Cobweb (http://bioinformatics.charite.de/cobweb).

<?xml version="1.0" encoding="UTF-8" ?>
<graph label="Apoptosis" directed="1" xmlns="http://www.cs.rpi.edu/XGMML" schemaLocation="http://www.cs.rpi.edu/~puninj/XGMML/xgmml.xsd">
  <att name="PICTURE_PATH" value="thumbnails/"/>
  <node id="Bad" label="Bad">
	<graphics type="hor_ellipsis" fill="#F8FF00"/>
	<att name="description" value="Bcl-2-associated death promoter"/>
	<att name="picture" value="apopbad.png"/>
  </node>
  <node id="Bid" label="Bid">
	<graphics type="hor_ellipsis" fill="#F8FF00"/>
	<att name="description" value="BH3 interacting domain death agonist"/>
	<att name="picture" value="apopbid.png"/>
  </node>
  <edge label="Inhibition" source="Puma" target="Bcl-2" weight="1.0">
	<att name="edge.shape" value="circle"/>
	<att name="edge.color" value="119,82,82"/>
  </edge>
  <edge label="Inhibition" source="Puma" target="Bcl-XL" weight="1.0">
	<att name="edge.shape" value="circle"/>
	<att name="edge.color" value="119,82,82"/>
  /edge>
</graph>