.xgmml
From BITS wiki
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>