What is XGMML?

XGMML is an XML version of GML.

XGMML in Cytoscape

In future releases, Cytoscape's standard format for saving graph layout will be XGMML. Users can save graph topology AND attributes in the same file.

XML Schema

The code to manipulate data element in XML file will be generated by data binding package, called Java Architecture for XML Binding (JAXB). JAXB automatically generate JAVA code based on XML Schema. XML schema for XGMML is available here.

Metanode and XGMML

In Cytoscape v2.3, a new concept called Metanode will be introduced. In XGMML, a metanode is a node which has a subgraph containing nodes and edges. For more information, please read Metanode_In_XGMML section.

File Format

Network file in XGMML has the following information:

JamesMcIninch 2006/04/20:

      <att value="YCK2" label="string" name="commonName"/>

      <att value="YCK2" type="string" label="Common Name" name="commonName"/>

Example

The example below describes a small graph in xgmml which will import successfully into Cytoscape v2.8.2

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<graph label="small example" 
    xmlns:dc="http://purl.org/dc/elements/1.1/" 
    xmlns:xlink="http://www.w3.org/1999/xlink" 
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
    xmlns:cy="http://www.cytoscape.org" 
    xmlns="http://www.cs.rpi.edu/XGMML"  
    directed="1">
  <node label="A" id="1">
    <att name="size" type="integer" value="24"/>
    <att name="confirmed" type="boolean" value="true"/>
  </node>
  <node label="B" id="2">
    <att name="size" type="integer" value="16"/>
    <att name="confirmed" type="boolean" value="false"/>
  </node>
  <node label="C" id="3">
    <att name="size" type="integer" value="13"/>
    <att name="confirmed" type="boolean" value="true"/>
  </node>
  <edge label="A-B" source="1" target="2">
    <att name="weight" type="integer" value="7"/>
  </edge>
  <edge label="B-C" source="2" target="3">
    <att name="weight" type="integer" value="8"/>
  </edge>
  <edge label="C-A" source="3" target="1">
    <att name="weight" type="integer" value="4"/>
  </edge>
</graph>

please note that:

XGMML (last edited 2012-03-03 00:48:59 by nworbnhoj)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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