=== What is XGMML? ===
[[http://www.cs.rpi.edu/~puninj/XGMML/|XGMML]] is an XML version of [[http://infosun.fmi.uni-passau.de/Graphlet/GML/|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 [[http://java.sun.com/webservices/jaxb/|Java Architecture for XML Binding (JAXB)]].  JAXB automatically generate JAVA code based on XML Schema.  XML schema for XGMML is available [[http://www.cs.rpi.edu/~puninj/XGMML/xgmml.xsd|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:

 * Interactions (Nodes/Edges)
 * Attributes (annotation for nodes/edges)
 * Graphical representation of nodes and edges
 * Network meta-info in RDF
  * This is general information for the network.  Generic information like network name, date modified, etc. will be inserted here.  The data format used for network meta-information is RDF (Resource Description Framework).  The supported attributes are taken from Dublin Core Metadata Element Set (DCMES):
   * Title
   * Creator
   * Subject
   * Description
   * Publisher
   * Contributor
   * Date
   * Type
   * Format
   * Identifier
   * Source
   * Language
   * Relation
   * Coverage
   * Rights

  * Although the internal data structure will support all of the above, GUI (Network Metadata Editor) supports a subset of the elements.  For more information about DCMES, please visit [[http://dublincore.org/documents/dces/|here]].

JamesMcIninch 2006/04/20:

 . Questions:
  * Previously, attributes could be any Java type -- java.net.URL for instance -- and XGMML supports "list", "integer", "real", and "string". What thought has been given to restoring the ability to use other types?
  * The examples in the testData directory put the '''type''' of the attribute
   . in the '''label'''. For example,

{{{
      <att value="YCK2" label="string" name="commonName"/>
}}}
 . instead of the correct XGMML

{{{
      <att value="YCK2" type="string" label="Common Name" name="commonName"/>
}}}
 . .. should that not be fixed? Is Cytoscape doing the the right thing?


=== 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:
 * every <graph>, <node> and <edge> element '''must''' contain a ''label'' attribute. Failure to do so will result in a null-pointer error during the import.
 * all of the ''xmsns'' attributes in the root <graph> element '''must''' be present
 * including data associated with <graph>, <node> and <edge> elements requires an <att> element with the attributes ''name'', ''type'' and ''value'' as shown