XGMML

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:

• 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 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