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There are three types of nodes in XGMML files.
 1. Base Node - node without children.
 2. Meta Node - node which has at least one child.
 3. Meta Node Reference - pointer to actual metanode data structure.

==== A Node ====

{{{
 * Test
 {{{
    * test2
 }}}
}}}

A Base Node is a node which has no internal structure. This type of entry has the following members.
 * '''ID'''
 * '''Label'''
 * '''Attributes'''
 * '''Graphics'''

==== A Metanode ====
 * ID
 * Label
 * Attributes
   * Normal attributes (Spices, canonical name, etc.)
   * Subgraph
 * Graphics

How Metanodes Are Stored In An XGMML File?

(Under construction)

There are three types of nodes in XGMML files.

  1. Base Node - node without children.
  2. Meta Node - node which has at least one child.
  3. Meta Node Reference - pointer to actual metanode data structure.

A Node

 * Test
 {{{
    * test2

}}}

A Base Node is a node which has no internal structure. This type of entry has the following members.

  • ID

  • Label

  • Attributes

  • Graphics

A Metanode

  • ID
  • Label
  • Attributes
    • Normal attributes (Spices, canonical name, etc.)
    • Subgraph
  • Graphics 

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<graph id="2" label="gal.gml" xmlns:ns1="urn:abc" xmlns:ns2="urn:def" xmlns="http://www.cs.rpi.edu/XGMML">
    <att>
        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
            <rdf:Description rdf:about="http://www.cytoscape.org">
                <dc:type xmlns:dc="http://purl.org/dc/elements/1.1/">Foo</dc:type>
                <dc:description xmlns:dc="http://purl.org/dc/elements/1.1/">N/A</dc:description>
                <dc:date xmlns:dc="http://purl.org/dc/elements/1.1/">2006-01-20 11:31:17</dc:date>
                <dc:identifier xmlns:dc="http://purl.org/dc/elements/1.1/">N/A</dc:identifier>
                <dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">gal.gml</dc:title>
                <dc:source xmlns:dc="http://purl.org/dc/elements/1.1/">http://www.cytoscape.org</dc:source>
                <dc:format xmlns:dc="http://purl.org/dc/elements/1.1/">N/A</dc:format>
            </rdf:Description>
        </rdf:RDF>
    </att>
    <node id="-332" label="gal">
        <att value="gal" name="commonName"/>
        <att value="gal " name="ALIASES"/>
        <att value="gal" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="50.0" w="50.0" fill="#eeeeee" outline="#000000" x="-0.5" y="-81.5" width="1" type="ellipse"/>
    </node>
    <node id="-333" label="ATP">
        <att value="ATP" name="commonName"/>
        <att value="ATP " name="ALIASES"/>
        <att value="ATP" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="-2.5" y="-10.5" width="1" type="ellipse"/>
    </node>
    <node id="-334" label="GAL3">
        <att value="GAL3" name="commonName"/>
        <att value="GAL3 " name="ALIASES"/>
        <att value="GAL3" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="115.5" y="-53.5" width="1" type="rectangle"/>
    </node>
    <node id="-335" label="GAL80">
        <att value="GAL80" name="commonName"/>
        <att value="GAL80 " name="ALIASES"/>
        <att value="GAL80" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#00ff00" outline="#000000" x="199.5" y="-53.5" width="1" type="rectangle"/>
    </node>
    <node id="-336" label="GAL4">
        <att value="GAL4" name="commonName"/>
        <att value="GAL4 " name="ALIASES"/>
        <att value="GAL4" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="199.5" y="67.5" width="1" type="rectangle"/>
    </node>
    <node id="-337" label="GAL2">
        <att value="GAL2" name="commonName"/>
        <att value="GAL2 " name="ALIASES"/>
        <att value="GAL2" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="9.5" y="223.5" width="1" type="rectangle"/>
    </node>
    <node id="-338" label="GAL1">
        <att value="GAL1" name="commonName"/>
        <att value="GAL1 " name="ALIASES"/>
        <att value="GAL1" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="96.5" y="223.5" width="1" type="rectangle"/>
    </node>
    <node id="-339" label="GAL7">
        <att value="GAL7" name="commonName"/>
        <att value="GAL7 " name="ALIASES"/>
        <att value="GAL7" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="169.5" y="222.5" width="1" type="rectangle"/>
    </node>
    <node id="-340" label="GAL10">
        <att value="GAL10" name="commonName"/>
        <att value="GAL10 " name="ALIASES"/>
        <att value="GAL10" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="249.5" y="222.5" width="1" type="rectangle"/>
    </node>
    <node id="-341" label="GAL5">
        <att value="GAL5" name="commonName"/>
        <att value="GAL5 " name="ALIASES"/>
        <att value="GAL5" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="327.5" y="220.5" width="1" type="rectangle"/>
    </node>
    <node id="-342" label="GAL6">
        <att value="GAL6" name="commonName"/>
        <att value="GAL6 " name="ALIASES"/>
        <att value="GAL6" name="canonicalName"/>
        <att value="Saccharomyces cerevisiae" name="species"/>
        <graphics h="30.0" w="50.0" fill="#eeeeee" outline="#000000" x="281.5" y="-53.5" width="1" type="rectangle"/>
    </node>
    <edge source="-334" target="-335" label="GAL3 (pp) GAL80">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-335" target="-336" label="GAL80 (pp) GAL4">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-336" target="-341" label="GAL4 (pp) GAL5">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-336" target="-339" label="GAL4 (pp) GAL7">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-336" target="-338" label="GAL4 (pp) GAL1">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-336" target="-337" label="GAL4 (pp) GAL2">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-332" target="-334" label="gal (pp) GAL3">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-333" target="-334" label="ATP (pp) GAL3">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-342" target="-336" label="GAL6 (pp) GAL4">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
    <edge source="-336" target="-340" label="GAL4 (pp) GAL10">
        <graphics fill="#000000" arrow="last" width="1" type="line"/>
    </edge>
</graph>

Metanode_In_XGMML (last edited 2012-03-03 00:39:39 by server2)

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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