Differences between revisions 7 and 8
← Revision 7 as of 2006-01-25 22:33:41 →
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Editor: KeiichiroOno
Comment:
← Revision 8 as of 2006-01-26 01:00:53 →
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Editor: KeiichiroOno
Comment:
Deletions are marked like this. Additions are marked like this.
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There are three types of nodes in XGMML files. There are three types of nodes in Cytoscape XGMML files.
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 3. Meta Node Reference - pointer to actual metanode data structure.  3. Node Reference - pointer to actual node data structure.
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==== A Node ==== === Base Node ===
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 * Test
 {{{
    * test2
 }}} 		<node id="GAL80" label="GAL80" name="base">
    <att value="GAL80" name="commonName"/>
    <att value="GAL80 " name="ALIASES"/>
    <att value="GAL80" name="canonicalName"/>
    <att value="Saccharomyces cerevisiae" name="species"/>
    <graphics fill="#00ff00" outline="#000000" h="30.0" w="50.0" x="199.5" y="-53.5" type="rectangle"/>
</node>
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 * '''ID'''
 * '''Label'''
 * '''Attributes'''
 * '''Graphics''' 		 * '''ID''' - ID of the node. Must be unique.
 * '''Label''' - Label of the node.
 * '''Name''' - '''''Type of the node.''''' Base, metaNode or reference. This is a bit confusing, but in XGMML standard, ''type'' attribute is used as XLink. So ''name'' is used to repredent node type in Cytoscape.
 * '''Attributes''' - Arbitrary number of user attributes.
 * '''Graphics''' - Graphical information, such as node shape, size, etc.
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==== A Metanode ====
 * ID
 * Label
 * Attributes
   * Normal attributes (Spices, canonical name, etc.)
   * Subgraph
 * Graphics 		=== Metanode ===

(The example below does not have edges. Will be updated shortly.)
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<?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> 		<node id="MetaNode_-14" label="MetaNode_-14" name="metaNode">
    <att value="GAL80,GAL4,GAL6" name="commonName"/>
    <att name="ALIASES"/>
    <att value="MetaNode_-14" name="canonicalName"/>
    <att value="Saccharomyces cerevisiae" name="species"/>
    <att name="metanodeChildren">
        <graph>
            <node id="GAL80" label="GAL80" name="reference"/>
            <node id="GAL4" label="GAL4" name="reference"/>
            <node id="GAL6" label="GAL6" name="reference"/>
        </graph>
Line 48: Line 45:
    <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>

 		    <graphics fill="#ffffff" outline="#000000" h="75.6939756606048" w="75.6939756606048" x="227.33333418100946" y="-12.666665818990552" type="rectangle"/>
</node>
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Most of the part is the same as base nodes. The difference is, metanode always has a subgraph, which contains child nodes and edges. To avoid redundancy, nodes and edges in metanodes are references to the actual XML data element. Also, metanode can have the other metanodes.

How Metanodes Are Stored In An XGMML File?

(Under construction)

There are three types of nodes in Cytoscape XGMML files.

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

Base Node

<node id="GAL80" label="GAL80" name="base">
    <att value="GAL80" name="commonName"/>
    <att value="GAL80 " name="ALIASES"/>
    <att value="GAL80" name="canonicalName"/>
    <att value="Saccharomyces cerevisiae" name="species"/>
    <graphics fill="#00ff00" outline="#000000" h="30.0" w="50.0" x="199.5" y="-53.5" type="rectangle"/>
</node>

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

  • ID - ID of the node. Must be unique.

  • Label - Label of the node.

  • Name - Type of the node. Base, metaNode or reference. This is a bit confusing, but in XGMML standard, type attribute is used as XLink. So name is used to repredent node type in Cytoscape.

  • Attributes - Arbitrary number of user attributes.

  • Graphics - Graphical information, such as node shape, size, etc.

Metanode

(The example below does not have edges. Will be updated shortly.) 

<node id="MetaNode_-14" label="MetaNode_-14" name="metaNode">
    <att value="GAL80,GAL4,GAL6" name="commonName"/>
    <att name="ALIASES"/>
    <att value="MetaNode_-14" name="canonicalName"/>
    <att value="Saccharomyces cerevisiae" name="species"/>
    <att name="metanodeChildren">
        <graph>
            <node id="GAL80" label="GAL80" name="reference"/>
            <node id="GAL4" label="GAL4" name="reference"/>
            <node id="GAL6" label="GAL6" name="reference"/>
        </graph>
    </att>
    <graphics fill="#ffffff" outline="#000000" h="75.6939756606048" w="75.6939756606048" x="227.33333418100946" y="-12.666665818990552" type="rectangle"/>
</node>

Most of the part is the same as base nodes. The difference is, metanode always has a subgraph, which contains child nodes and edges. To avoid redundancy, nodes and edges in metanodes are references to the actual XML data element. Also, metanode can have the other metanodes.

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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