Diff for "Metanode_In_XGMML"

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 ([http://www.w3.org/TR/2001/REC-xlink-20010627/ XML Linking Language]). 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="MetaNode_-16" label="MetaNode_-16" 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 metanodes as children.