User:Lindenb/Notebook/UMR915/20110131

=Project 'B'= merging files =interactome for project 'B'= tried to open BIOGRID human in cytoscape= out of memory

converted PSI to GEXF, the networks can be openeded in gephi   

    

  

     </g:graph> </xsl:template>

<xsl:template match="p:entry"> <g:graph mode="static" defaultedgetype="directed"> <xsl:apply-templates select="p:interactorList"/> <xsl:apply-templates select="p:interactionList"/> </g:graph> </xsl:template>

<xsl:template match="p:interactorList">  <xsl:apply-templates select="p:interactor"/> </g:nodes> </xsl:template>

<xsl:template match="p:interactor"> <xsl:element name="g:node"> <xsl:attribute name="id"><xsl:value-of select="@id"/></xsl:attribute> <xsl:attribute name="label"><xsl:value-of select="p:names/p:shortLabel"/></xsl:attribute> </xsl:element> </xsl:template>

<xsl:template match="p:interactionList"> <g:edges> <xsl:apply-templates select="p:interaction"/> </g:edges> </xsl:template>

<xsl:template match="p:interaction"> <xsl:element name="g:edge"> <xsl:attribute name="id"><xsl:value-of select="@id"/></xsl:attribute> <xsl:attribute name="source"><xsl:value-of select="p:participantList/p:participant[1]/p:interactorRef"/></xsl:attribute> <xsl:attribute name="target"><xsl:value-of select="p:participantList/p:participant[2]/p:interactorRef"/></xsl:attribute> </xsl:element> </xsl:template>

</xsl:stylesheet> But it's slow & not very useful.

I transformed the PSI to GXMML with the following xslt stylesheet: <?xml version='1.0' encoding="UTF-8" ?> <xsl:stylesheet xmlns:xsl='http://www.w3.org/1999/XSL/Transform' 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" xmlns:p="net:sf:psidev:mi" version='1.0' > <xsl:output method="xml" indent="yes"/>

<xsl:template match="/"> <xsl:apply-templates select="p:entrySet"/> </xsl:template>

<xsl:template match="p:entrySet"> <xsl:apply-templates select="p:entry"/> </xsl:template>

<xsl:template match="p:entry"> <graph directed="0" label="Network"> <att name="documentVersion" value="1.1"/> <att name="networkMetadata"> <rdf:RDF> <rdf:Description rdf:about=""> <dc:type>Protein-Protein Interaction</dc:type> <dc:description>N/A</dc:description> <dc:identifier>N/A</dc:identifier> <dc:date>2011-01-31 10:37:20</dc:date> <dc:title>Network</dc:title> <dc:source>http://www.cytoscape.org/</dc:source> <dc:format>Cytoscape-XGMML</dc:format> </rdf:Description> </rdf:RDF>

<xsl:apply-templates select="p:interactorList"/> <xsl:apply-templates select="p:interactionList"/> </xsl:template>

<xsl:template match="p:interactorList"> <xsl:apply-templates select="p:interactor"/> </xsl:template>

<xsl:template match="p:interactor"> <xsl:element name="node"> <xsl:attribute name="id"><xsl:value-of select="@id"/></xsl:attribute> <xsl:attribute name="label"><xsl:value-of select="p:names/p:shortLabel"/></xsl:attribute> </xsl:element> </xsl:template>

<xsl:template match="p:interactionList"> <xsl:apply-templates select="p:interaction"/> </xsl:template>

<xsl:template match="p:interaction"> <xsl:element name="edge"> <xsl:attribute name="source"><xsl:value-of select="p:participantList/p:participant[1]/p:interactorRef"/></xsl:attribute> <xsl:attribute name="target"><xsl:value-of select="p:participantList/p:participant[2]/p:interactorRef"/></xsl:attribute> <xsl:attribute name="label"><xsl:value-of select="p:names/p:shortLabel"/></xsl:attribute> </xsl:element> </xsl:template>

</xsl:stylesheet>



Again... too much information...