orthoxml_example_v0.4.xml

<?xml version="1.0" encoding="utf-8"?>
<orthoXML xmlns="http://orthoXML.org/2011/" version="0.4" origin="inparanoid"
  originVersion="7.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://orthoXML.org/2011/ http://www.orthoxml.org/0.4/orthoxml.xsd">
  <notes>
    Example OrthoXML file. Stripped down version of a real InParanoid 7.0 file.
  </notes>
  <species name="Caenorhabditis elegans" NCBITaxId="6239">
    <database name="WormBase" version="Caenorhabditis-elegans_WormBase_WS199_protein-all.fa"
      geneLink="http://www.wormbase.org/db/gene/gene?name=" 
      protLink="http://www.wormbase.org/db/seq/protein?name=WP:">
      <genes>
        <gene id="1" geneId="WBGene00000962" protId="CE23997" />
        <gene id="5" geneId="WBGene00006801" protId="CE43332" />
      </genes>
    </database>
  </species>
  <species name="Homo Sapiens" NCBITaxId="9606">
    <database name="Ensembl" version="Homo_sapiens.NCBI36.52.pep.all.fa"
      geneLink="http://Dec2008.archive.ensembl.org/Homo_sapiens/geneview?gene="
      protLink="http://Dec2008.archive.ensembl.org/Homo_sapiens/protview?peptide=">
      <genes>
        <gene id="2" geneId="ENSG00000197102" protId="ENSP00000348965" />
        <gene id="6" geneId="ENSG00000198626" protId="ENSP00000355533" />
        <gene id="7" protId="ENSP00000373884" />
      </genes>
    </database>
  </species>
  <scoreDefs>
    <scoreDef name="bit" desc="BLAST score in bits of seed orthologs" />
    <scoreDef name="inparalog" desc="Distance between edge seed ortholog" />
    <scoreDef name="bootstrap" desc="Reliability of seed orthologs" />
  </scoreDefs>
  <propertyDefs>
    <propertyDef name="seed" desc="Marks seed orthologys" />
    <propertyDef name="foo" desc="Defines the foo level" />
  </propertyDefs>
  <groups>
    <orthologGroup id="1">
      <score name="bit" value="5093" />
      <property name="foo" value="bar"/>
      <geneRef id="1">
        <score name="inparalog" value="1" />
        <score name="bootstrap" value="1.00" />
        <property name="seed"/>
      </geneRef>
      <geneRef id="2">
        <score name="inparalog" value="1" />
        <score name="bootstrap" value="1.00" />
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score name="bit" value="3795" />
      <property name="foo" value="bar"/>
      <geneRef id="5">
        <score name="inparalog" value="1" />
        <score name="bootstrap" value="1.00" />
      </geneRef>
      <geneRef id="6">
        <score name="inparalog" value="1" />
        <score name="bootstrap" value="1.00" />
      </geneRef>
      <geneRef id="7">
        <score name="inparalog" value="0.4781" />
      </geneRef>
    </orthologGroup>
  </groups>
</orthoXML>