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wikipathways / reactome2gpml-converter

Converts Reactome pathways to GPML format
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Dovitinib is not annotated with a structure identifier in GPML (but is in original) #65

Open egonw opened 6 years ago

egonw commented 6 years ago

The resulting GPML has this, but looking at Dovitinib in Reactome (https://reactome.org/PathwayBrowser/#/R-HSA-5655302&DTAB=MT), it seems annotated with a PubChem compound identifier:

  <DataNode TextLabel="Dovitinib " GraphId="ba4b1" GroupRef="d4f5d">
    <Attribute Key="cellular_location" Value="cytosol" />
    <Attribute Key="complex_id" Value="R-ALL-2045079" />
    <Attribute Key="copies_num" Value="1" />
    <Graphics CenterX="0.0" CenterY="0.0" Width="0.0" Height="0.0" ZOrder="32768" FontSize="10" Valign="Middle" />
    <Xref Database="" ID="" />
  </DataNode>
egonw commented 6 years ago

It should be working:

https://github.com/wikipathways/reactome2gpml-converter/blob/1a82248811402d22bc738e17360a424f360ec98c/src/org/gk/gpml/ReactometoGPML2013.java#L355-L356