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GPML2013a vs GPML2017

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Martina Summer-Kutmon edited this page Aug 14, 2017 · 22 revisions

Complete GPML files

Pathway element

GPML2013a:

<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Acetylcholine Synthesis" Organism="Homo sapiens">
  <Graphics BoardWidth="829.0515247108307" BoardHeight="621.8666666666666" />
  <BiopaxRef>dbc</BiopaxRef>
  ...
</Pathway>

GPML2017:

<Pathway xmlns="http://pathvisio.org/GPML/2017" name="Acetylcholine Synthesis" organism="Homo sapiens" width="829.0515247108307" height="621.8666666666666">
  <Xref dataSource="" identifier="" /> <!-- Pathways can now have an Xref to link to WikiPathways -->
  <CitationRef citationID="dbc" /> <!-- biopax replaced by CitationRef-->
  ...
</Pathway>

DataNode element

GPML2013a:

  <DataNode TextLabel="PCYT1A" GraphId="a69" Type="GeneProduct">
    <Attribute Key="org.pathvisio.model.BackpageHead" Value="PCYT1A | phosphate cytidylyltransferase 1 chol..." />
    <Graphics CenterX="656.9484752891697" CenterY="200.46971608832808" Width="60.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
    <Xref Database="Entrez Gene" ID="5130" />
  </DataNode>

GPML2017:

  <DataNode elementID="a69" textLabel="PCYT1A" type="GeneProduct" centerX="656.9484752891697" centerY="200.46971608832808" width="60.0" height="20.0" zOrder="32768" fontSize="10" vAlign="Middle">
    <Attribute key="org.pathvisio.model.BackpageHead" value="PCYT1A | phosphate cytidylyltransferase 1 chol..." />
    <Xref dataSource="Entrez Gene" identifier="5130" />
  </DataNode>

Interaction element

GPML2013a:

  <Interaction GraphId="be454">
    <Graphics ZOrder="12288" LineThickness="1.0">
      <Point X="114.71819137749738" Y="572.8666666666666" GraphRef="e42" RelX="0.0" RelY="-1.0" />
      <Point X="114.66666666666676" Y="339.86666666666673" GraphRef="dfe" RelX="0.0" RelY="1.0" ArrowHead="Arrow" />
    </Graphics>
    <Xref Database="" ID="" />
  </Interaction>

GPML2017:

  <Interaction elementID="be454" lineThickness="1.0" zOrder="12288">
    <Xref dataSource="" identifier="" />
    <Point elementID="f2ed9" elementRef="e42" x="114.71819137749738" y="572.8666666666666" relX="0.0" relY="-1.0" />
    <Point elementID="b0ef5" elementRef="dfe" arrowHead="Arrow" x="114.66666666666676" y="339.86666666666673" relX="0.0" relY="1.0"/>
  </Interaction>

Groups

GPML2013a:

  <DataNode TextLabel="PDHA1" GraphId="ba5" Type="GeneProduct" GroupRef="dc39d">
  ...
  </DataNode>
  <DataNode TextLabel="PDHA2" GraphId="a93" Type="GeneProduct" GroupRef="dc39d">
  ...
  </DataNode>
  <Group GroupId="dc39d" GraphId="d74e5" />

GPML2017:

  <DataNode elementID="a93" textLabel="PDHA2" type="GeneProduct" groupRef="d74e5" centerX="183.33648790746582" centerY="266.7" width="60.0" height="20.0" zOrder="32768" fontSize="10" vAlign="Middle">
  ...
  </DataNode>
  <DataNode elementID="ba5" textLabel="PDHA1" type="GeneProduct" groupRef="d74e5" centerX="183.33648790746582" centerY="246.7" width="60.0" height="20.0" zOrder="32768" fontSize="10" vAlign="Middle">
  ...
  </DataNode>
  <Group elementID="d74e5" />

Citations

GPML2013a:

  <BiopaxRef>dbc</BiopaxRef>
  ...
  <Biopax>
    <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="dbc">
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">6867732</bp:ID>
      <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:DB>
      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Choline and cholinergic neurons.</bp:TITLE>
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Science</bp:SOURCE>
      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1983</bp:YEAR>
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Blusztajn JK</bp:AUTHORS>
      <bp:AUTHORS rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Wurtman RJ</bp:AUTHORS>
    </bp:PublicationXref>
  </Biopax>

GPML2017:

  <CitationRef citationID="dbc" />
  ...
  <Citations>
    <Citation citationID="dbc" URL="" title="Choline and cholinergic neurons." year="1983" source="Science">
      <Xref dataSource="PubMed" identifier="6867732" />
      <Author name="Blusztajn JK" />
      <Author name="Wurtman RJ" />
    </Citation>
  </Citations>

Ontology Tags

GPML2013a:

  <!-- no reference in the pathway -->
  <Biopax>
    <bp:openControlledVocabulary xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#">
      <bp:TERM xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">acetylcholine metabolic pathway</bp:TERM>
      <bp:ID xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PW:0000408</bp:ID>
      <bp:Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pathway Ontology</bp:Ontology>
    </bp:openControlledVocabulary>
  </Biopax>

GPML2017:

  <OntologyTermRef ontologyTermID="PW:0000408" /> <!-- reference in the pathway element -->
  ...
  <OntologyTerms>
    <OntologyTerm ontologyTermID="PW:0000408" term="acetylcholine metabolic pathway" ontology="Pathway Ontology" />
  </OntologyTerms>
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