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PathVisio / GPML

Graphical Pathway Markup Language
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GPML vs. wpTypes vocab #12

Open ariutta opened 7 years ago

ariutta commented 7 years ago

ArrowHead type names are not consistent across our projects. For just one example:

wp vocab: Binding wpTypes vocab: MimBinding Actual GPML: mim-binding

  <Interaction>
    <Graphics ZOrder="12288" LineThickness="1.0">
      <Point X="419.0" Y="208.0" GraphRef="e9078" RelX="-1.0" RelY="0.0" />
      <Point X="160.75" Y="103.25" GraphRef="f2588" RelX="0.0" RelY="1.0" ArrowHead="mim-binding" />
      <Anchor Position="0.4" Shape="None" />
    </Graphics>
    <Xref Database="" ID="" />
  </Interaction>

If the purpose of the wpTypes vocab is to help keep our projects harmonized, it needs to be in sync with actual GPML.

mkutmon commented 7 years ago

Yes! In the wp vocab it's different because it's the real semantics described there (so if we would support sbgn then sbgn-binding would also be mapped to WP vocab Binding). As said - I didn't look at the WPType vocab in detail yet but there is definitely still lots of work to do! And yes it should be the same as in the GPML!

ariutta commented 7 years ago

Thanks @mkutmon! We can either change wpTypes to match PathVisio's GPML, or we can use this GPML update to make PathVisio's GPML reflect what's in wpTypes. Do you have a preference?

ariutta commented 7 years ago

Does this issue belong in the PathVisio/pathvisio repo? The 2013a xsd doesn't reference any of the mim types.