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geneontology / noctua-visual-pathway-editor

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Update VPE to allow use and proper display of 'has primary input' and 'has primary output' #84

Open vanaukenk opened 2 weeks ago

vanaukenk commented 2 weeks ago

To make sure we are consistently representing inputs and outputs in our GO-CAMs, standard annotations, and the ontology, we need to be able to use 'has primary input' and 'has primary output' in the visual pathway editor.

The relations need to be available as annotation extensions and as translations in the graphical view relating inputs and outputs to MFs and BPs.

More implementation details needs to be discussed and added to this ticket.

vanaukenk commented 2 weeks ago

In the VPE, we'll need to update:

  1. The Causal Relation Form between a chemical and an MF to replace 'input of' with 'primary input of' and 'output of' with 'primary output of', noting that the latter relations do not seem to be in RO, so we'd need to add them.
  2. Update the Annotation Extension relations for MFs in the Activity Unit and Protein Complex forms to include 'has primary input' and 'has primary output'.