Update input/output/transports relations to primary input/primary output in GO-CAMs

[vanaukenk]

This is to discuss the work that will need to be done to update 'has input', 'has output', and 'transports or maintains localization of' in GO-CAM models to 'has primary input' and 'has primary output'.

The draft TSV is here.

Note that we need to decide how to treat imported pathway models wrt these changes. Ticket for that discussion is here.

[vanaukenk]

A high-level task summary for this work based on the 2024-10-03 Noctua workbenches call:

• [ ] Update noctua-dev models to latest version of production models (optional, but would be nice)
• [ ] Write SPARQL queries based on specifications for which models to update and perform a test data update on noctua-dev for QC. TSV for relation changes.
• [ ] Specify requirements for updates to the VPE Causal Relations Form between chemicals and activity units and annotation extension entries for Activity Unit and Protein Complex tools
• [ ] Implement VPE UI changes and test creation of new models and display of existing models on noctua-dev
• [ ] Check on impacts to pipeline, i.e. annotation files via GOA
• [ ] Check on impacts to NDeX
• [ ] Check on impacts to Pathway Preview
• [ ] Once fully tested, make data and UI changes on production Noctua, Alliance

@kltm @balhoff @tmushayahama @pgaudet