To discuss: how to handle Reactome and Yeast Pathways imported GO-CAMs wrt input/output data updates

[vanaukenk]

I'm putting this ticket here; we can move it to another repo, if need be.

As part of aligning the ontology and GO-CAM data model, we want to make sure that the Noctua curation interfaces and existing models use, where applicable, 'has primary input' and 'has primary output' instead of 'has input' and 'has output'.

However, we can't just perform an automatic update on all models, since that will then change pathway models that have been imported from external sources like Reactome or SGD.

Before moving forward with the model and ShEx updates, I want to confirm that:

1. The automatic updates we perform will not touch the imported Reactome models, or any models that have GOC:reactome_curators as contributors.

2. The automatic updates we perform will not touch the imported yeast pathways models or any models that have GOC:sgd_curators as contributors. Related question: It looks like SGD curators are manually reviewing the pathways models and then marking those models as production. Do we want manual review to ever include updating input/output relations or is this something we will tackle later, programmatically, when we can make use of the list of proposed currency chemicals?

[vanaukenk]

See: https://github.com/geneontology/noctua-models-migrations/blob/main/ontology_replacements/WIP_input_output_relation_replacements.tsv

[vanaukenk]

For Reactome models, exclude from updates any model with GOC:reactome_curators as a contributor.
For SGD models, exclude from updates any model with GOC:sgd_curators as a contributor.
I will check with Rossana and Steven tomorrow about the FlyBase metabolism models.

[vanaukenk]

Update from 2024-10-03 Pathways2GO call:

For Reactome models, exclude from updates any model with GOC:reactome_curators as a contributor.
For SGD models, exclude from updates any model with GOC:sgd_curators as a contributor.
For a subset of MGI models: https://orcid.org/0000-0001-7476-6306 as a contributor AND the string 'R-HSA' is included in a Comment.