Decide how to handle annotating interacting taxons

[vanaukenk]

For some BP terms, e.g. defense response to bacterium, curators capture the taxon of the interacting organism.

We need to decide how we want to handle this in the standard annotation form, but note that this also touches on how we can capture this in the underlying data model.

[vanaukenk]

From 2024-06-06 workbenches call:

Adding NCBITaxon:1 to the list of closures for annotation extensions.

We are proposing to model dual taxon annotations with 'has input' 'NCBITaxonxx' , similarly to what was done for the whole genome imports.

We still need to discuss harmonizing this information in standard annotations more generally.

[vanaukenk]

Issue of harmonizing dual taxon annotations added to managers agenda for 2024-06-12

[vanaukenk]

We weren't able to discuss this on the manager's call, so I'm putting a proposal here for discussion on the workbenches call:

1. In Noctua, dual taxon annotations will be made by adding a 'has input' annotation extension that uses an NCBITaxon id as the object of the extension.
2. For the GPAD output, the annotation extension would be converted an NCBITaxon id in the Interacting_taxon_field, i.e. no extension relation.
3. This would keep things consistent with how we currently model interacting taxon curation and not require changes to existing file specifications, how the information is captured in curation tools, or how it is modeled in the GO-CAM data store.
4. We will need to make sure this information gets through to the GAF according to GAF specs.
5. Future iterations of GO standard annotation tools or data stores could revisit this issue.

ACTION ITEM: Kimberly will make a minerva ticket for the GPAD work.

[vanaukenk]

See https://github.com/geneontology/minerva/issues/545

[vanaukenk]

This issue should be addressed with the minerva work on GPAD output, but I'm leaving the ticket open until all the minerva updates and testing are done.