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geneontology / noctua-standard-annotations

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Annotations to protein-containing complex need to display on the table #10

Closed vanaukenk closed 1 month ago

vanaukenk commented 3 months ago

To reproduce:

Enter: gp protein-containing complex 'part of'

No annotation displays on the table and the representation in the graph editor displays protein-containing complex 'has part' gp

In the table, curators will want to see:

gp 'part of' protein-containing complex

tmushayahama commented 2 months ago

@vanaukenk I have made a temporary solution on this one because the way we used to determine the protein containing complex on NF, VPE is it should not be a stand alone but connected to MF by enabled by. So to simplify for future, we must come to this so the other apps are not affected. In other words this is the function like workbench Macromolecular Complex Creator

The bug will arise if the incoming "NF activity unit model" has both enabled by and has part, it will read as 2 standard annotations

Also tagging @pgaudet for VPE (in the future in case if the bug leaks)

vanaukenk commented 2 months ago

Tested with different types of annotation subjects (i.e. gene, sequence, protein, protein-containing complex) and adding 'part of' relation before selecting GO term or selecting GO term first and letting the tool default to the gp2term relation for a PCC annotation.

All is working as expected, except when a protein-containing complex is the subject, I could select a PCC GO term, no relation was selected either by default or manually by a curator, but the SAVE button wasn't disabled so I could click SAVE but no annotation was saved.

@tmushayahama @thomaspd - generally this is all working fine, but we need to decide what we're going to do with protein-containing complexes as subjects of standard annotation. I'll make a separate ticket for that.

vanaukenk commented 1 month ago

This is now fixed.