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geneontology / noctua-visual-pathway-editor

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cannot always import existing annotations #78

Open ValWood opened 2 months ago

ValWood commented 2 months ago

sometimes, I cannot import existing annotations, although I can see them, and select them, they do not appear in the activity unit?

this is happening for me now on http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A662af8fa00000499 after importing mug56 and trying to select the cytochrome b5 activity

pgaudet commented 2 months ago

This seems to be an ongoing issue - it has been reported before

@tmushayahama @vanaukenk

ValWood commented 2 months ago

I just encountered this again. It seems to be specific to some genes/annotations. Try fission yeast pqr1 and then try to import the existing IMP annotation for ubiquitin ligase, nothing appears. However if you click in the MF box the term is there, just hidden below the test box. You can select this term, but still the evidence does not appear.

If I delete, and repeat with all evidence :

Screenshot 2024-05-08 at 08 24 12
ValWood commented 2 months ago

This happens quite a lot so I'm inclined to hold off model building until it is fixed. In some cases I have repeated the existing annotation but I don't know what happens to these I don't want to create new redundant annotations?

ValWood commented 1 month ago

I see the problem, Noctua is ignoring IEA. Most of our compound annotations are EXP. Could this be prioritised? We are going to have to go back and update a lot of models.....

ValWood commented 1 month ago

Actually, I have a workaround. If I select no evidence at all, it brings in the EXP evidence !

vanaukenk commented 1 month ago

Noting that this functionality works in the Noctua form editor and I could even still import the annotations correctly from the Function Companion in the graph editor, so I'll move this ticket to the VPE tracker.