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do not show the "phase" branch in biological process #1794

Open ValWood opened 5 years ago

ValWood commented 5 years ago

This branch is all "do not annotate" only for use in extensions. It would be good if we could not display these terms in BP selection.

Maybe GO will need to add a subset designation if there is not one already.

do not show phase branch subset

ValWood commented 5 years ago

Do we have the technology to do this already? Or do we need a subset created?

kimrutherford commented 5 years ago

Do we have the technology to do this already? Or do we need a subset created?

If that branch was a subset then we could exclude it just by changing the configuration. Without a subset it could still be done but it would be more work, probably a small Canto code change.

ValWood commented 2 years ago

From Pascale:

You can look for the stanzas with

subset: gocheck_do_not_annotate
subset: gocheck_do_not_manually_annotate

Also, you can get the list from the list of slims :

kimrutherford commented 2 years ago

Sorry, I misunderstood the problem. Canto already obeys the gocheck_do_not_annotate subset, that's why it says the term should not be used for direct annotations. But I (and Canto) assumed that when a term is in the gocheck_do_not_annotate subset it will always have a child term that can be used for annotation. For the phase branch that's not true.

I'll have a think about how that can be handled in Canto.

ValWood commented 2 years ago

Ah right, what you are doing is correct.

This is because 'phase ' is different. The entire branch is "do not annotate" This isn't a big issue, but I guess the rule would be not to show a. branch if every term beneath is "do not annotate"

Putting as "low priority" the comment works in the interim, and I have never seen a community session with a direct annotation to a phase term, so it isn't actually a pressing issue.