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geneontology / noctua-standard-annotations

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Display NOT on table for negative annotations #47

Closed krchristie closed 1 month ago

krchristie commented 2 months ago

Hi,

@LiNiMGI and I have noticed that the table of annotations does not display a "NOT" to indicate when a negative annotation has been made.

We were looking at previously existing annotations in the model for Dmrtb1 and I have added some additional ones. It is clear that the Standard Annotations form completely fails to indicate the existence of the NOT qualifier when it is supposed to be present.

The original NOT annotation was "NOT sequence-specific DNA binding". I have added two other NOT annotations (to "NOT RNA polymerase I activity" and "NOT RNA polymerase II activity" with various evidence codes and both annotations show up, but the NOT qualifier is not shown in the table in the Standard Annotations editor.

Below are screen shots of the Form Editor and the Standard Annotations editor for the gene-centric model for Dmrtb1 from mouse. In both screenshots, I have highlighted the capitalized form of the word "NOT":

NOTannots-FormEditor NOTannots-StandardAnnotations

LiNiMGI commented 2 months ago

Also, for some reason, Standard Annotations form missing the IKR evidence for "NOT sequence-specific DNA binding". thanks, Li

krchristie commented 2 months ago

Also, for some reason, Standard Annotations form missing the IKR evidence for "NOT sequence-specific DNA binding". thanks, Li

I'm planning to put this in a separate ticket. There appears to be an issue with displaying annotations that are displayed as "one" annotation with multiple evidence codes in the Form Editor; in the Standard Annotations Editor, it looks like one evidence code is not displayed.

vanaukenk commented 2 months ago

Thanks @krchristie and @LiNiMGI I'll also go through this carefully and let you know if we need any more discussion.

vanaukenk commented 1 month ago

Thanks @tmushayahama

@krchristie @LiNiMGI

Tremayne put a fix in on noctua-dev and I've tested adding new annotations and displaying existing annotations with 'NOT'. The display for 'NOT' looks okay to me (the multiple evidence issue is in a separate ticket). Please double-check and let me know if this looks okay to you. If so, we will put the fix in during next week's maintenance outage. Thanks.

suzialeksander commented 1 month ago

@krchristie This should be resolved in the last outage. I noticed the NOT is not removable, but if that is needed/expected it should be a new ticket. Can you just confirm the NOT appears as expected? OK to close if so.

krchristie commented 1 month ago

@krchristie This should be resolved in the last outage. I noticed the NOT is not removable, but if that is needed/expected it should be a new ticket. Can you just confirm the NOT appears as expected? OK to close if so.

@vanaukenk @suzialeksander - yes, thanks. The NOT does appear in an appropriate place now.

@LiNiMGI - Once you're back, we should look at this together and talk about whether we want to request that the NOT qualifier should be editable in the Standard Annotations form.