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pombase / fypo

Fission Yeast Phenotype Ontology
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unexpected drop in annotated phenotypes #4140

Open ValWood opened 2 years ago

ValWood commented 2 years ago
FYPO_queru

Hi @kimrutherford when you get chance could you do a query on an old database (anything > say 10 days ago) and provide me with the list of genes annotated to "normal chromatin organization during vegetative growth'.

i had a look on the tracker and I can't see anything that would cause this drop.

ValWood commented 2 years ago

Even normal chromatin organization only has 214 annotations. I am baffled.

kimrutherford commented 2 years ago

Here's the database from 2022-04-21: https://desktop.kmr.nz/ https://desktop.kmr.nz/results/from/id/876c6786-4411-4151-b4e0-41a17556362c

I'll investigate the drop too.

kimrutherford commented 2 years ago

I think I can see what's changed but I can't see why.

Since 2022-04-22, "normal nucleosome positioning" (FYPO:0000856) has had a different parent in Chado. It was "normal chromatin organization during vegetative growth" (FYPO:0002891) but it's now "normal cellular process during vegetative growth" (FYPO:0001319). This is 2022-04-21: https://desktop.kmr.nz/term/FYPO:0000856 This is now: https://www.pombase.org/term/FYPO:0000856

The weird thing is that I looked in the Git history of fypo-edit.obo and the parent of "normal nucleosome positioning" hasn't changed there for months. It's "normal cellular process during vegetative growth" (FYPO:0001319)

But in the generated files like "fypo-simple-pombase.obo" the parent changed on 2022-04-22. Before then it was "normal chromatin organization during vegetative growth". Now it's "normal cellular process during vegetative growth".

I don't have any idea how that could happen.

kimrutherford commented 2 years ago

Even normal chromatin organization only has 214 annotations. I am baffled.

How many should it have?

That term was only added to Chado on 2022-04-22 so it's not on desktop.kmr.nz, which is from 2022-04-21

ValWood commented 2 years ago

thanks, I know what it is! will explain shortly....

ValWood commented 2 years ago

The reason for the drop in annotation number is that "nucleosome positioning" has been removed from GO as a process (nucleosome positioning is now an activity). You can't see it in Git because this parent was only inferred by the reasoner based on the GO structure and logical def.

I am still not sure what actually happens to logical relations when a term that they contain disappears, but maybe this will enlighten me. I presume the logical relation is wiped and it the term is positioned under the instantiated subclass.

It is worrying that there does not seem to be any alerting for this, so potentially GO relations could be being removed all and I do not spot them. I only noticed this one by chance because I had an active query in my history.

ValWood commented 2 years ago

This is how it looks

Screenshot 2022-05-06 at 15 21 09

I presume there is a file somewhere reporting these.

Action: add the correct logical def or instantiate the parent to make it appear under "normal chromatin organization during vegetative growth"

ValWood commented 2 years ago

Also find the others....

kimrutherford commented 2 years ago

It is worrying that there does not seem to be any alerting for this

What sort of alerting do you mean? Aren't changes discussed and announced?

ValWood commented 2 years ago

Well they  are discussed and announced, but there are so many I don't keep track of them or check on a case-by-case basis to check if they are used in FYPO. I expected them to be in a log file by ODK checks. Maybe they are and I have forgotten where/how.