changes in transcription annotations

[ValWood]

I can't figure out what is causing this, so i need some help...

Historically, everything annotated to "regulation of process X", used to also be annotated to "process X"

This clearly isn't the case here for transcription:

Although if this is a general phenomena I can't see why the slim isn't extremely adversly affected:
https://www.pombase.org/browse-curation/fission-yeast-go-slim-terms
(i.e things annotated to "regulates" would no longer be annotated to the process)

I'm baffled....

[kimrutherford]

I'm baffled too but mostly because this involves ontologies. :-)

I had a look at one of the genes that's in the "regulation of transcription, DNA-templated" list but not in the "transcription, DNA-templated" list:
https://www.pombase.org/gene/SPAC140.03

OWLTools says these two terms are descendants of "regulation of transcription, DNA-templated" but not descendants of "transcription, DNA-templated":

• chromatin silencing at centromere
• chromatin silencing by small RNA

Here's the ancestry:
https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/%7Bids%7D/chart?ids=GO:0006355%2CGO:0030702%2CGO:0031048

[mah11]

That actually makes a perverse kind of sense, because there are 78 genes found by

(regulation of transcription, DNA-templated (GO:0006355) NOT transcription, DNA-templated (GO:0006351))

All are annotated to terms in the chromatin silencing branch of GO BP except for a few annotated to 'sterol regulatory element binding protein cleavage' (GO:0035103) (cdc48, dsc1-5, rbd2, rpn12, ubc4, ubr1, ufd1).

What does OWLTools say about 'carbon catabolite repression of transcription' (GO:0045013)? That one looks as though it has similar ancestry to GO:0006342, but genes annotated to it do inherit both GO:0006351 and GO:0006355 ... and I can't see a reason for the difference.

[ValWood]

Yes I think its a recent change in that now "regulation is not inherited over regulation".

But I don't know when this change happened? I don't think it was announced, and it's a major change.....
@cmungall @pgaudet

@cmungall - I think this change will fix panther enrichment issues too.

[ValWood]

What does OWLTools say about 'carbon catabolite repression of transcription' (GO:0045013)? That one looks as though it has similar ancestry to GO:0006342, but genes annotated to it do inherit both GO:0006351 and GO:0006355 ... and I can't see a reason for the difference.

I think it is possible because "'carbon catabolite repression of transcription' (GO:0045013)" is is_a "regulation of transcription", but the others were "regulation" of "regulation of transcription"

[ValWood]

There is something very sinister going on here:
We didn't change anything. Look at the totals for last week, vs this week.
This is an extreme example of the random flip-flopping I keep 'going -on' about. I'm convinced it is some arbitrary effect of owl tools traversing different regulates paths. Beyond that I don't know what I am talking about. But what I am seeing is a big issue.

I will transfer this to the GO tracker.

compare
how it was

and how it is today

Note that, despite the number of annotations to "regulation of transcription" being identical, the number of annotations to transcription changes radically.

[ValWood]

Moved to the GO tracker

[pgaudet]

Hi Val, When is the first screenshot from? As far as I know there has been no release since March 19th. Pascale Le jeu. 18 avr. 2019 à 3:17 PM, Val Wood <[email protected]> a écrit :

…

Reopened #722 <#722>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#722 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABEPWUEVO46KXOKTQBQEU6DPRBYFBANCNFSM4HF2IMPA> .

[ValWood]

last week some time.....

[ValWood]

but it changes day by day. It will be different tomorrow! And we didn't annotate anything. I'll do another screen shot tomorrow.....

[kimrutherford]

I found something odd in the owtools output that might explain some of this. I've commented here: geneontology/go-ontology#17171 (comment)

[ValWood]

since this seems to be a duplicate of
#678
closing

(even though Its an external issue I'll keep the first ticket open for now as a reminder)