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This repository hosts the tracker for issues pertaining to GO annotations.
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Review annotations to GO:0043044 ATP-dependent chromatin remodeling #3833

Closed pgaudet closed 3 years ago

pgaudet commented 3 years ago

Discussing with @colinlog and as part of the work on ATPases

GO:0043044 ATP-dependent chromatin remodeling will be merged into GO:0006338 chromatin remodeling, see https://github.com/geneontology/go-ontology/issues/21732

We suggest people consider using the new term, GO:0140658 ATP-dependent chromatin remodeler activity, to capture ATP-dependent chromatin remodelers.

Annotations are here: https://docs.google.com/spreadsheets/d/1dlmmkswk6CU6cvIL5eTDDj7fEO9Gn3PFQbMbCLbAH9Q/edit#gid=0 @colinlog and I tried to mark ATP-dependent remodelers that we could easily spot, this may not be exhaustive.

Special note for yeast: These are the ATP-dependent chromatin remodelers in yeast: ISW1, ISW2, STH1, SNF2, FUN30, INO80, SWR1, yfr038w, CHD1 (note that not all of them are annotated to GO:0043044 ATP-dependent chromatin remodeling, but you may want to annotate the MF for all of them).

Thanks, Pascale

hdrabkin commented 3 years ago

MGI done using suggested term.

ValWood commented 3 years ago

Will annotate the pombe MFs today. Very happy for the others to merge into chromatin remodeling

ValWood commented 3 years ago

A question, I got a bit lost in the series of changes here.

Some of our GO:0140658 ATP-dependent chromatin remodeler activity are now annotated to

GO:0070615 | nucleosome-dependent ATPase activity

will this term merge into GO:0140658 ATP-dependent chromatin remodeler activity and are/will there be there more specific terms to represent the histone/nucleosome loaders?

ValWood commented 3 years ago

A question, I got a bit lost in the series of changes here.

ignore, I found the ticket about GO:0070615 | nucleosome-dependent ATPase activity

I agree it should be obsoleted. It has name mappings to divergent ATPases acting on DNA (helicases), and nucleosomes (loaders)

ValWood commented 3 years ago

Pombase done

bmeldal commented 3 years ago

@pgaudet I picked this up from the Jenkins report. No-one is yet assigned to this ticket.

RLovering commented 3 years ago

ucl done

pgaudet commented 3 years ago

For today's ontology call - what remains:

bmeldal commented 3 years ago

I'm on it, 36 complexes remaining! (The GO search doesn't find them all so I always do my internal one.)

bmeldal commented 3 years ago

I'm on it, 36 complexes remaining! (The GO search doesn't find them all so I always do my internal one.)

CP done :)

srengel commented 3 years ago

i can work on this towards the end of next week.

hattrill commented 3 years ago

FB done

pgaudet commented 3 years ago

Merge has been done @srengel do you still want to review these?

srengel commented 3 years ago

oops, sorry for the delay, i think the change has already been made on the GO side. i went through our list and added the suggested annotations to GO:0140658 ATP-dependent chromatin remodeler activity

pgaudet commented 3 years ago

Thanks!