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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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GO:0005677 | chromatin silencing complex, grouping term obsoletion (silencing as a process no longer in GO) #19574

Open ValWood opened 4 years ago

ValWood commented 4 years ago

SInce the " chromatin silencing " terms are going, probably this grouping term should also be removed.

GO:0005677 | chromatin silencing complex

related to https://github.com/geneontology/go-annotation/issues/3070

ValWood commented 4 years ago

It's odd. There are direct annotations, although I had assumed this was a "process grouping term"

For example http://europepmc.org/article/MED/16085498 for mouse Baz2a, but this isn't the actual complex (there is a complex with a different name). SNF2h-containing chromatin-remodeling complex NoRC which has an actual term https://www.ebi.ac.uk/QuickGO/term/GO:0090536

In other cases it is not clear that the annotated protein ios a member of a complex, for example Suv39h1 for mouse "Functional and physical interaction between the histone methyl transferase Suv39H1 and histone deacetylases." Vaute O., Nicolas E., Vandel L., Trouche D. Nucleic Acids Res. 30:475-481(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HISTONE DEACETYLASE COMPLEX.

(SuV39H1 are adaptors/recruiters for histone deacetylases)

I would obsolete , with something along the lines of This term was intended as a grouping term for complexes involved in "silencing". However, the concept of silencing as a process is no longer included in GO (refer to the obsoletion of silencing) Please reannotate to a specific complex term (chromatin remodelling complex or one of its descendants is also a possibility).

There are only 30 EXP annotations (and some of these will be OK, for example the SGD annotations to "RENT COMPLEX" which is currently a descendant of "chromatin silencing complex"

pgaudet commented 4 years ago

Discussion will @ValWood We propose to merge this term into 'nuclear protein-containing complex' when that is created in #19952

Thanks, Pascale

pgaudet commented 4 years ago

Annotations are here:https://docs.google.com/spreadsheets/d/1cezH8B6MNIaJwLOPSrbqUZ84RvDyyefWSAIcwPbUVew/edit#gid=0

ValWood commented 3 years ago

There are 34 EXP annotations that could be more specific. Obsoletion might be better?

pgaudet commented 2 years ago

How about if I change the label to 'gene silencing complex'? I am not sure why this term is a problem. Although many annotations can be improved, see https://docs.google.com/spreadsheets/d/1cezH8B6MNIaJwLOPSrbqUZ84RvDyyefWSAIcwPbUVew/edit#gid=0

ValWood commented 2 years ago

I think it is a weird term.

It's definition is Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.

so transcriptional silencing would. be more [precise BUT it has only a tiny fraction of "transcriptional silencing complexes" as children. And what do we mean precisely by transcriptional silencing (negative regulation of transcription?)