Obsoletion request: GO:1990343 heterochromatin domain

[ValWood]

Please provide as much information as you can:

GO:1990343 heterochromatin domain

• GO term ID and Label

• Reason for deprecation Put an x in the appropriate box:

• The reason for obsoletion is that this term was added in error.

• "Replace by" term (ID and label)
  If all annotations can safely be moved to that term

• "Consider" term(s) (ID and label)
  Suggestions for reannotation

• Are there annotations to this term?

• How many EXP:

1 PomBase

• Any other information

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Checklist for ontology editor

Check term usage and metadata in Protégé

• check term usage in the ontology
• check internal mappings: RHEA, EC, MetaCyc
• check subset usage
• check taxon constraints

Check annotations

• create Annotation Review spreadsheet
• • Annotation Review template: https://docs.google.com/spreadsheets/d/1izV3q1jnq_Ybg5MJ53O_b5BCTkGtjl_Fi-cOg3-7eBE/edit#gid=0
• • Instructions: https://wiki.geneontology.org/Annotation_Review_Request
• create annotation review ticket: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D
• find external mappings (via IEAS), include in obsoletion notice
• tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Notification

• create obsoletion announcement
• announce to GO friends (go-friends@mailman.stanford.edu)
• paste the text in the ontology ticket

[pgaudet]

The phrase "heterochromatin domain" is used in the definition of certain terms:

• piRNA-mediated heterochromatin formation: The formation of heterochromatin into a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process mediated by a small interfering piRNA.
• siRNA-independent facultative heterochromatin formation: similar def
• siRNA-mediated facultative heterochromatin formation: similar def

We should reformulate these terms if we dont have a concept for "heterochromatin domain".

Thanks, Pascale

[ValWood]

well it has no children, but I believe "heterochromatin domain" is a collective term for "regions of constitutive heterochromatin". Although, in that case, I am not sure why it is in the facultative definitions? (these are islands)

Maybe need to confirm with @colinlog

[colinlog]

In the sequence ontology 'Heterochromatin do ain does not exist. SO has http://www.sequenceontology.org/browser/current_release/term/SO:0002257, 'The knob', with synonym 'heterochromatin knob'. Is there now a term that stems from the chromatin interaction field (HiC, etc...) where the A and B compartments have been re-discovered and described interms of their cohesive properties? A is euchromatin and B is heterochromatin. As for Domains, I think it is now TADs that people discuss, and these are based on CTCF-anchored chromatin loops. I think this term should be a CC and is heterochromatin. We could update the labels to B and A compartments? Friday again?

…

On Mon, Jan 22, 2024 at 1:58 PM Val Wood ***@***.***> wrote: well it has no children, but I believe "heterochromatin domain" is a collective term for "regions of constitutive heterochromatin". Although, in that case, I am not sure why it is in the facultative definitions? (these are islands) Maybe need to confirm with @colinlog <https://github.com/colinlog> — Reply to this email directly, view it on GitHub <#26839 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALZVLKBQCDRRSGMW6727Q4TYPZPAZAVCNFSM6AAAAABCEFA4WGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBTHE2TMOBYGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>