Obsoletion request: GO:2001268 - negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway

[slaulederkind]

Please provide as much information as you can:

• GO term ID and Label

• negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)

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

  • [ ] The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
  • [ ] The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
  • [ ] The reason for obsoletion is that this term represent an assay and not a GO process.
  • [ ] The reason for obsoletion is that this represents a phenotype.
  • [ ] The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using [appropriate GO term].
  • [ ] The reason for obsoletion is that this term represents a molecular function.
  • [ ] The reason for obsoletion is that this term represents a gene product.
  • [ ] The reason for obsoletion is that this term refers to a class of proteins.
  • [ ] The reason for obsoletion is that this term was added in error.
  • [ ] The reason for obsoletion is that more specific terms were created.
  • [ ] The reason for obsoletion is that this term was an unnecessary grouping term.
  • [ ] The reason for obsoletion is that the meaning of the term is ambiguous.
  • [ ] The reason for obsoletion is that is not known to be catalyzed by any gene product.
  • [ ] The reason for obsoletion is that it more specific than the specificity of any known gene product.
  • [ ] The reason for obsoletion is that there is no evidence that this function/process/component exists.

This term is not a node term but an end of branch leaf node, yet it is labelled "Not4Curation"

• "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:

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

• Is this term in a subset? (check the AmiGO page for that term)

• 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

[sjm41]

All these related terms MF and BP should probably go too:

id: GO:0097153 name: cysteine-type endopeptidase activity involved in apoptotic process namespace: molecular_function

id: GO:0097199 name: cysteine-type endopeptidase activity involved in apoptotic signaling pathway namespace: molecular_function

id: GO:0097200 name: cysteine-type endopeptidase activity involved in execution phase of apoptosis namespace: molecular_function

==

id: GO:0006919 name: activation of cysteine-type endopeptidase activity involved in apoptotic process namespace: biological_process

id: GO:0043154 name: negative regulation of cysteine-type endopeptidase activity involved in apoptotic process namespace: biological_process

id: GO:0043280 name: positive regulation of cysteine-type endopeptidase activity involved in apoptotic process namespace: biological_process

id: GO:0043281 name: regulation of cysteine-type endopeptidase activity involved in apoptotic process namespace: biological_process

id: GO:0097296 name: activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway namespace: biological_process

id: GO:1990001 name: inhibition of cysteine-type endopeptidase activity involved in apoptotic process namespace: biological_process

id: GO:2001267 name: regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway namespace: biological_process

id: GO:2001268 name: negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway namespace: biological_process

id: GO:2001269 name: positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway namespace: biological_process

id: GO:2001270 name: regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis namespace: biological_process

id: GO:2001271 name: negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis namespace: biological_process

id: GO:2001272 name: positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis namespace: biological_process

[pgaudet]

Definitely the BPs should be obsoleted.

WRT MFs: these terms were created to represent 'caspase activity', but the intention was not to explicitly name 'caspase' because that represents a gene product (or a class of gene products). These can be merged up but I wonder if the community expects to be able to find 'caspase' in GO; it's really widely used, we may want to keep it.

[sjm41]

WRT MFs: these terms were created to represent 'caspase activity', but the intention was not to explicitly name 'caspase' because that represents a gene product (or a class of gene products). These can be merged up but I wonder if the community expects to be able to find 'caspase' in GO; it's really widely used, we may want to keep it.

Ah, OK, then it makes sense to keep those MFs.

But given we have those apoptotic-specific terms, then I'd remove the two caspase synonyms from the more general parent term: id: GO:0004197 name: cysteine-type endopeptidase activity def: "Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." synonym: "caspase activity" NARROW [GOC:mtg_apoptosis] synonym: "lysosomal cysteine-type endopeptidase" NARROW [] synonym: "metacaspase activity" NARROW [GOC:mtg_apoptosis] synonym: "thiol endopeptidase activity" EXACT [] xref: EC:3.4.22.- is_a: GO:0004175 ! endopeptidase activity is_a: GO:0008234 ! cysteine-type peptidase activity

[pgaudet]

@raymond91125 Would you please run an annotation review so we can decide how to proceed?

[raymond91125]

@raymond91125 Would you please run an annotation review so we can decide how to proceed?

Annotation review for MF's also?