Obsoletion request: GO:0006507 GPI anchor release

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

This term is problematic in 2 ways.

1. it's a single step process (phospholipase activity)
2. It's positioned under
   GO:0006505 GPI anchor metabolic process, but this isn't metabolising the anchor, it is cleaving the anchor from the protein

and considering that the ADDITION of the GPI anchor (a multistep process) is NOT under GPI anchor metabolism
(it is under GO:0180046 JSON
GPI anchored protein biosynthesis)

I am not sure what the process should be without seeing the context, but possibly part of some catabolic process?
(there are only 16 manual annotations, all to GPLD1 and Notum (but most of the annotations to notum are "NOTS"

SUMMARY single step process in the wrong place

• 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.

• "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

---

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 ([email protected])
• paste the text in the ontology ticket

[raymond91125]

If we obsolete this term, the NOT annotations may have no specific term to transfer to.

[ValWood]

I wonder if that's a problem? presumably the annotations were only made to prevent annotations to this term? so if the term goes away the NOT is no longer required.... I'm not sure but I know it is useful to have NOT annotations to provide a negative annotation set but in this case it might not be necessary to preserve.

Should we report NOT annotations in the obsoletion to give people the opportunity to migrate them?

[raymond91125]

Should we report NOT annotations in the obsoletion to give people the opportunity to migrate them?

NOT's are included in the report already.

[raymond91125]

PMID: 26563290 reference review.

[ValWood]

the equivalent MF term appears to be
glycosylphosphatidylinositol phospholipase D activity
but are there multiple steps?

[raymond91125]

There are multiple sequence motifs in GPI-anchored proteins that affect release PMID:15470092. In addition to GPI-PLD, there are other GPIases: PMID:15665832, PMID:19503825.
But I've found no evidence for multi-step (involving multiple gene products) process in GPI-anchor enzymatic release.

[pgaudet]

@ValWood what should be the process? post-translational protein modification?

[raymond91125]

@ValWood what should be the process? post-translational protein modification?

Yes, that would fit. @pgaudet Are you suggesting replaced_by post-translational protein modification?

[pgaudet]

Discussion on the ontology editor's call: this applies more to localization or even membrane location - or secretion ? if the protein is outside

“Cell-surface GPI-APs are released by GPIase activity in many important biological events, including cellular proliferation, development, neurogenesis, and reproduction.” (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4808780/)

[raymond91125]

@pgaudet This term has already been obsoleted. I'd close this ticket if all necessary is done. One question is that I added Consider GO:0004621 glycosylphosphatidylinositol phospholipase D activity. Is Consider an MF appropriate?

[pgaudet]

Perfect.

Some examples where papers clearly describe protein secretion: PMID:2017684, PMID:17720976