Obsoletion request: GO:0033383 geranyl diphosphate metabolic process

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

GO:0033386 geranylgeranyl diphosphate biosynthetic process

GO:0033383 geranyl diphosphate metabolic process

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

• The reason for obsoletion is that this term was an unnecessary grouping term. (pathway intermediate)

(pathway intermediate, only has 3 pombe annotations)

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

[pgaudet]

The reason for obsoletion is that this term was an unnecessary grouping term.

Is it? There are 2 MetaCyc pathway
and there are no children.. how is it a grouping class?

[ValWood]

After discussion with @pgaudet also look at

'geranyl diphosphate metabolic process' http:https://purl.obolibrary.org/obo/GO_0033383
'geranyl diphosphate biosynthetic process' http:https://purl.obolibrary.org/obo/GO_0033384
'geranylgeranyl diphosphate catabolic process' http:https://purl.obolibrary.org/obo/GO_1902247
'geranylgeranyl diphosphate metabolic process' http:https://purl.obolibrary.org/obo/GO_0033385 OK
'geranylgeranyl diphosphate biosynthetic process' http:https://purl.obolibrary.org/obo/GO_0033386 OK
'farnesyl diphosphate catabolic process' http:https://purl.obolibrary.org/obo/GO_0045339
'farnesyl diphosphate metabolic process' http:https://purl.obolibrary.org/obo/GO_0045338
'farnesyl diphosphate biosynthetic process' http:https://purl.obolibrary.org/obo/GO_0045337 OK
 'farnesyl diphosphate biosynthetic process, mevalonate pathway' http:https://purl.obolibrary.org/obo/GO_0010142 OK
 
 
And these look like MFs, but I haven’t checked.
• 'peptidyl-S-geranylgeranyl-L-cysteine biosynthetic process from peptidyl-cysteine' http:https://purl.obolibrary.org/obo/GO_0018228
• 'peptidyl-S-farnesyl-L-cysteine biosynthetic process from peptidyl-cysteine' http:https://purl.obolibrary.org/obo/GO_0018226
• 'peptidyl-S-12-hydroxyfarnesyl-L-cysteine biosynthetic process from peptidyl-cysteine' http:https://purl.obolibrary.org/obo/GO_0018227

(NOTE "I think farnesyl diphosphate biosynthetic process, mevalonate pathway" is OK (major branch point, FPP is the precursor for farnesylation, dolichol, heme A ubiquinone, gernylgerenylation, and precedes squalene the first dedicated step in sterol biosynthesis) but will review the others. It seems the catabolism terms have been used to model consumption of the metabolite by the next pathway component (i..e NOT catabolism).

[ValWood]

@pgaudet what should the obsoletion reason be? as you say it isn't really grouping class, it's pathway intermediate (but in this case it is sometimes used as grouping for preceding steps, but it isn't an 'end point')

[ValWood]

GO:0033386 geranylgeranyl diphosphate biosynthetic process is fine
GO:0033383 geranyl diphosphate metabolic process is questionable? (20EXP)

[pgaudet]

If you can explain why the MetaCyc pathways are incorrect then we can consider obsoletion.

[ValWood]

yes I requested the wrong term - I meant
GO:0033383 geranyl diphosphate metabolic process

(the reactions are all performed by the same enzyme PANTHER FARNESYL-PYROPHOSPHATE SYNTHETASE)

GO:0033386 geranylgeranyl diphosphate biosynthetic is OK
GO:0045337 farnesyl diphosphate biosynthetic process is OK.

It seems that "GO:0033383 geranyl diphosphate metabolic process" was requested because curators probably wanted a specific process to match the 'output' of each reaction, but GPP doesn't need one (see image above)

I will change the title.

[pgaudet]

OK. I think this was created because it was standard to create the metabolic/biosynthetic/catalytic triad for any compound.

Depending on the group, 'metabolism' may mean synthesis or degradation :(