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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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consistency issues (phosphatidylinositol) #29055

Open ValWood opened 1 month ago

ValWood commented 1 month ago

Term names use variously: phosphatidylinositol-3-phosphate synthesis phosphatidylinositol 5-phosphate synthesis

and 1-phosphatidyl-1D-myo-inositol or phosphatidylinositol

@pgaudet @deustp01 @rozaru @sjm41

ValWood commented 1 month ago

Rhea uses 1-phosphatidyl-1D-myo-inositol but in practice everyone uses "phosphatidylinositol" (at lease for the terms I looked at)

Chebi seem inconsistent

Since we are supposed to use the most commonly used by the community should we use phosphatidylinositol

ValWood commented 1 month ago

was from this comment, https://github.com/geneontology/go-ontology/issues/28898#issuecomment-2407383697

pgaudet commented 1 month ago

Since we are supposed to use the most commonly used by the community should we use phosphatidylinositol

Are you talking about term names or definitions?

For term names >>> absolutely For definitions: we have been copying RHEA definitions, for consistency, but that may not be complete.

ValWood commented 1 month ago

For the names.

ValWood commented 1 month ago

@pgaudet do we prefer phosphatidylinositol to 1-phosphatidyl-1D-myo-inositol i the labels?

pgaudet commented 1 month ago

In the labels I would prefer phosphatidylinositol if the meaning is the same. I know RHEA uses 1-phosphatidyl-1D-myo-inositol.

sjm41 commented 1 month ago

According to Google AI: Phosphatidylinositol and 1-phosphatidyl-1D-myo-inositol are both lipids that play important roles in the body, but they differ in structure and function. Phosphatidylinositol is made up of a glycerol backbone, two fatty acids, a phosphate, and an inositol headgroup. 1-phosphatidyl-1D-myo-inositol is a type of phosphatidylinositol where the inositol moiety is the 1D-myo isomer.

I find "1D-myo" in these term 12 labels: name: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolic process name: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate catabolic process name: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process name: regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate catabolic process name: negative regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate catabolic process name: positive regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate catabolic process name: regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process name: negative regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process name: positive regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process name: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process name: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate catabolic process name: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate biosynthetic process

Compared to the rest of this branch, it seems reasonable to use just "phosphatidylinositol" in those labels, but I'm not expert in this area (we haven't got to lipid metabolism yet - next on the list)

phosphatidylinositol metabolic process
|__1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process
|   |__1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate biosynthetic process
|   |__1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate catabolic process
|__1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolic process
|   |__1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
|   |__1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate catabolic process
|__GPI anchor metabolic process
|   |__GPI anchor biosynthetic process
|   |__GPI anchor release
|   |__mannosyl diphosphorylinositol ceramide metabolic process
|__phosphatidylinositol 5-phosphate metabolic process
|   |__phosphatidylinositol 5-phosphate biosynthetic process
|__phosphatidylinositol acyl-chain remodeling
|__phosphatidylinositol biosynthetic process
|   |__GPI anchor biosynthetic process
|   |__phosphatidylinositol phosphate biosynthetic process
|__phosphatidylinositol catabolic process
|   |__1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate catabolic process
|   |__1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate catabolic process
|__phosphatidylinositol dephosphorylation
ValWood commented 1 month ago

I checked this but now I am not sure, because although I have seen the names used interchangeably in labels they have separate entries in CHEBI

1-phosphatidyl-1D-myo-inositol
https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:57880

phosphatidylinositol https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:28874

ValWood commented 1 month ago

I'm going to leave this one for now!