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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Scope of fungal-type cell wall biogenesis (GO:0009272) #22008

Open ValWood opened 3 years ago

ValWood commented 3 years ago

I have been wondering about the scope of fungal-type cell wall biogenesis (GO:0009272)

Definition A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a fungal-type cell wall. The fungal-type cell wall contains beta-glucan and may contain chitin.

Is this supposed to include all of the processing that occurs in the ER? for example the glycosylation, does it include chaperones? does it include transport? (I am thinking about ribosome biogenesis as an analogy)

I pick up quite a lot of mappings to this term from SGD to things which have cell wall compromised phenotypes, but this does seem to fit because the scope is very broad. However I would not make these as GO annotations.

pgaudet commented 3 years ago

@ValWood What types of activities do you think would be relevant for this ? It may help redefine to exclude other activities.

ValWood commented 3 years ago

Most of the children are "biosynthetic process" which is different from "biogenesis" And many terms in. this branch represent activities: fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process (GO:0071970 cell wall mannoprotein biosynthetic process

I'm also not sure if we need fungal and plant specific terms... We have organization, assembly and disassembly for the things which are making the cell wall components. Although the assembly terms are not much used. The terms are confusing because it isn't clear what belongs to biosynthesis and what belongs to assembly, and we have a grouping term : cell wall organization or biogenesis (GO:0071554).

Anyway this isn't super urgent so I would put it at low priority.