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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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obsoletion "protein exit from endoplasmic reticulum" #19122

Open ValWood opened 4 years ago

ValWood commented 4 years ago

should protein exit from endoplasmic reticulum be part_of "vesicle-mediated transport"?

(occurs via COPII vesicles?)

ValWood commented 4 years ago

@pgaudet discuss/add today

pgaudet commented 4 years ago

@ValWood to check her annotations

ValWood commented 4 years ago

The term "protein exit from endoplasmic reticulum" should be obsoleted.

It is used for 3 unrelated processes. It has a child GO:0030970 retrograde protein transport, ER to cytosol The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon. PMID:11994744

This, term and annotations to it, are fine.

Quite a lot of the other annotation to "protein exit from endoplasmic reticulum" are for
some are retrograde (move to the existing child )

Others are for 1) transmembrane transport of small molecules from ER to cytosol e..g human TM9SF4 | Transmembrane 9 superfamily member 4 human TMED9 mouse Slc51b. pthr36129

2) some are trafficking from the ER via COPII vesicles e.g TLG2 | Syntaxin-like t-SNARE

Part of the problem is that there isn't a term to describe this process, as a child of vesicle-mediated transport https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016192 so people are finding the term in the other branch which does not reference v-m-t at all

we have a term for the component: GO:0030134 COPII-coated ER to Golgi transport vesicle

but not for the process ER to Golgi vesicle transport