Rename GO:0036228 protein targeting to nuclear inner membrane -> protein *localization* to nuclear inner membrane

[pgaudet]

Hello,

I am working on #13754 trying to make smaller issues whenever possible. @ValWood writes

For nucleocytoplasmic transport this one is a localization, GO:0036228 protein targeting to nuclear inner membrane because things are not "targeted" to the inner membrane. They are only targeted to the nuclear pore.

I also propose to change the definition: OLD: The process of targeting a protein to, and inserting it into, the nuclear inner membrane; usually uses signals contained within the protein. NEW: The process of transporting or maintaining the localization of another protein into the nuclear inner membrane.

Manual annotations are only by SGD and Flybase; @srengel @hattrill would you be OK these changes ?

[hattrill]

I am fine with this. But the new definition doesn't scan for me. Suggest something like:

"The process of transporting a protein to, or maintaining its localization in, the nuclear inner membrane."

[pgaudet]

Thanks @hattrill I used a slightly different definition from other terms in the neighborhood:

[Term] id: GO:0036228 -name: protein targeting to nuclear inner membrane +name: protein localization to nuclear inner membrane namespace: biological_process -def: "The process of targeting a protein to, and inserting it into, the nuclear inner membrane; usually uses signals contained within the protein." [GOC:dgf, PMID:16929305] -synonym: "protein targeting to INM" EXACT [PMID:16929305] -is_a: GO:0006612 ! protein targeting to membrane -intersection_of: GO:0006605 ! protein targeting +def: "A process in which a protein is transported to, or maintained in, a location within the nuclear inner membrane." [GOC:dgf, PMID:16929305] +synonym: "protein targeting to INM" RELATED [PMID:16929305] +synonym: "protein targeting to nuclear inner membrane" RELATED [] +intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005637 ! nuclear inner membrane

Thanks, Pascale

[ValWood]

I looked at the paper used to support the original term, and this does appear to be describing a transport process not just any localization process.

https://www.ncbi.nlm.nih.gov/pubmed/16929305

So should it be something like The process of transporting a protein into the nucleus to a location on the nucleus inner membrane ? (this really is proper targeting actually)

[srengel]

Joining late, but I think I'm fine with this. I like Helen's proposed definition.

[pgaudet]

Hi @ValWood There is at least one protein annotated to this process that seems involved in localization rather than transport, NUP155, see http://europepmc.org/abstract/MED/22718353

Should I create a new term for the transport ? Unless you think NUP155 would be OK annotated to 'protein transport to nuclear inner membrane? (this is also a question for @hattrill since this is a fly annotation.

Thanks, Pascale

[hattrill]

For NUP155, I would think that from the evidence in the paper it would be a localization thing (although there isn't much mechanistic data). Certainly not transport.

[pgaudet]

Right, so I am leaving this as 'localization. We can add transport if needed - if someone wants it. please create a new issue.

Thanks !

Pascale