#11211 establishment of nucleus localization is defined as "transport"

[Valerie Wood]

GO:0040023 establishment of nucleus localization
is defined
The directed movement of the nucleus to a specific location within a cell.
but this is the “transport” definition, not the localisation definition

localization : should be transported to, and/or maintained in, a specific location.

nuclear migration is defined
The directed movement of the nucleus.
(which again is a transport def. I think this is correct here, this is transport , but it doesn’t have a transport parent).

val

[Valerie Wood]

This one is really quick too.

similar to 11213 which we just closed.

[David Osumi-Sutherland]

The def is consistent with the pattern throughout the 'establishment of localization' branch:

label "establishment of localization"^^string
definition "The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location."^^string
subClassOf: localization

label "establishment of localization in cell"^^string
definition "The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell."^^string
subClassOf: "establishment of localization"

label "establishment of nucleus localization"^^string
definition "The directed movement of the nucleus to a specific location within a cell."^^string
subClassOf: "establishment of localization in cell"

Its only when we get up to 'localization' that we get 'and/or maintained in' as part of the def.

"establishment of localization" has a sibling term that covers the maintenance side of things:

label "maintenance of location"^^string
definition "Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere."^^string

So. I think this is OK as is. Closing as works-for-me.

[Valerie Wood]

I'm sure that this is wrong. Or at least it's a conundrum.

I always thought that "Directed movement" was transport:

transport
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.

Localization is:
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to or maintained in a specific location.

So, if localization is being split into "transport" and "maintenance", then logically establishment MUST be equivalent to transport?

I guess my question is what is the difference between "transport" and "establishment of localization" (their defs appear to be the same). Can the localization of something be established without transport (or is this maintenance?).

Help, I got stuck in a loop....

[David Hill]

Hi Val,

You can establish localization of something by degrading it in one place and stabilizing it in another. No transport is required. Not sure that is the case here, but in the general case that can be true.

-D

[Valerie Wood]

OK, I thought there was a difference, i wasn't sure how. Do you agree though that its definition is the same as the transport def ?

[David Osumi-Sutherland]

Narrow answer

transport: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore."^^string
subClassOf: 'establishment of localization'

1. Seems to apply only to substances. Not organelles (may be some grey area with macromolecular complexes).
2. It seems unlikely that establishment of localization of an organelle would involve selective degredation (although I suppose it is possible if there are a large number in one cell). This is certainly not possible for the nucleus.

So, there is a case for changing some defs to refer to localization by selective degredation - specificaly those where localized thing is a molecule.

Big picture:

There is a long JIRA discussion on the tangles and inconsitencies in this branch. I think we concluded that radical overhaul needed for complete consistency would be more that we could take on, given the massive amount of existing annotation. At the end there is a proposal for better refactoring and automation of what we have. But I'm reluctant to touch this until we have better tools for managing inference in our pipeline.

[Valerie Wood]

OK I can cope with "transport" for small things and "establishment of localization" for organelles etc.

[David Osumi-Sutherland]

OK I can cope with "transport" for small things and "establishment of localization" for organelles etc.

Not that simple unfortunately. As David pointed out, small things can be localized either as a result of transport or spatially variable stablization / degredation (although maybe worth looking in to how many annotations are to anything involving the non-transport mechanism). So, for any molecule, we could potentially have both a general 'establishment of localization' class and a more specific transport class. But we actually only have the general classes for protein and RNA.