merge: GO:0040023 and GO:0007097

[gocentral]

Based on their text definitions, these should be merged, as the top def is subsumed by the bottom one:

~~ is_a GO:0040023 ! establishment of nucleus localization [DEF: "The directed movement of the nucleus to a specific location within a cell."]

Furthermore, the transport rules don't appear to be consistently
applied. For example, "nuclear migration along a microtubule" is
considered a subclass of transport:

~is_a GO:0006810 ! transport
~~is_a GO:0046907 ! intracellular transport
~~~is_a GO:0030705 ! cytoskeleton-dependent intracellular transport
`is\_a GO:0010970 \! microtubule-based transport
`~is_a GO:0072384 ! organelle transport along microtubule
```~~is_a GO:0030473 ! nuclear migration along microtubule *** 

However, "nuclear migration" itself is not a subtype of
transport. This is fairly odd. 

Reported by: cmungall

Original Ticket: [geneontology/ontology-requests/8980](https://sourceforge.net/p/geneontology/ontology-requests/8980)

[gocentral]

• assigned_to: nobody --> tairtb

Original comment by: jl242

[gocentral]

I think part of the problem (transport vs. migration) lies in the definition of transport and child terms. For 'transport' down to 'cytoskeleton-dependent intracellular' transport what moves are substances (such as macromolecules, small molecules, ions). No mention of organelles. Once we hit 'microtubule-based transport', now we are moving "organelles or other particles".

We need to reconcile definitions. Transport needs to include organelles.

What do you think of making 'establishment of localization' a child of 'transport' instead of the reverse situation which is the case right now? The DAG is pretty darned confusing but I think this might solve the problem of 'nuclear migration' not being a subtype of transport since NM (merged into est of nucleus localization) is_a est of localization.

EOL = The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.

T = 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.

biological process --[i] localization ----[p] establishment of localization ----[p] maintenance of localization --[i] establishment of localization ----[i]transport

I must be missing something obvious or this would have been done a while ago. Let's discuss.

Original comment by: tberardini

[gocentral]

Ok. discussing with David had brought up that 'establishment of localization' is not defined as well as it could be. We definitely need to revisit the whole 'establishment of localization' node.

Original comment by: tberardini

[pgaudet]

I don't see why these two terms shouldn't be merged. 'nuclear migration' is the only sub-type of 'establishment of nucleus localization'. The other term we have is cell-type and process specific: establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification

So, unless there are objections I will merge and keep 'nuclear migration' as the main label. References: PMID:10725321 PMID:24563363

[tberardini]

@pgaudet, sure, please roll into your next set of edits. Thank you.

[ValWood]

The merge is OK, but we have used child terms like "microtubule polymerization based movement" As these terms are directed movement, I think they should probably be a type of transport?

[pgaudet]

Hi @hattrill

To do this I need to first deal with the children terms. I am trying to understand the difference between ‘establishment of localization to x’ and ‘transport to x’. (looking at issue https://github.com/geneontology/go-ontology/issues/13754)

GO:0040023 ! establishment of nucleus localization has two children

• GO:0030722 establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification (3 EXP flybase annotation) — GO:0007312 oocyte nucleus migration involved in oocyte dorsal/ventral axis specification (about 30 annotations)

Are these two terms really different ? I tried to look at the annotations for GO:0030722 establishment of… but I couldn’t see that the proteins localize the nucleus, I might have missed something.

Do you think these can be merged ?

Thanks, Pascale

[hattrill]

Not sure .....they sound equivalent, but I'll have a look either today or tomorrow.

"I tried to look at the annotations for GO:0030722 establishment of… but I couldn’t see that the proteins localize the nucleus, I might have missed something."

......I assume that it doesn't matter where the proteins localize but the organelle itself.

[hattrill]

Can't see any difference in the ways that the terms have been used. Go ahead a merge away!

[pgaudet]

Hello again @hattrill

I just noticed that the parent of these two occyte nuclear migration terms, 'oocyte nucleus localization involved in oocyte dorsal/ventral axis specification' has the same definition as the two other terms.

GO:0051663 'oocyte nucleus localization involved in oocyte dorsal/ventral axis specification'

The directed movement of the nucleus to a specific location within a cell during the establishment and maintenance of the dorsal/ventral axis of the oocyte.

-- GO:0030722 'establishment of oocyte nucleus localization involved in oocyte dorsal/ventral axis specification' The directed movement of the nucleus to a specific location within the cell during the establishment and maintenance of the dorsal/ventral axis of the oocyte. In the insect oocyte, for example, the nucleus is repositioned to a dorso-anterior position.

---- GO:0007312 'oocyte nucleus migration involved in oocyte dorsal/ventral axis specification' The directed movement of the oocyte nucleus within the cell as part of the establishment and maintenance of the dorsal/ventral axis of the oocyte. An example of this is found in Drosophila melanogaster.

Localization should have meant 'migration' OR 'maintenance of location'. Do you want to check whether these should be moved to the 'nuclear migration...' term?

There is a small number of FlyBase IMP annotations:

Q9VEX5 | Asun | PMID:24333177 P42271 | gammaTub37C | PMID:21852952 A0A0B4K682 | jvl | PMID:21989913 A0A0B4K6H8 | jvl | PMID:21989913 A0A0B4K6X6 | jvl | PMID:21989913 Q6NNB4 | jvl | PMID:21989913 Q7KSJ6 | jvl | PMID:21989913 Q960P5 | jvl | PMID:21989913 Q9VFG3 | jvl | PMID:21989913 A1ZBL5 | par-1 | PMID:16753562 A1ZBL7 | par-1 | PMID:16753562 A1ZBL9 | par-1 | PMID:16753562 E1JGM9 | par-1 | PMID:16753562 E1JGN0 | par-1 | PMID:16753562 Q6NPA6 | par-1 | PMID:16753562 Q7K9Q9 | par-1 | PMID:16753562 Q7YU80 | par-1 | PMID:16753562 Q8IGD5 | par-1 | PMID:16753562 Q8MQR8 | par-1 | PMID:16753562 Q95T80 | par-1 | PMID:16753562 Q95U75 | par-1 | PMID:16753562 Q963E5 | par-1 | PMID:16753562 Q963E6 | par-1 | PMID:16753562 Q9V8V7 | par-1 | PMID:16753562 Q9V8V8 | par-1 | PMID:16753562

Thanks, Pascale

[hattrill]

Moved most: oocyte nucleus localization involved in oocyte dorsal/ventral axis specification to oocyte nucleus migration involved in oocyte dorsal/ventral axis specification. (and dumped par-1 as evidence quite weak)