search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
220 stars 40 forks source link

NTR: regulation of mitotic spindle elongation (spindle phase one) and two children #23318

Open manulera opened 2 years ago

manulera commented 2 years ago

Related to #23317

Please provide as much information as you can:

A term and two children

These definitions should be analogous to GO:0110162, GO:0110163 and GO:0110164, but ending with "during mitotic prophase (spindle phase one)"

mitotic spindle elongation (spindle phase one):

Any process that modulates the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase (spindle phase one) PMID:27697865

negative regulation of mitotic spindle elongation (spindle phase one):

Any process that stops, prevents or reduces the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase anaphase B (spindle phase three). PMID:27697865

positive regulation of mitotic spindle elongation (spindle phase one):

Any process that activates or increases the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase anaphase B (spindle phase three). PMID:27697865

Will be added through pombase

Parentage should be arranged as for GO:0110162 and its children (they should be children of GO:0032888)

graph TD;
      GO:0110162["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0110162>GO:0110162</a><br>regulation of mitoti<br>c spindle elongation<br> (spindle phase thre<br>e)"]-->GO:0110164["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0110164>GO:0110164</a><br>positive regulation <br>of mitotic spindle e<br>longation (spindle p<br>hase three)"];
      GO:1902846["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:1902846>GO:1902846</a><br>positive regulation <br>of mitotic spindle e<br>longation"]-->GO:0110164["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0110164>GO:0110164</a><br>positive regulation <br>of mitotic spindle e<br>longation (spindle p<br>hase three)"];
      GO:0032888["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0032888>GO:0032888</a><br>regulation of mitoti<br>c spindle elongation"]-->GO:1902846["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:1902846>GO:1902846</a><br>positive regulation <br>of mitotic spindle e<br>longation"];
      GO:0110162["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0110162>GO:0110162</a><br>regulation of mitoti<br>c spindle elongation<br> (spindle phase thre<br>e)"]-->GO:0110163["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0110163>GO:0110163</a><br>negative regulation <br>of mitotic spindle e<br>longation (spindle p<br>hase three)"];
      GO:1902845["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:1902845>GO:1902845</a><br>negative regulation <br>of mitotic spindle e<br>longation"]-->GO:0110163["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0110163>GO:0110163</a><br>negative regulation <br>of mitotic spindle e<br>longation (spindle p<br>hase three)"];
      GO:0032888["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0032888>GO:0032888</a><br>regulation of mitoti<br>c spindle elongation"]-->GO:0110162["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0110162>GO:0110162</a><br>regulation of mitoti<br>c spindle elongation<br> (spindle phase thre<br>e)"];
      GO:0032888["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:0032888>GO:0032888</a><br>regulation of mitoti<br>c spindle elongation"]-->GO:1902845["<a href=https://www.ebi.ac.uk/QuickGO/term/GO:1902845>GO:1902845</a><br>negative regulation <br>of mitotic spindle e<br>longation"];
manulera commented 2 years ago

Hi @ValWood,

So this I believe is related to the other issue #23317.

I also wonder whether the intent of the terms GO:0110159 (regulation of mitotic spindle formation (spindle phase one)) and children was actually regulation of mitotic spindle elongation (spindle phase 1). Otherwise, I don't see the difference between GO:0110159 and GO:1901673 (regulation of mitotic spindle assembly vs. regulation of mitotic spindle formation - this always happens during prophase / phase 1)

manulera commented 2 years ago

Sometimes it is hard to tell the difference between spindle assembly and elongation during phase I / prophase.

Some clear cases that can be annotated to elongation only are deletions that would cause the spindle to be longer than usual by the end of prophase / during metaphase, such as kinesin-8. This typically would make overly long kinetochore microtubules that would make the spindle longer by the end of prophase / during metaphase. However, kinesin-8 deletions would not lead to monopolar spindles (or spindle assembly problems).

There are also examples in which some genes should be annotated to both spindle assembly and elongation, since they have been shown to affect the length of the spindle, but also be required to achieve bipolarity, examples are cut7 and ase1 (synthetically lethal in the cut7D pkl1D showing that ase1 also contributes to spindle formation)

ValWood commented 2 years ago

I agree that GO:0110159 and GO:1901673 are referring to the same thing & could merge. I think this is a hang-over from before we added the phase 1-3 terms and separated assembly/formation from elongation.

manulera commented 2 years ago

Ok, so looking a bit more in detail it seems that the term GO:0061804 (mitotic spindle formation (spindle phase one) ) actually encompasses both things:

The cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase.

As such, 61804 is part_of mitotic spindle elongation and part_of mitotic spindle assembly. As I said before, the two are often hard to distinguish, so I would agree with this, probably this is sufficient and I will annotate the genes to the children of GO:0061804

ValWood commented 2 years ago

Assembly vs elongation is something we struggled with a lot trying to get this right. Takashi Toda helped me with the terms and defs...I think there will still be tweaks needed...

manulera commented 2 years ago

Having seconds thoughts about this as I annotate some genes to it. It makes little sense to say that a protein like kinesin-8 "negative regulates mitotic spindle formation". It is important for its homeostasis, but it makes it shorter. Perhaps worth discussing with someone else.

ValWood commented 2 years ago

Generally, if something is involved directly in a process, we would not annotate also to the "regulation of process" term. I will discuss the use of "regulation of process" with you soon. https://wiki.geneontology.org/Annotating_regulation is out of data.

My rule of thumb is to try to reserve regulation for 'signalling' that is upstream of a pathway. Everything else is annotated directly to the process.

pgaudet commented 2 years ago

Maybe this is relevant #13461 as well ?

Please let me know if you want new terms or updates to GO:0110159 & children.

Thanks, Pascale

ValWood commented 2 years ago

https://github.com/geneontology/go-ontology/issues/13461 is quite an old ticket. It predates where we renamed to include 'spindle phase I' II and III in the term names. There was quite a bit of work on this since this ticket. There are 31 closed tickets with a search on "spindle elongation". It will probably be more confusing to try to revisit any old tickets than to just identify any remaining biological inconsistencies in the existing arrangement with expert input from @manulera and fix them.

Let's wait until I discuss regulation terms with @manulera and then we can have a call to fix anything maybe? I will take the ticket for now.