[Ontology-editors] DASH complex - two part_of parents

[Valerie Wood]

It just seems that it would be more accurate to remove the 'microtubule' 
parent totally.
I don't think that DASH would be considered to be part of the 
microtubule would it?
The interaction with the spindle  will be captured by  the processes 
like 'kinetochore-microtubule attachment' (or whatever it is)
val

Midori Harris wrote:

> I haven't committed any changes yet, so at the moment the live copy 
> still has the structure I put below (the "after that work" bit).
>
> That said, I don't think it's ideal either way round. The problem is 
> that part_of doesn't do a very good job of representing the actual 
> relationship between things that are "associated" in the sense of 
> being adjacent or connected to each other. I also think you're right 
> in saying the difference between the two newer DASH terms is temporal, 
> but there is precedent with the different proteasome terms (nuclear 
> proteasome, ER proteasome, etc.).
>
> I guess that leaves two options (at least until we add new 
> relationship types, which may not happen very soon):
>
>  - have one DASH complex term, part_of condensed chromosome 
> kinetochore, but with no relationship to microtubule term; or
>
>  - have two terms, where 'microtubule associated DASH complex' has 
> parents is_a DASH complex and part_of kinetochore microtubule.
>
> The first one misses out the connection with microtubules entirely 
> because it isn't always true. The second is more fiddly, and has the 
> problem that part_of isn't quite right.
>
> For now I just won't commit the merges, so we'll still have the three 
> terms we had before you opened SF 2573002. Let's see if anyone else 
> has insightful comments.
>
> m
>
> On Mon, 23 Feb 2009, Valerie Wood wrote:
>
>> I'm still not sure about this.
>>
>> The DASH complex is usually considered part of the kinetochore. It 
>> associated with spindle microtubules, when they attach to the 
>> kinetochore..
>> I'm not sure it is correct to position under 'spindle microtubule' as 
>> this would imply it was a constituent of the microtubule.
>> According to the ref genome discussion recently microtubule should 
>> only be used to annotatate tubulins, and other things which assoicate 
>> with the microtubule should be annotated with microtubule binding, or 
>> the appropriate microtubule cytoskeleton component term.
>>
>> In this case I don't think  the DASH complex would be considered as 
>> part of the microtubule, or  microtubule cytoskeleton?
>>
>> I'm also not sure that the 2 children microtubule associated DASH 
>> complex and kinetochore associated DASH complex are required?
>> As far as I'm aware DASH complex is always associated with the 
>> kinetochore when it exists. When the spindles attach it is also 
>> associated with the microtubules. Is there a precedent for having 
>> separate componet terms in this situation when we are referring to an 
>> identical complex ? (It seems  the terms are being used to describe 
>> temproal aspects of the complexes interactions)
>>
>> VAl
>>
>> Midori Harris wrote:
>>
>>> Hi,
>>>
>>> This is just to record that Val and I have looked at the literature 
>>> on the DASH complex (GO:0042729), and agreed that it's OK for it to 
>>> have two part_of parents for now.
>>>
>>> Background: the DASH complex term was originally added with two 
>>> part_of parents, GO:0000778 condensed nuclear chromosome kinetochore 
>>> and GO:0005828 kinetochore microtubule. It was duly flagged by 
>>> Chris' QC report, and at a meeting involving Jane, David and me, 
>>> Jane created two
>>> child terms to avoid true path violations. After that work we had:
>>>
>>>   DASH complex GO:0042729
>>>   [i] kinetochore-associated DASH complex GO:0043926
>>>   [i] microtubule-associated DASH complex GO:0043925
>>>
>>>   condensed nuclear chromosome kinetochore
>>>   [p] kinetochore-associated DASH complex GO:0043926
>>>
>>>   kinetochore microtubule
>>>   [p] microtubule-associated DASH complex GO:0043925
>>>
>>> But Val and I confirmed that, as far as is known in the field, every 
>>> DASH complex that forms is part of a kinetochore and associated with 
>>> kinetochore microtubules. I think using a different relationship 
>>> type, perhaps associated_with or connected_to or adjacent_to, 
>>> between DASH complex and kinetochore microtubule would improve our 
>>> representation of the biology, but until we add new relationship 
>>> types, allowing the original DASH complex term to have two part_of 
>>> parents is the most biologically accurate thing we can do.
>>>
>>> Accordingly, I've merged the newer terms into the parent, restoring 
>>> the part_of relationships (and removing the newer term names from 
>>> the synonym list -- looks like nobody uses them).
>>>
>>> midori
>>>
>>>
>>>
>>
>>
>>
>>
>
>
>



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