[Ontology-editors] DASH complex - two part_of parents

[Midori Harris]

In that case, option 1 would do - just keep the original DASH complex 
term, part_of kinetochore, no relation to MTs. Want me to do that?

m

On Mon, 23 Feb 2009, Valerie Wood wrote:

> 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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