[Ontology-editors] DASH complex - two part_of parents

[Midori Harris]

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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