[Ontology-editors] DASH complex - two part_of parents

[Chris Mungall]

On Feb 23, 2009, at 6:50 AM, 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.

Should this decision not be reflected in the comment tag? Seems like a  
very specific rule.

Would colocalizes_with to microtubule be allowed for non-tubulins?

When we have the MF->CC links in the ontology we will be able to make  
inferences of the form: a gene product that is executing a function of  
X binding must, at the least, be in the vicinity of some X. Here I  
would think vicinity_of would translate to colocalizes_with, and would  
be treated appropriately in AmiGO

I think it's especially important to be thinking about this if people  
are making MF annotations as proxies for CC annotations

>
> 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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