[Ontology-editors] DASH complex - two part_of parents

[Chris Mungall]

I've added this as a use case here:

http://wiki.geneontology.org/index.php/XP:molecular_function_xp_cellular_component#Use_Cases

On Feb 24, 2009, at 9:14 AM, Chris Mungall wrote:

>
> 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
>>>
>>>
>>>
>>
>>
>>
>> -- 
>> The Wellcome Trust Sanger Institute is operated by Genome Research  
>> Limited, a charity registered in England with number 1021457 and a  
>> company registered in England with number 2742969, whose registered  
>> office is 215 Euston Road, London, NW1 2BE.  
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