[Ontology-editors] DASH complex - two part_of parents

[Valerie Wood]

Thats what I think but it would be good if someone from SGD could comment.
(that would do as DASH is only present in fungi)

val

Midori Harris wrote:

> 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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