[Ontology-editors] [Transport] calcium ion transport question

[Jane Lomax]

Should be part_of - e.g. transmembrane transport during release of 
sequestered calcium ion into cytosol part_of release of sequestered 
calcium ion into cytosol. Otherwise you'll probably run into tpvs later 
down the line.

Jane

Jennifer Deegan (nee Clark) wrote:
> Is that a problem?
>
> Jen
>
> Jane Lomax wrote:
>> But surely 'release of sequestered calcium ion into cytosol' is a 
>> process that /involves/ transmembrane transport rather than being 
>> transmembrane transport itself?
>>
>> Jane
>>
>> Jennifer Deegan (nee Clark) wrote:
>>> Hi,
>>>
>>> If it's through a transmembrane transporter then I agree that it's 
>>> very straightforward and that the relationship should be made.
>>>
>>> Jen
>>>
>>> Valerie Wood wrote:
>>>> I don't know.
>>>>
>>>> I can't think of any of these processes which don't involve 
>>>> transmembrane transporters as they are crossing compartmental 
>>>> boundaries.
>>>>
>>>> As the current def says
>>>> "The process by which calcium ions sequestered in the endoplasmic 
>>>> reticulum or mitochondria are released into the cytosolic compartment"
>>>>
>>>> then we can assume that this is transmembrane transport
>>>>  and at some level a a calcium transporter is activated (usually a 
>>>> voltage gated ion channel) for the release to occur. So it could 
>>>> probably  be under 'transmembrane transport"
>>>>
>>>>
>>>>
>>>> Val
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Midori Harris <midori at ebi.ac.uk> wrote:
>>>>> Thanks for the comments so far; looking forward to hearing more 
>>>>> from the transport experts.
>>>>>
>>>>> I'm adding Varsha to the recipients so she can see what's 
>>>>> happening (the SF request that prompted this was hers).
>>>>>
>>>>> m
>>>>>
>>>>> On Fri, 6 Feb 2009, Jennifer Deegan (nee Clark) wrote:
>>>>>
>>>>>> Yes I agree. I think that the transport definition is very 
>>>>>> general and I'm in some doubt about how general it was intended 
>>>>>> to be, and whether we still stand by that intention. How 
>>>>>> 'directed' should the transport be, and do we really mean 'via, 
>>>>>> or with the assistance of a transporter protein complex'?
>>>>>>
>>>>>> I would be interested to hear whether the domain experts think 
>>>>>> that release of sequestered calcium ions into cytosol should 
>>>>>> count as directed. If the calcium ions had been transported from 
>>>>>> one location to another in vesicles, and then released, then I 
>>>>>> think that this could count as directed. However this def 
>>>>>> specifies that the ions are released from the endoplasmic 
>>>>>> reticulum or mitochondrion. This seems less directed, but I would 
>>>>>> like to have a better idea of the background of this process. 
>>>>>> Does anybody know off-hand?
>>>>>>
>>>>>> Does anybody else have any idea of how restrictive the transport 
>>>>>> terms were intended to be, or how restrictive they should be now? 
>>>>>> In our usual GO way, I could see the top transport term being 
>>>>>> general enough to capture all transport.
>>>>>>
>>>>>> Jen
>>>>>>
>>>>>>
>>>>>>
>>>>>> Chris Mungall wrote:
>>>>>>>  thought transport sensu GO meant *directed* movement.
>>>>>>>
>>>>>>> If I were to sneak into a zoo at night and unlock all the cages, 
>>>>>>> would I be directing all the monkeys and lions into the 
>>>>>>> surrounding city? I guess it depends on my intentions.
>>>>>>>
>>>>>>> I think it's similar here. There is a hidden notion of agency in 
>>>>>>> the GO definition of transport. Of course, cells have no 
>>>>>>> intentions, but gene products have evolved to carry out some 
>>>>>>> role, so there is a form of agency here. Even so it may be 
>>>>>>> easier if describe processes rather than ascribing goals.
>>>>>>>
>>>>>>> On Feb 5, 2009, at 4:00 AM, Midori Harris wrote:
>>>>>>>
>>>>>>>> just re-sending with a subject line ...
>>>>>>>>
>>>>>>>> On Thu, 5 Feb 2009, Midori Harris wrote:
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> Is anyone aware of any reason why 'release of sequestered 
>>>>>>>>> calcium ion into cytosol' (GO:0051209) has no relationship to 
>>>>>>>>> 'calcium ion transport' (GO:0006816)? If not, I think it would 
>>>>>>>>> make sense to add.
>>>>>>>>>
>>>>>>>>> This came up as part of SF 2560505:
>>>>>>>>>
>>>>>>>>> https://sourceforge.net/tracker/index.php?func=detail&aid=2560505&group_id=36855&atid=440764 
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Midori
>>>>>>>>> _______________________________________________
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>>>>>>>>>
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>>>>
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>>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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