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

[Jane Lomax]

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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>>>>>>> Transport at geneontology.org
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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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