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

[Jennifer Deegan (nee Clark)]

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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>