[Ontology-editors] calcium ion transport question

[Midori Harris]

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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>>>> http://fafner.stanford.edu/mailman/listinfo/transport
>>>> 
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>> 
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