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

[Jennifer Deegan (nee Clark)]

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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