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

[Jennifer Deegan (nee Clark)]

Hi Jane,

> 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.

I think perhaps the transmembrane transport that you are thinking of 
that is part of this process is a function. As I understand it you are 
talking about the part_of relationship below and I am talking about the 
is_a. (The term names are paraphrased)

[i]transport process
---[i]release of sequestered calcium ion into cytosol
------[p]some specific transmembrane transport function

Would that be right?

Jen


> 
> 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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