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

[Midori Harris]

what are the other parts?

m

On Fri, 6 Feb 2009, Jane Lomax wrote:

> 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.
>
> Jane
>
> 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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>>>>>> 
>>>>> 
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