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

[Jane Lomax]

Well that's the question! But there must be something more to it 
otherwise the term could just be called 'transmembrane transport of 
calcium into cytosol'. Or maybe it could be renamed that?

Perhaps someone who actually knows something about the process could 
comment?!

Jane


Midori Harris wrote:
> 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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>>>>
>>>>
>>
>>
>>


-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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