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

[Jennifer Deegan (nee Clark)]

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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