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

Jane Lomax jane at ebi.ac.uk
Fri Feb 6 06:27:58 PST 2009 

There we are then - we just need an exact synonym: 'calcium ion 
transport into cytosol' and everyone's happy.

Jane

Alexander Diehl wrote:
> Hi,
>
> "Release" of calcium from the endoplasmic reticulum involves calcium 
> channels in the ER, and thus fulfills the directional nature of 
> calcium transport (PMID:11244045, PMID:17267286, PMID:18365243, 
> PMID:17499354, among many others; this has, not surprisingly, been 
> studied extensively in immunological signaling).  The use of the word 
> "release" while imprecise, probably reflects the history of the way 
> this phenomenon was discovered and described.  I imagine the linkage 
> between the terms 'release of sequestered calcium ion into cytosol' 
> (GO:0051209) and 'calcium ion transport' (GO:0006816) reflects mostly 
> that they were created by separate individuals at different times who 
> were unaware of the other terms.  This has been fairly common in the 
> GO over its history and other examples exist even today.
>
> I would like to remind people that Pubmed is a great source of answers 
> to straightforward questions like this.  It doesn't make sense to 
> deconstruct the meaning of a term endlessly without recourse to the 
> literature, and better referencing of GO terms to the actual source 
> literature, would help.
>
> As for Jane's point, I would argue that the "release of sequestered 
> calcium ion into cytosol" is_a calcium transport under a different 
> name.  However the term clearly needs regulation terms attached to it, 
> since a variety of signaling pathways trigger this type of transport.  
> I do not see any TPV here, just language that matches the scientific 
> literature.
>
> Thanks,
>
> Alex
>
>
> 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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>>>>>>>>>>> Transport at geneontology.org
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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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