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

Midori Harris midori at ebi.ac.uk
Fri Feb 6 06:30:49 PST 2009 

Ok, I'll take care of it since I'm working on the SF item that started it 
all.

(Alex - thanks for consulting the literature; due to its importance in 
immunology you probably had a better idea than I where to start looking.)

m

On Fri, 6 Feb 2009, Jane Lomax wrote:

> 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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>>>>> 
>>>>> 
>>> 
>>> 
>> 
>> 
>
>
>

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