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

Alexander Diehl adiehl at informatics.jax.org
Fri Feb 6 06:17:53 PST 2009 

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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>
>


-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131

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