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

Alexander Diehl adiehl at informatics.jax.org
Fri Feb 6 06:30:51 PST 2009 

Works for me.

-- Alex


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


-- 
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
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fax:  +1 (207) 288-6131

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