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

Jennifer Deegan (nee Clark) jdeegan at ebi.ac.uk
Fri Feb 6 06:58:24 PST 2009 

Sounds good.

Jen

Midori Harris wrote:
> Actually, we already have a term for 'calcium ion transport into 
> cytosol' (GO:0060402), which does not have the negative regulation of 
> sequestering parentage that GO:0051209 has. So I'll make GO:0060402 an 
> additional parent of GO:0051209. That's consistent with everything here 
> and in the ontology.
> 
> m
> 
> On Fri, 6 Feb 2009, Alexander Diehl wrote:
> 
>> 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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