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

Midori Harris midori at ebi.ac.uk
Fri Feb 6 06:52:47 PST 2009 

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
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Transport mailing list
>>>>>>>>>>>>> Transport at geneontology.org
>>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/transport
>>>>>>>>>>>>> 
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Ontology-editors mailing list
>>>>>>>>>>>> Ontology-editors at geneontology.org
>>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>>>>>>>> 
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Ontology-editors mailing list
>>>>>>>>>>> Ontology-editors at geneontology.org
>>>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>>>>> _______________________________________________
>>>>>>>>> Transport mailing list
>>>>>>>>> Transport at geneontology.org
>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/transport
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Ontology-editors mailing list
>>>>>>> Ontology-editors at geneontology.org
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>> 
>>>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>
>
>

More information about the Ontology-editors mailing list