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

Chris Mungall cjm at berkeleybop.org
Fri Feb 6 11:04:55 PST 2009 




On Feb 6, 2009, at 6:52 AM, 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.

is_a parent?

That means GO:0060402 will have an only is_a child, which invites the  
question, what kinds of GO:0060402 ! calcium ion transport into  
cytosol are not kinds of GO:0051209 ! release of sequestered calcium  
ion into cytosol?

Also, shouldn't we make GO:0060402 an is_a child of
GO:0007204 ! elevation of cytosolic calcium ion concentration
?

>
> 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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