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

Fri Feb 6 11:33:59 PST 2009

On Fri, Feb 6, 2009 at 11:04 AM, Chris Mungall <cjm at berkeleybop.org> 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?

Legend:

GO:0051209 = release of sequestered calcium ion into cytosol
GO:0060402 = calcium ion transport into cytosol
GO:0014808 = release of sequestered calcium ion into cytosol by sarcoplasmic
reticulum

 GO:0051209 refers specifically release from "...endoplasmic reticulum or
mitochondria ...into the cytosolic compartment."    A sibling for this under
60402 should be 'GO:0014808 release of sequestered calcium ion into cytosol
by sarcoplasmic reticulum' (Varsha's new term).  I'm not too sure about
14808 being a child of 51209 since 51209 refers to release from ER or
mitochondria but not SR.

Either: rename 51209 to include the ref to ER or mitochondria (not so
satisfactory because of the 'OR') or refine its definition to be more broad
(to include SR) and create child terms specific to mitochondria and ER.

Tanya

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

Yes.  Looks like Midori has already done so.

>
>
>
>> 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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>>>>>>>>>>>>>>> Transport at geneontology.org
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>>>>>>>>>>>>>>>
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-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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