[Transport] [Ontology-editors] calcium ion transport question
Tanya Berardini
tberardi at acoma.stanford.edu
Fri Feb 6 12:36:11 PST 2009
okey dokey!
On Fri, Feb 6, 2009 at 11:53 AM, Alexander Diehl <adiehl at informatics.jax.org
> wrote:
> Tanya,
>
> According to CC, SR is a type of ER (which agrees with my understanding as
> well). Therefore GO:0014808 should be a child of GO:0051209, not a sibling.
>
> Thanks,
>
> Alex
>
>
>
> Tanya Berardini wrote:
>
>>
>>
>> On Fri, Feb 6, 2009 at 11:04 AM, Chris Mungall <cjm at berkeleybop.org<mailto:
>> 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
>> <mailto: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
>> <
>> https://sourceforge.net/tracker/index.php?func=detail&aid=2560505&group_id=36855&atid=440764>
>> Thanks,
>> Midori
>>
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>>
>> --
>> Tanya Berardini
>> TAIR Curator
>> www.arabidopsis.org <http://www.arabidopsis.org>
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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
> work: +1 (207) 288-6427
> fax: +1 (207) 288-6131
>
>
--
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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