[Transport] [Ontology-editors] calcium ion transport question
Alexander Diehl
adiehl at informatics.jax.org
Fri Feb 6 11:53:40 PST 2009
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
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