Re: [sbgn-libsbgn] [sbgn-discuss] Parent-child relations in SBGN-ML

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Hi Nicolas and Frank,

Thank you very much for your replies and examples. That clarifies the issue.

Best wishes,

Alexander

On Fri, Oct 7, 2016 at 12:49 PM, Frank T. Bergmann <fbe...@ca...>
wrote:

> Hello Alexander,
>
> just answering about SBGN-ML ... there we have an attribute
> "compartmentOrder" that does allow us to resolve this issue.
>
> see also the test cases:
>
> http://svn.code.sf.net/p/libsbgn/code/trunk/test-files/
> PD//compartmentOrder1.sbgn
> http://svn.code.sf.net/p/libsbgn/code/trunk/test-files/
> PD//compartmentOrder2.sbgn
>
> example renderings:
>
> http://sysbioapps.dyndns.org/RenderComparison/Home/ProcessDescription
>
> cheers
> Frank
>
> On Fri, Oct 7, 2016 at 12:11 PM, Alexander Mazein <am...@ei...>
> wrote:
> > Than you, Nicolas.
> >
> > 1. How de we know it is in cytosol? Because it is a bit more in cytosol
> than
> > in extracellular space? The center of the shape is within a certain
> > compartment - this is how we read it?
> >
> > 2. SBGN-ML encodes coordinates AND depth? Would it be encoded that a) one
> > compartment is on the top of another and that b) CHT1 belongs to synaptic
> > button and not to synaptic cleft? Coordinates themselves do not clarify
> > that?
> >
> > Best regards,
> >
> > Alexander
> >
> > On Fri, Oct 7, 2016 at 11:33 AM, Nicolas Le Novere <n.l...@gm...
> >
> > wrote:
> >>
> >> On 07/10/16 09:50, Alexander Mazein wrote:
> >>>
> >>> Hello,
> >>
> >>
> >>>
> >>> In SBGN-ML file, how parent-child relations are handled?
> >>
> >>
> >>>
> >>> Please find the diagrams attached, they are posted as examples on
> >>> sbgn.org <http://sbgn.org> (http://sbgn.github.io/sbgn/examples).
> >>
> >>
> >>>
> >>> 1. In case of "Insulin signaling": how a software supposed to know
> >>> where complex IGF-IGFR belongs to? The membrane location is implied
> >>> but is not shown: should we avoid that? We probably should we update
> >>> our examples too?
> >>
> >>
> >> The "membrane location" is actually not part of SBGN. Here the complex
> >> IGF-IGFR belong to the cytosol compartment, not the membrane. If you
> want to
> >> explicitly put it in a membrane, you have to create a membrane
> compartment.
> >>
> >> Putting it anywhere does not change the semantics of the map. Think
> about
> >> all the maps with signalling lipids (e.g. PIP3 or DAG). In reality,
> they are
> >> in membrane, but are almost always represented as floating around in the
> >> cytosol. Because we don't care about their location. When the location
> is
> >> important (for instance to represent the recruitment of Akt) people
> >> generally represent a big membrane.
> >>
> >> However, SBGML-ML encodes the coordinates so the visual implicit
> location
> >> would be conserved. SBGN-ML stores all that is not SBGN :-)
> >>
> >>> 2. "Neuro-muscular junction": do we have depth in SBGN-ML? One
> >>> compartment is shown on the top of another.
> >>
> >>
> >> This drawing was made on purpose, to show that there is no compartment
> >> nesting in SBGN. The compartment is indeed on top of the other, not
> inside.
> >> The respective location needs not to be conserved. For an example of map
> >> with compartments in different respective locations, see:
> >>
> >> http://sbgn.github.io/sbgn/faq/pd#how-can-i-represent-
> multi-compartment-reactions-without-multiplying-the-ugly-
> compartment-boundaries
> >>
> >>
> >>
> >>>
> >>> Thank you,
> >>>
> >>> Alexander
> >>>
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> >>>
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> >>
> >>
> >> --
> >> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22
> 3AT
> >> Tel: +441223496433   Mob:+447833147074   n.l...@gm...
> >> orcid.org//0000-0002-6309-7327  http://lenoverelab.org/perso/lenov/
> >> Skype:n.lenovere  twitter:@lenovere  http://nlenov.wordpress.com/
> >>
> >>
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