Re: [sbml-qual] Design choices for SBML Logic Models

Sorry for not attaching the links to the Figures, here are the links in
case the Figures don't shown up in the previous email.
Figure 1
<https://1.bp.blogspot.com/-fs90lVuf2xw/WVypEN9zJGI/AAAAAAAAGfY/gsEbiGH228w9ocY1hgg0v7cDlwxpkllQgCLcBGAs/s320/or-simple.png>
Figure 2
<https://2.bp.blogspot.com/-u_5AitRQqfw/WVypIP5Rz0I/AAAAAAAAGfc/CeQGeo3Ua6gOmDqT8KJeuvbj_-ze3_ddQCLcBGAs/s1600/or-simple-new.png>
Figure 3
<https://4.bp.blogspot.com/-gmKV5sxzvbs/WWhtqdAzU_I/AAAAAAAAGiY/Rx1m2l5Z9Gw5aXIUmJn9tdg75udVW-R_wCLcBGAs/s1600/compartment.png>

Thank you again!
Haoran

On Fri, Jul 14, 2017 at 2:55 AM, Haoran Yu <hal...@gm...> wrote:

> Hi all,
>
> I have a couple of questions regarding how to design Logic Models when
> writing SBML from scratch. The questions might not be specifically for SBML
> 'qual', but I thought it might be convenient to have all my questions in
> one place rather than across different mailing lists.
>
> I'm currently implementing the following bidirectional converters between
> SBML and SBGN-ML:
>
> (1) SBML 'core'+'layout'+'render' <-> SBGN-ML PD
> (2) SBML 'core'+'qual' <-> SBGN-ML AF
>
> I have made some progress in both converters (1) and (2). All the
> questions I have is for the SBGN - > SBML conversion. The questions were
> posted on my blog over the last 2 weeks, Week 10
> <http://haleyyew-gsoc.blogspot.ca/2017/07/week-10.html> (section 2) and Week
> 11 <http://haleyyew-gsoc.blogspot.ca/2017/07/week-11.html> (section 1.1).
>
> The SBGN examples that motivated the questions are
> libsbgn/test-files/PD/or.sbgn
> <https://github.com/sbgn/libsbgn/blob/master/test-files/PD/or-simple.png>
> and libsbgn/test-files/AF/compartment.sbgn
> <https://github.com/sbgn/libsbgn/blob/master/test-files/AF/compartment.png>
>
> *Question 1:*
> There are 2 alternative mappings for SBGN PD->SBML for the example
> "or.sbgn" that involves choosing between 'layout' SpeciesGlyphs,
> ReactionGlyphs and GeneralGlyphs.
> I included a color coded diagram to illustrate the 2 mapping alternatives, Blue
> is SpeciesGlyphs, Green is ReactionGlyphs and Red is GeneralGlyphs.
> [Figure 1]
> [Figure 2]
>
> In Figure 1, I mapped the 'OR' SBGN Glyph to a ReactionGlyph ,and
> therefore all Arcs connecting the 'OR' glyph should become
> SpeciesReferences. But I found this mapping to be inadequate. Arc [1] is a
> ModifierSpeciesReference, and by *Rule 21111* in the
> *sbml-level-3-version-1-core-release-2* specification, the *species *attribute
> must refer to an existing Species. Which means Arc [1] refers to the 'OR'
> glyph and 'OR' must be a Species, otherwise Arc [1] can't be a
> ModifierSpeciesReference of the green reaction. That is why I had to make
> Arc [1] a GeneralGlyph instead without associating with any core Model
> components.
>
> In Figure 2, the reason that the 'OR' SBGN Glyph is changed from a
> ReactionGlyph to a SpeciesGlyph is to fix the problem with the Arc [1] in
> Figure 1. The 2 Logic Arcs below *Enzyme1 *and *Enzyme2 *become
> GeneralGlyphs, and the 'OR' SBGN Glyph becomes a Species. Then Arc [1] can
> be a ModifierSpeciesReference in the green reaction below, and associate
> with the 'OR' Species. The 2 Logic Arcs should be GeneralGlyphs because
> they are not real Model components anyway.
>
> I have implemented the mapping in Figure 1, but later changed the
> implementation to the mapping in Figure 2. *Since neither of the 2
> alternatives are perfect, I'm wondering if there is a third alternative
> that might be a better mapping? Or any suggestions that improve the
> mappings in either Figure 1 or Figure 2? *
>
>
> *Question 2:*
> While working on converter (2), the "compartment.sbgn" example in SBGN AF
> is more complex than I thought, and I have trouble mapping it to SBML
> 'qual'. I can map an SBGN Logic Arc to a SBML 'qual' Transition, where the
> Input and Output QualitativeSpecies could be anything connected to the
> Logic Arc.
> [Figure 3]
> ​
> But in the more complex case where many Logic Arcs meet with a Logic
> Operator, and then output an Arc to connect to the target Glyph. All of
> these Arcs and Glyphs would belong to a single Transition in 'qual'. Each
> Logic Arc has an Input. Then each of them would have a separate
> FunctionTerm. But each FunctionTerm must have a resultLevel. The problem is
> that in Logic Models, the possible Input and Ouput values could only be 0
> or 1. *Are there are only 2 possible FunctionTerms in all Transitions
> (resultLevel 0 or 1)?*
>
> Due to my current choice mapping: the 'AND' glyph would be mapped to a
> QualitativeSpecies, and for each SBGN Glyph that is connected to a Logic
> Arc, I map the Glyph to a QualitativeSpecies. Then I create SpeciesGlyphs
> that correspond to the QualitativeSpecies. But the 'AND' Logic Operator is
> part of a Transition, and the Arc that acts as the Output must connect to
> only one QualitativeSpecies. Therefore the 'AND' glyph does not have a
> mapping, i.e. it is lost in the mapped SBML Model.
>
> *Is there a better mapping that is able to preserve the 'AND' glyph? *
> I have thought about storing the 'AND' as part of the Math element in a
> FunctionTerm. But I have trouble coming up with a good algorithm to map the
> SBGN Glyph+Arcs to a Transition containing multiple FunctionTerms. It would
> be great if someone could help me trace an algorithm for mapping of the
> "compartment.sbgn" example.
>
>
> Thank you for all your help!
> Haoran
>
>