SBGN-compliance

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How far are we from being SGBN-complaint? We don't need to support SBGN PD 
notation fully but supporting the basics would be nice. Please investigate how 
much work is involved to do so.

Original issue reported on code.google.com by ugurdogr...@gmail.com on 30 Apr 2012 at 12:35

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Original comment by ugurdogr...@gmail.com on 30 Apr 2012 at 12:35

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1. Single entry and exit points for inputs and outputs
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We don't want to support this because it messes up the layout.

2. Special glyphs for association and dissociation
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It does not make sense to use special glyphs for association and dissociation 
because reactions don't have to be pure associations or dissociations. Two 
things may come together while one of them being modified. So is this an 
association or a biochemical reaction? Or consider this reaction "A-B + C --> A 
+ B-C". Is this an association or dissociation? I think this is not a very well 
thought concept and I suggest we skip it.

3. Different glyphs for effector edges
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The shape of our effector edges is similar to "trigger" in SBGN-PD. We are 
color coding positive and negative edges without changing the shape. SBGN-PD 
inhibition is similar to PATIKA inhibitions. We can switch to this notation. 
Then if we also keep the color coding, it will be similar to PATIKA. I don't 
know how easy is to customize arrow ends in Chisio framework.

There are 3 more effector edge types in SBGN-PD: modulation, catalysis, and 
necessary stimulation. We can ignore those for now.

4. Small molecules are represented with circles
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As far as I understood, this is a feature that no one likes. ChiBE 
differentiates small molecules not with shape but with color coding. They have 
white background while PhysicalEntities are colored according to their 
EntityReference. We are drawing ubiquitous small molecules smaller than the 
normal ones.

Original comment by ozgunba...@gmail.com on 23 May 2012 at 9:17

• Changed state: Started

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I made small molecules rounder than macromolecules. The ones with short names 
(e.g. P) look like a circle, others look like something between an ellipse and 
a rounded rectangle. This didn't affect the length of labels.

I also implemented clone markers for ubiques. SBGN says that clone markers are 
necessary when the node is duplicated in the drawing. Currently we don't check 
if the ubique is duplicated. We draw the clone marker anyway. SBGN does not say 
clone markers should not be drawn if the node is not duplicated ;) Besides 
that, I still think that adding clone markers to duplicated ubiques do not 
improve anything in the graph, on the contrary, it harms it by adding a detail 
to the less emphasized part of the graph. This is something we should discuss 
with the SBGN community.

Original comment by ozgunba...@gmail.com on 6 Jun 2012 at 4:32

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SBGN "Nucleic Acid Feature" glyph corresponds to "DNARegion" and "RNARegion" in 
BioPAX. We can support it, but it is not urgent. There are no instance of these 
classes in Pathway Commons.

Original comment by ozgunba...@gmail.com on 6 Jun 2012 at 4:46

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Q: Is it possible to fully represent BioPAX Controls using SBGN logical 
operators?
A: No. In BioPAX a Control may be controlling other Controls, and specifically 
a Modulation controls a Catalysis. In SBGN, we cannot point an effector edge 
(like stimulation or inhibition) to an AND node. They have to point to a 
process node. So the closest representation is to AND the catalyzers and 
modulators. But in that case we lose the information of who is the catalyzer 
and who is the modulator.

Original comment by ozgunba...@gmail.com on 6 Jun 2012 at 5:37

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Implemented multimers. If a complex contains only one member with stoichiometry 
> 1, the complex is not drawn, but the member shown as a multimer. For other 
cases where the member have stoichiometry > 1, it is shown as multimer inside 
the complex.

Original comment by ozgunba...@gmail.com on 6 Jun 2012 at 10:58

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Merve, can you please implement SBGN effector edge glyphs? Current shape is 
similar to Stimulation. Addition to that, we need to have Catalysis, 
Modulation, and Inhibition glyphs. The mapping between BioPAX and SBGN should 
be:

BioPAX Catalysis --> SBGN Catalysis
BioPAX Modulation --> SBGN Modulation
BioPAX Control (anything other than Catalysis and Modulation) --> if 
(activating) SBGN Stimulation else SBGN Inhibition.

Original comment by ozgunba...@gmail.com on 8 Jun 2012 at 6:32

• Changed state: Accepted

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I now notice that ChiBE effector edge is not identical to SBGN stimulation 
glyph. They are identical to SBGN product glyph, and they both are identical to 
ChiBE product edges. ChiBE differentiates product and effector edges with 
color. So it looks like we also need to implement SBGN Stimulation glyph for 
the related subset of ChiBE effector edges. This glyph have a hollow interior, 
as opposed to the filled interior of product edge arrowheads.

Original comment by ozgunba...@gmail.com on 11 Jun 2012 at 8:59

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Merve and I implemented effector glyphs. Nothing else remains. Issue is fixed.

Original comment by ozgunba...@gmail.com on 13 Jun 2012 at 10:11

• Changed state: Fixed

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I just noticed that SBGN Modulation and BioPAX Modulation are totally different 
concepts, and they cannot simply be mapped to each other. 

BioPAX Modulation is defined as a secondary control over a Catalysis (not the 
Conversion). It has a sign. An example can be some ions making an enzyme more 
or less efficient. 

SBGN Modulation is a control over the process node, and it has no sign. SBGN 
advices to use Modulator when the sign of the control is not known. 

So I changed the mapping in ChiBE as:

if control is BioPAX Catalysis --> show with SBGN Catalysis
else if control sign is null --> show with SBGN Modulation
else if control is positive --> show with SBGN Stimulation
else (it is negative) --> show with SBGN Inhibition

Original comment by ozgunba...@gmail.com on 18 Jun 2012 at 7:25