PD development

On reversible arcs

One of the questions discussed at COMBINE 2010 (as in several past meetings) was the representations of reversible processes. In PD L1V1, the "production" node is overloaded, meaning only production for an irreversible reaction, but meaning production *and* consumption for a reversible reaction. Several solutions have been discussed to disentangle the glyphs. The current survey addresses two related issues: 1) the representation of the consumption. 2) the representation of reversible processes. Note that contrary to the questions discussed in previous surveys, there was no consensus reached in COMBINE2010. We therefore do not seek ratification of a solution by the community to be implemented immediately. Rather we would like the opinion of everyone for future developments.

For a detailed presentation of the different solutions, see here

For the discussion about different solutions at HARMONY 2011, see here

A vote was opened on January 14th 2011 and closed on February 11th. 7 votes have been expressed.

At the question "Are-you satisfied with the current representation of irreversible reactions, where a consumption arc does not carry an arrowhead. Or would-you like to adopt a representation that expresses the direction of consumption?", voters answered:

At the question "The solutions for the reversible processes that have been discussed at COMBINE 2010 would be: 0. Current situation. We do not change anythings. Advantage: it is already implemented. There is an overload at the level of the arc, but this is clear at the level of the process. 1. three types of arcs: consumption, production and bidirectional. The bidirectional would carry the same arrowheads. This solution would work for both the current and alternative consumption arc (see question 2). 2. three types of arcs: bidirectional would carry half arrows to remind that they are both consuming and producing. The representation would be a bit different according to the answer to question 2. 3. Two arcs from the entity pool node to the process node, one input and production on either side. The representation would be a bit different according to the answer to question 2. This solution was discussed and rejected at SBGN -2 in Yokohama. A scaling out would transform 3a) into 0) and 3b) into 1). The number of arcs may become esthetically unbearable. 4. Annotation inside the process node (">"). This solution does not change the arcs themselves, but makes clear that the process is or not reversible. Multiple choices are allowed." voters answered:

Further discussion on that topic was held at HARMONY 2011.

Multiplication of source and sink

In SBGN PD L1 V1, the source and sink, although represented by the same symbol (empty set), are separate SBGN glyphs. They follow different syntactic rules. In addition, an "empty-set" symbol can only be connected to one arc, either consumption (for source) or production (for sink). Although this situation arose from the need to be semantically clear, it is contrary to many usage, results in a sometimes large duplication of glyphs, and does not fully correspond to what is intended (a boundary condition with size null).

The question that was debated at COMBINE 2010 was "Are all "empty-set" glyphs members of a clone?"

The conclusion of the (long and animated) discussion was Yes.

Therefore:

1. The glyph Sink and Source are to be replaced by a single glyph called Empty Set. The symbol associated to those glyph does not change.
2. A given "empty-set" symbol can be connected to one or more arcs.
3. The sources and the sinks symbols are all members of the same clone. They all represent the same underlying object.
4. The Empty Set glyph does not belong to a compartment.

A vote was organized to validate the result of the discussion. The question was "Do-you agree with the conclusions of the discussion held at COMBINE 2010, and the corresponding change in SBGN Process Description Level 1 Version 2 ". The vote was opened on December 16th 2010 and closed on December 31st. 11 votes have been filed. The results are:

Process Identity and Cloning

One of the questions discussed at COMBINE 2010 was the cloning of processes in PD. Because the identity of a process is currently only given by the arcs it connects to, the L1 V1.2 specification allows process to be cloned implicitly. Two processes linked to exactly the same EPNs are de facto graphical representation of the same underlying biological process. Alternative discussed:

1. Keep the current situation
2. Each process node is an independent node with its own identity
3. Allow users to decide and use a clone marker

Option is not sustainable, because one cannot represent two reactions with different intrinsic rates. At the end, it was felt that option 2 was the only non-confusing solution for the time being.

A vote was organized to validate the result of the discussion. The question was "When it comes to process node cloning, would-you prefer?". The vote was open on December 16th 2010 and closed on December 31st. 8 votes have been filed. The results are: