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LibSBGN meeting during HARMONY, April 20 2011

  1. Introductions

Participants

Martijn, Stuart, Ugur, Huaiyu, Augustin, Gael, Martina, Alice (via Skype), Katja, Tobias

  1. SBGN-ML

   - ER    - AF    - PD: z ordering/containment

  • road map: release milestone 2 covering PD, ER and AF at COMBINE 2011

AF

  • development plan for AF: derive test cases from the specification ACTION: drawing test cases during HARMONY 2011 (Thursday or Friday)

ER

  • update on the status for ER

   proposals for ER were presented at HARMONY 2011    all proposal were accepted/discussed before HARMONY 2011

  • discussion about the name for the grouping element for ternary interactions

   proposed names: hyperarc, superglyph, hyperglyph, arcgroup    decision: arcgroup    proposal: outcomes should not be a child glyph of the circle element

but a top glyph in the group

PD: z ordering/containment

  • clarification of the PD specification regarding compartments

   There is always an implicit compartment (not visible) containing all

elements except process nodes and the empty set.

   If one compartment is drawn all elements have to be within a visible

compartment.

  • Compartment reference will be added as attribute to the glyph element - Canvas size (bounding box) will be added as attribute to the map element - We should have a vote to determine if the implicit compartment should be added as an actual element to the map or if it can be handled implicitly by the library. - Z order will be added as attribute to all elements (integer value 32 bit).

   proposal: the higher number is on top, numbers should be unique

  1. LibSBGN

Validation

  • Schematron might not be able to cover all validation rules which are needed (e.g. overlap). - advantage of schematron: language independent - 3 layers of validation needed?

   schema validation (implicitly)    schematron validation where possible    language dependent validation for all other rules

  • Some rules will be implemented in schematron as a test.

   SBGN syntactic rules    SBGN-ML syntactic rules    layout rules (overlap)    semantic rules (clone marker validation, reversible and irreversible

reaction at the same time) - validation rule numbering (this is a proposal to SBGN editors)

   We will use similar system as SBML.    Each rule has 5-digit id. First three digits are category, then 2

sequential digits. - categories numbering

   Categories 100-899 are for general SBGN use. SBGN-ML syntactic rules

start from category 900.

   Categories will be adapted from SBML (errors, recommendations, ...).        

  1. Paper
  • suggestion by Stuart, Katja, and Huaiyu to wait for a bigger paper
  1. Round table
  • Stuart: We should vote to increase the priority for defining color for graphics. Stuart wants to get to this before validation - Ugur: There should be interaction between people from Paxtools and LibSBGN regarding conversion. - Tobias: We need clarification about arc coordinates (Where does an arc end?) [Request by Frank]

           Proposal: The coordinates of an arc specify the end

points of the drawing and not the points where the arc is connected to glyphs (important for catalysis and inhibition).

Action items

  • ACTION: Tobias, Martijn, Huaiyu: create AF test-cases covering all aspects of AF. (everybody is welcome to join in)
  • ACTION: Martijn: implement "arcgroup" in ER examples, grouping interactions and making outcomes a child of the arcgroup wherever applicable.
  • ACTION: Tobias: hold a vote on compartmentRef: should it be required or not?
  • ACTION: Tobias: hold a vote on implicit compartments: should there be an explicit implicit compartment?
  • ACTION: Tobias: hold a vote on the zorder field, should it be optional? should they be unique?
  • ACTION: Martijn, Augustin: experiment with schematron rules to get a better idea of suitability (everybody is welcome to join in)
  • ACTION: Alice: Propose 5-digit rule numbering system to SBGN editors (also: unify and renumber existing lists of rules).
  • ACTION: Tobias: hold vote on increasing priority of color attributes
  • ACTION: Tobias: write detailed proposal on the end-points of arcs (make sure this contains really detailed drawings because we tend to speak past each other on this topic).
  • ACTION: Martijn will organize an online meeting in May (US-EU time)