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Augustin Luna edited this page Jun 11, 2016 · 2 revisions

LibSBGN Meeting notes, March 10 2011

Present: Alice, Anatoly, Augustin, Falk, Martijn, Tobias

Report from Gatersleben

  • Alice, Tobias, Martijn and Falk met in Gatersleben. We worked on ER implementation, which resulted in several test cases and proposals.
  • We also started writing up a manuscript.
    • Anatoly asks if the library is mature enough for publication? - It is definitely mature enough for somebody who wants to add SBGN-ML support to a tool. Our main goal now is to draw new developers.
    • Augustin is in favor, he remarks that validation will be important for the reviewers.
    • Which journal to choose?

ACTION: Falk will send a presubmission enquiry.

Discussion of proposals

Proposals 1 and 3

  • Anatoly remarks that proposal 1 and 3 have the issue that the position of the port could be outside the parent arc, this must be validated. Alice: yes, and we've seen this problem in PD with arcs pointing to process nodes, the coordinates of the arc don't have to match the coordinates of the port.
  • Anatoly asks who is responsible for validation, the reader or the writer? - Both must do validation. You have to validate upon reading because external files could be corrupted. You have to validate upon writing to guard against bugs in your own code.
  • Anatoly asks if SBGN-ML can be used to store a graph without coordinates? - Alice: no it was decided a long time ago that this is outside the scope of LibSBGN.

Proposals 1 and 3 are passed without further discussion.

Proposals 2 and 4

  • Regarding proposal 2, the part before the implicit xor in an assignment arc doesn't really have a name, although it has its own look (i.e. no arrow head)
  • For proposal 4, there are two options to group elements belonging to an interaction. 4a proposes a utility function, 4b proposes a grouping element
    • Solution 4b has the advantage of being platform-independent
    • 4b looks a bit like a hyperedge
    • If we go for 4b, we might also want to revisit the solution for proposal 2, which has a similar hyperedge-like quality

ACTION: Alice will raise naming of assignment arcs to the SBGN editors.

ACTION: Martijn will adjust proposal 2, and put 4a and 4b up for a vote.

Proposal 5

  • Proposal 5: there isn't much opposition to this proposal anymore. Anatoly recognizes the extra effort that maintaining multiple namespaces bring.
  • GraphML was brought up. Why don't we use GraphML?
    • GraphML must be heavily extended for our purposes, these extensions will be proprietary (from a non-LibSBGN standpoint).
    • Tobias: exchange of GraphML between tools doesn't work in practice.
    • GraphML doesn't have tool support that is as good as XML proper.

ACTION: Martijn will put up proposal 5 for a vote for confirmation


  • We want to build a validation layer with schematron. For each validation rule, we'll need
    • an identifier
    • textual description
    • A schematron rule
    • SBGN-ML negative test-case
    • SBGN-ML positive test-case
  • We'll start gathering rules on this wiki page: ValidationRules
    • For Alice, this can go hand in hand with her SBGN editorial duties.
    • According to Augustin, textual description can be stored in schematron xml.
    • Augustin also suggests to also include "warning rules" for usage that is not wrong but goes against recommendation.
  • A schematron rule and ant target to run is already checked into subversion by Augustin

ACTION: everybody can start adding rules to the ValidationRules wiki page

ACTION: Martijn and Augustin will create a SchematronHowto wiki page

ACTION: everybody: read up on schematron before Harmony, start playing with a couple of rules.


  • After the release, we have to update our Roadmap. After some discussion, we came up with this:
    • Milestone 2: Support for ER and AF. Addition of schematron validation rules. Release targeted around COMBINE 2011.
    • Milestone 3: Detailed graphical specification, and extensibility
    • Milestone 4: Annotations, linking with external models (e.g. BioPAX), and MIRIAM compliance.
  • Extensibility support, i.e. opening SBGN-ML to third-party extensions, was briefly discussed.
    • Advantage: allows to support more use cases, which can draw in more users
    • Disadvantage: if an extension becomes too popular, this might cause the same issues as any non-standard format.
    • Falk: let's put exensibility support in M3, after finalizing ER and AF support.

Bug tracker update

  • The bug tracker was quickly updated to reflect the new roadmap.


  • During the Harmony meeting in NY we'll try to set aside a session just for creating rules. This could be any day but Friday, as Falk has to leave early.
  • We'll also set up an informal dinner on Sunday evening, for those who are there.

Final items

  • There won't be another online meeting before Harmony.
  • A recording of this meeting is available from Martijn upon request.
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