#142 Mathematical framework

closed
Michael Hucka
5
2014-05-27
2009-04-17
Andreas Dräger
No

In contrast to previous versions of SBML Level 4, the specification of Version 4 states that the SBO term for a model should be choosen from the "interaction" branch of the SBO (SBO:0000231), page 33, lines 14-22. However, on page 71, lines 19-27 describe the connection between the mathematical framework of how to simulate a model and the SBO terms of the kinetic laws. This seems to be a bit misleading due to the fact that "mathematical framework" should not longer be used for the annotation of a model. In my opinion, in this paragraphs statements referring to the mathematical framework of a model should be removed, especially because it seems that there may be conflicts of how to interprete a model anyways due to the problem that kinetic laws could point to a different mathematical framework than the model annotation (in previous Versions of Level 2).

Discussion

  • Michael Hucka
    Michael Hucka
    2009-05-09

    I am accepting this issue as valid.

     
  • Michael Hucka
    Michael Hucka
    2009-05-09

    • milestone: --> 678078
    • assigned_to: nobody --> mhucka
     
  • Michael Hucka
    Michael Hucka
    2009-05-09

    The paragraph on p.71 is wrong; it should not be there at all.

    When the specification was edited for L2v4 to change the SBO term assignment, we thought we banished all the old references to Model using mathematical framework, but apparently we missed this very large paragraph.

    Thank you for reporting this.

     
  • Stefan Hoops
    Stefan Hoops
    2009-05-09

    I am accepting this issue as valid.

     
  • Frank Bergmann
    Frank Bergmann
    2009-05-09

    I am accepting this issue as valid.

     
  • Sarah Keating
    Sarah Keating
    2009-05-11

    I am accepting this issue as valid.

     
  • Michael Hucka
    Michael Hucka
    2009-05-15

    Per our standard procedure, changing the status to Pending because 4/5 majority of the editors indicated they consider this a valid issue.

     
  • Michael Hucka
    Michael Hucka
    2009-05-15

    • status: open --> pending
     
  • Frank Bergmann
    Frank Bergmann
    2009-05-15

    I agree with the proposed change and that it should be done.

     
  • Sven Sahle
    Sven Sahle
    2009-05-15

    I am accepting this issue as valid.

     
  • Sven Sahle
    Sven Sahle
    2009-05-15

    I agree with the proposed change and that it should be done.

     
  • Sarah Keating
    Sarah Keating
    2009-05-15

    I agree with the proposed change and that it should be done.

     
  • Stefan Hoops
    Stefan Hoops
    2009-05-15

    I agree with the proposed change and that it should be done.

     
  • Michael Hucka
    Michael Hucka
    2009-05-16

    • milestone: 678078 --> Accepted:_Changes_with_conformance_implications
     
  • Michael Hucka
    Michael Hucka
    2009-05-16

    Per procedures, since 4/5 editors agree with the proposed change, the group of this item can be changed to "Accepted". It seems to me this may have performance implications for implementors, if they followed the spec blindlly in this section, so we had better call this "Accepted with conformance implications".

     
    • status: pending --> closed
     
  • This Tracker item was closed automatically by the system. It was
    previously set to a Pending status, and the original submitter
    did not respond within 730 days (the time period specified by
    the administrator of this Tracker).

     
  • Lucian Smith
    Lucian Smith
    2012-05-24

    • status: closed --> pending
     
  • Lucian Smith
    Lucian Smith
    2012-05-24

    Re-set to 'pending'. I believe this is an l2v5 issue.

     
  • Lucian Smith
    Lucian Smith
    2014-05-27

    • status: pending --> closed
    • Group: Accept-conformanc-implication --> Accept-conformance-implications
     
  • Lucian Smith
    Lucian Smith
    2014-05-27

    Fixed in SVN for L2v5, and will be part of the forthcoming release of that specification.