#96 Reversible and irreversible reaction or process

open
new term (59)
5
2013-02-13
2013-02-12
No

Layout graphs within SBML files can be more elaborated than the underlying computational models. In case that for the sake of simplicity a mathematical model has been reduced to very fiew reactions, it might still be useful to have a very detailled graphical representation of the entire pathway. In this case, many reaction glyphs might not have corresponding core reactions. Due to the design of the SBML layout extension it is in these cases not possible to indicate if the reaction glyph (without core reaction) is to be drawn as a reversible reaction. Therefore, a specialized SBO term "reversible reaction" would be useful. In addition, the term "irreversible reaction" would be a good complement. In case that the term "reaction" is too biochemical, it would be possible to name the terms "reversible process" and "irreversible process". See the specification of the SBML Layout Extension for details (http://otto.bioquant.uni-heidelberg.de/sbml/level2/20050425/SBMLLayoutExtension-20050425.pdf).

Discussion

  • Nick Juty

    Nick Juty - 2013-02-13

    I prefer the 'process' view, and would suggest something like:
    SBO:0000375 - process
    SBO:0000xxx - process directionality
    SBO:0000xxx - reversible process
    SBO:0000xxx - irreversible process

    I'll wait for some feedback, and look at the specification and see if that fits...
    Thanks for the suggestion!

     
  • Nick Juty

    Nick Juty - 2013-02-13
    • assigned_to: nobody --> njuty
     
  • Nicolas Le Novère

    I think that would brake the truth path. "process directionality" is not a "process". I would just create reversible process and irreversible process as children of process.

     

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