#109 Destinguishing flux bound parameters

[Andreas Dräger]

Hi SBO team,

Following the discussion on the SBML-Flux mailing list and the proposals brought up by Lucian Smith, I am here proposing a collection of new terms for the annotation of flux bounds.

As a consensus it was proposed that with version 2 of the SBML-FBC package we will move from specific FluxBound objects to generic Parameter objects. An appropriate annotation would be helpful to indicate the purpose and meaning of these flux bound parameters.

We propose there should be a root term "flux bound" under SBO:0000613 ("reaction parameter"). This term would have the following child terms:

• "default flux bound", this could indicate a parameter for the COBRA default flux bound (often a value like ±1000, ±99999 or ±∞).
• "flux bound from reaction", which would identify "a flux bound determined by the reaction itself"
• "flux bound from environment", this is to describe "a flux bound determined from environmental conditions"

It should be further discussed if each of these terms should be further extended with two children for "upper flux bound" and "lower flux bound" or if there should be upper/lower flux bound directly under "flux bound", of which each would have child terms described above. In order to keep it simple, it would already be sufficient just to have certain "flux bound" terms and make the distinction between upper/lower bounds in the model.

Thanks
Andreas

[Nick Juty]

After discussion with Andreas Dräger and Brett Olivier, the following terms have been created:
http://identifiers.org/biomodels.sbo/SBO:0000625
http://identifiers.org/biomodels.sbo/SBO:0000626
Thanks to both for their contribution,

cheers

Nick