Re: SBML L2v2 specification vote #4: References to controlled vocabularies
04 Jan '06 09:46
Hello Nicholas and Mike,
On Wed, 04 Jan 2006 11:02:15 +0000 (GMT)
Nicolas Le Novere <email@example.com> wrote:
> On Tue, 3 Jan 2006, Stefan Hoops wrote:
> >> Also suggest: If a tool does not understand SBO terms it should be
> >> able to ignore them completely, i.e., not required to write any of
> >> the SBO terms back out. I would suggest the following:
> > No, I disagree I see the sboTerm similar to annotation(s) where it
> > is good practise to keep them as long as you do not modify the
> > annotated object itself. Again, a little effort from the tool
> > developer helps the community a lot :)
> Very dangerous although I agree with the principle. The situation is a
> bit different than for the annotation elements. The content of the
> latter does not affect the way the model itself is interpreted, while
> bogus sboTerms would potentially result in a wrong interpretation.
You are both correct that this is slippery territory. I think as long as
the rate law or user defined function and the reaction are not modified
the sboTerms can be preserved (if it was correct to begin with).
However, one could envision a situation where the sboTerm attached to a
kinetic law or user defined function makes this rate law invalid for a
reaction. A simple example is changing a reversible reaction into an
irreversible without modifying the rate law.
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Bioinformatics Facility I
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606