Re: SBML L2v2 specification vote #4: References to controlled vocabularies
05 Jan '06 05:29
MH>> c) Tools reading SBML should behave as follows:
>> 2) If a tool understands only sboTerms and not the math
>> formulas, it is like other tools today that do not
>> understand SBML maths. Users should be made aware of
>> how the tool is interpreting the SBML, and it might be
>> perfectly acceptable to the tool's users. As with
>> other tools that do not interpret the math, the tool
>> would not pass all parts of the SBML validation suite
>> and would not be considered fully SBML compliant.
NLN>That goes in favor of possible kineticLaws with only sboTerms IMHO.
I disagree for the following reasons:-
If you have connectivity to the sboTerm and, (as some suggest) it has to
have a mathematical translation attached to it so that the symbols are in
a standard order, then there is no excuse for not writing the mathML.
If you don't have the connectivity, a <notes> <B>kineticlaw is mass
action</B></notes> avoids problems of spelling errors that we have
sometimes seen when using some of the named equations. It is at least as
informative as the kineticLaws with only sboTerms.
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