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Here's my point: reactions may include more than one parameter, and
we need to identify which parameter is which. For example, suppose we
know that a reaction is Michaelis-Menten-Henri, and we know the k1
and the kD. We can not specify this information without giving the
entire math field, because even though the kineticlaw is optional,
if the kineticLaw is present the math is required, and the parameters
are inside of the kinetic law.

Because of this, the sboterms are completely redundant - we can't
have an sboterm on a parameter unless we also have the math.

For example, in the following the SBO terms can be safely ignored:

<reaction id="mmhex" name="Michaelis-Menten-Henri Example"
reversible="false" fast="false">
<listOfReactants>
<speciesReference species="S"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="P"/>
</listOfProducts>
<listOfModifiers/>
<kineticLaw timeUnits="time" substanceUnits="substance"
sboTerm="http://biomodels.net/SBO/#SBO:2222222"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci>k1</ci>
<ci>S</ci>
</apply>
<apply>
<plus/>
<ci>kD</ci>
<ci>S</ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k1" value="1" sboTerm="http://biomodels.net/SBO/
#SBO:3333333"//>
<parameter id="kD" value="1" sboTerm="http://biomodels.net/SBO/
#SBO:4444444"//>
</listOfParameters>
</kineticLaw>
</reaction>

but in the following, which is INVALID SBML because it does not have
a math field, All THREE sboterms are needed. If any of the SBOTerms
are omitted, its not possible to figure out the reaction law.

<reaction id="mmhex" name="Michaelis-Menten-Henri Example"
reversible="false" fast="false">
<listOfReactants>
<speciesReference species="S"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="P"/>
</listOfProducts>
<listOfModifiers/>
<kineticLaw timeUnits="time" substanceUnits="substance"
sboTerm="http://biomodels.net/SBO/#SBO:2222222"/>
<listOfParameters>
<parameter id="k1" value="1" sboTerm="http://biomodels.net/SBO/
#SBO:3333333"//>
<parameter id="kD" value="1" sboTerm="http://biomodels.net/SBO/
#SBO:4444444"//>
</listOfParameters>
</kineticLaw>
</reaction>


BES



On Dec 21, 2005, at 5:48 AM, Michael Hucka wrote:

> MH> But, won't a parameter declared as (e.g.) "rate
> MH> constant for first-order mass action" remain the same
> MH> no matter if the kinetic law itself is changed? Or
> MH> (e.g.) "Michaelis constant"?
>
> hds> But the name is OPTIONAL in the spec. There is
> hds> nothing to say that the parameter must be declared
> hds> with such a meaningfull name [...]
>
> Of course. The "declarations" I was referring to are
> sboTerm references, not the names. Parameter would look
> like the following example:
>
> <listOfParameters>
> <parameter id="k" sboTerm="http://biomodels.net/SBO/#SBO:
> 3333333"/>
> </listOfParameters>
>
> where the value of sboTerm is an identifier standing for
> (e.g.) "rate constant for first-order mass action" in the
> controlled vocabulary.
>
> MH
>