qual: Input Species not in FunctionTerm

[sbmlsecretary]

I'm not sure if this is the best place to ask this question, I apologize if this question isn't relevant here and would appreciate any suggestions for a better place to ask it.

I have encountered a model (originally found here http://ginsim.org/node/41 and converted to SBML using GINSIM, the converted SBML file, Level 3 Version 1 Qual Version 1 is attached) that appears to be valid (according to libsbml and http://sbml.org/Facilities/Validator/. In this model, there are a number of Transitions that have a Species listed in the ListOfInputs, but then not appear in the corresponding FunctionTerm. I'm curious if this is documented behavior, or if this is an error in this model.

Here is an example from this model:

      <qual:transition qual:id="tr_STAT1">
        <qual:listOfInputs>
          <qual:input qual:qualitativeSpecies="IFNgR" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_STAT1_in_1"/>
          <qual:input qual:qualitativeSpecies="IFNbR" qual:transitionEffect="none" qual:sign="positive" qual:id="tr_STAT1_in_6"/>
        </qual:listOfInputs>
        <qual:listOfOutputs>
          <qual:output qual:qualitativeSpecies="STAT1" qual:transitionEffect="assignmentLevel" qual:id="tr_STAT1_out"/>
        </qual:listOfOutputs>
        <qual:listOfFunctionTerms>
          <qual:defaultTerm qual:resultLevel="0">
          </qual:defaultTerm>
          <qual:functionTerm qual:resultLevel="1">
            <math xmlns="http://www.w3.org/1998/Math/MathML">            
              <apply>
                <or/>
                <apply>
                  <and/>
                  <apply>
                    <eq/>
                    <ci> IFNgR </ci>
                    <cn type="integer"> 0 </cn>
                  </apply>
                  <apply>
                    <eq/>
                    <ci> IFNbR </ci>
                    <cn type="integer"> 1 </cn>
                  </apply>
                </apply>
                <apply>
                  <eq/>
                  <ci> IFNgR </ci>
                  <cn type="integer"> 1 </cn>
                  <!--Should there be a value for IFNbR in this apply group?-->
                </apply>
              </apply>
            </math>
                    </qual:functionTerm>
          <qual:functionTerm qual:resultLevel="2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">            
              <apply>
                <eq/>
                <ci> IFNgR </ci>
                <cn type="integer"> 2 </cn>
              </apply>
            </math>
                    </qual:functionTerm>
        </qual:listOfFunctionTerms>
      </qual:transition>

Perhaps if an input isn't listed then it applies to any value of that Species? I wasn't able to find this in the specification, so I don't want to jump to that conclusion unless this is accepted behavior.

Any input would be helpful! Thank you in advance.

Reported by: colelyman

Original Ticket: sbml/sbml-specifications//368

[luciansmith]

Th17.sbml.txt