sbml-qual Mailing List for Systems Biology Markup Language (SBML)

Hi Cole,

thanks Sarah for forwarding this question!

I don't see anything wrong with this model. The function to reach level 1
is "IFNgR OR IFNbR", which is encoded in GINsim (for technical reasons) as
"(IFNgR=0 AND IFNbR=1) OR IFNgR=1"

In this function, IFNbR does appear in the root apply, but not in all
sub-branches, which should be fine. Maybe the validator is being a bit too
picky here?

Best


On Mon, Sep 7, 2020 at 11:10 AM Sarah Keating <ske...@ca...> wrote:

>
> Hi Cole
>
> Best place for this question is the sbml qual list (included in forward).
>
> Sarah
>
>
> -------- Forwarded Message --------
> Subject: [sbml:sbml-specifications] #368 qual: Input Species not in
> FunctionTerm
> Date: Fri, 04 Sep 2020 17:04:50 -0000
> From: Cole Lyman <col...@us...>
> Reply-To: Ticket #368: qual: Input Species not in FunctionTerm
> <36...@sb...>
> To: Ticket #368: qual: Input Species not in FunctionTerm
> <36...@sb...>
>
>
>
>
> ---
>
> ** [sbml-specifications:#368] qual: Input Species not in FunctionTerm**
>
> **Status:** open
> **Group:** Reported-Proposed
> **Created:** Fri Sep 04, 2020 05:04 PM UTC by Cole Lyman
> **Last Updated:** Fri Sep 04, 2020 05:04 PM UTC
> **Owner:** nobody
> **Attachments:**
>
> -
> [Th17.sbml](
> https://sourceforge.net/p/sbml/sbml-specifications/368/attachment/Th17.sbml)
>
> (34.1 kB; application/octet-stream)
>
>
> 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.
>
>
> ---
>
> Sent from sourceforge.net because you indicated interest in
> <https://sourceforge.net/p/sbml/sbml-specifications/368/>
>
>
>
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> <https://sourceforge.net/auth/subscriptions/>
>
>
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>


-- 
Aurélien Naldi

Hi Cole

Best place for this question is the sbml qual list (included in forward).

Sarah


-------- Forwarded Message --------
Subject: [sbml:sbml-specifications] #368 qual: Input Species not in 
FunctionTerm
Date: Fri, 04 Sep 2020 17:04:50 -0000
From: Cole Lyman <col...@us...>
Reply-To: Ticket #368: qual: Input Species not in FunctionTerm 
<36...@sb...>
To: Ticket #368: qual: Input Species not in FunctionTerm 
<36...@sb...>




---

** [sbml-specifications:#368] qual: Input Species not in FunctionTerm**

**Status:** open
**Group:** Reported-Proposed
**Created:** Fri Sep 04, 2020 05:04 PM UTC by Cole Lyman
**Last Updated:** Fri Sep 04, 2020 05:04 PM UTC
**Owner:** nobody
**Attachments:**

- 
[Th17.sbml](https://sourceforge.net/p/sbml/sbml-specifications/368/attachment/Th17.sbml) 
(34.1 kB; application/octet-stream)


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.


---

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