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Posts: 33
Registered:
March 2007
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Re: Did anyone care about SpeciesType?
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25 Aug '09 19:13
 
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The example in the L2v3r2 spec is:
<model>
34 ...
35 <listOfSpeciesTypes>
36 <speciesType id="ATP"/>
37 </listOfSpeciesTypes>
38 <listOfCompartments>
39 <compartment id="cytosol"/>
40 <compartment id="mitochon"/>
41 </listOfCopartments>
42 <listOfSpecies>
43 <species id="ATPc" speciesType="ATP" compartment="cytosol" initialConcentration="1"/>
44 <species id="ATPm" speciesType="ATP" compartment="mitochon" initialConcentration="2"/>
45 </listOfSpecies>
46 ...
47 </model>
This illustrates nicely one of the principal motivations for SpeciesType. In some sense SpeciesType was invented to fix the non-normalized concept of Species. For example, ATPc and ATPm (above) require the subscripts c and m because the species id must be unique, but at the same time the information conveyed by the c and m subscripts is already present in the definition of the species because the compartment is explicitly specified in the compartment attribute.
Among other things, SpeciesType permits software to infer that one of these species is "ATP in cytosol" and the other is "ATP in mitochon" instead of the redundant/nonsense species, "ATPc in cytosol."
Less importantly, but still usefully, SpeciesType allows software to draw an icon representing a compartment and then place correctly labeled icons within that compartment corresponding to the molecules that are present there. Returning to the Spec example, the software could draw two containers, one labeled cytosol and one labeled mitochon, and then place an icon inside each labeled ATP. In the absence of SpeciesType these molecule icons would have to be labeled ATPc and ATPm.
From my perspective, it would be a mistake to allow two species in the same compartment with the same SpeciesType. Would SBML ask us to write two differential equations for the species "ATP in cytosol" if multiple species ids have the same SpeciesType (ATP) and the same Compartment (cytosol)?
Allowing two species with the same SpeciesType in the same compartment seems to me to demolish all the gains that we made by introducing SpeciesType in the first place.
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