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Qualitative Models (qual)

The package which describes a model whose entities carry a level.

A qualitative model does not integrate rate laws over time. Its entities carry a level, a whole number which stands for a range of activity, and a rule says which level an entity takes next given the levels of the entities which act on it. It is how a regulatory network is written down when the kinetics are unknown, which is the usual case for a network of genes, and it covers the logical models of the Boolean school as well as Petri nets.

The qual package holds what such a model needs beyond the core: the qualitative species with their levels, and the transitions with the inputs they read, the outputs they change and the function terms which decide between them.

The report shows the qualitative species and the transitions of a model as sections of their own, the inputs of a transition with the sign of their influence, and the function terms as the transition table they are.

Validation rules

  • 3010101 (error): To conform to Version 1 of the Qualitative Models package specification for SBML Level 3, an SBML document must declare the use of the following XML Namespace: 'http://www.sbml.org/sbml/level3/version1/qual/version1'
  • 3010102 (error): Wherever they appear in an SBML document, elements and attributes from the Qualitative Models package must be declared either implicitly or explicitly to be in the XML namespace 'http://www.sbml.org/sbml/level3/version1/qual/version1'
  • 3020101 (error): In all SBML documents using the Qualitative Models package, the SBML object must include a value for the attribute 'qual:required' attribute.
  • 3020102 (error): The value of attribute 'qual:required' on the SBML object must be of the data type Boolean.
  • 3020103 (error): The value of attribute 'qual:required' on the SBML object must be set to 'true' if if the model contains any <transition> objects.
  • QualitativeSpecies: an entity of a qualitative model, which carries a level instead of an amount
  • Transition: what the level of a qualitative species becomes, and under which condition
  • Input: a qualitative species a transition reads, with the sign of its influence
  • Output: a qualitative species a transition changes, with the effect it has on it
  • FunctionTerm: one row of the transition table: a condition and the level it results in

Specification

SBML Level 3 Package: Qualitative Models, Version 1 Release 1 (Chaouiya et al. 2013, BMC Syst Biol 7:135).