Skip to content

FunctionTerm

One row of the transition table: a condition and the level it results in.

A function term is a condition and a level. The condition is ordinary MathML which returns a boolean value and reads the levels of the qualitative species of the transition; where it holds, the outputs take the result level of the term.

The terms of a transition are read in order and the first one which holds decides, so the list of terms with the default term behind it is the state transition table of the transition.

Attributes

attribute type required meaning specification
resultLevel integer required the level the outputs take where the condition of the term holds qual 3.6.5
math Math required the condition under which the term decides the level qual 3.6.5

Every element of a model also carries the common attributes of SBase.

resultLevel

The result level is a whole number which cannot be negative. An assignmentLevel output takes it as its new level, a production output gains it multiplied by its output level. The attribute is required.

The report shows it in the column "result level" of the table of the terms in the inspector of the transition.

  • 3020805 (error): The attribute 'qual:resultLevel' in <functionTerm> must be of the data type 'integer'.
  • 3020806 (error): The attribute 'qual:resultLevel' in <functionTerm> must not be negative.

math

The math is an expression which returns a boolean value, usually a comparison of the level of a species with the threshold of an input combined with and, or and not. A symbol in it is the identifier of a qualitative species, which means its level, of an input, which means its threshold level, or of an output, which means its output level.

The report renders the condition in the table of the terms in the inspector of the transition and links every element the condition reads.

  • 3010201 (warning): The MathML <math> element in a <functionTerm> object should evaluate to a value of type Boolean.
  • 3010202 (warning): The MathML <math> element in a <functionTerm> object should not use the <csymbol> elements 'time' and 'delay' as these explicitly introduce time into the model. As yet time is not considered within the Qualitative Models package specification.
  • 3020804 (error): A <functionTerm> object may contain exactly one MathML <math> element. No other elements from the SBML Level 3 Qualitative Models namespace are permitted on a <functionTerm> object.

Validation rules

  • 3020801 (error): A <functionTerm> object may have the optional 'metaid' and 'sboTerm' defined by SBML Level 3 Core. No other attributes from the SBML Level 3 Core namespace or the Qualitative Models namespace are permitted on a <functionTerm> object.
  • 3020802 (error): A <functionTerm> object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespaces are permitted on a <functionTerm>.
  • 3020803 (error): A <functionTerm> object must have the required attributes 'qual:resultLevel'. No other attributes from the SBML Level 3 Qualitative Models namespace are permitted on a <functionTerm> object.
  • 3020804 (error): A <functionTerm> object may contain exactly one MathML <math> element. No other elements from the SBML Level 3 Qualitative Models namespace are permitted on a <functionTerm> object.
  • Transition: what the level of a qualitative species becomes, and under which condition
  • DefaultTerm: the level of a transition in every state no function term covers
  • QualitativeSpecies: an entity of a qualitative model, which carries a level instead of an amount
  • Qualitative Models (qual): the package which describes a model whose entities carry a level

Specification

SBML Level 3 Package: Qualitative Models, Version 1 Release 1, Section 3.6.5 (Chaouiya et al. 2013, BMC Syst Biol 7:135).