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Input

A qualitative species a transition reads, with the sign of its influence.

An input names the qualitative species whose level a transition reads. Together with the outputs of the transitions the inputs are the influence graph of the model, the picture a reader of a regulatory model actually wants: who acts on whom, and whether the action activates or inhibits.

It is an element of the report and not a row of its transition, because the specification derives it from SBase: it may carry an identifier, a name, an SBO term, notes and annotations, and the reference to its species starts here, not at the transition around it.

Attributes

attribute type required meaning specification
qualitativeSpecies SIdRef required the species whose level the transition reads qual 3.6.1
thresholdLevel integer optional the level of the species at which the input acts qual 3.6.1
transitionEffect transitionInputEffect required whether the transition consumes the level of the species it reads qual 3.6.1
sign sign optional whether the influence of the species activates or inhibits qual 3.6.1

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

qualitativeSpecies

The attribute is required and names a qualitative species of the model. The report links it, and the inspector of that species shows the input under "referenced by", which is how the transitions that read an entity are found.

  • 3020508 (error): The value of the attribute 'qual:qualitativeSpecies' in an <input> object must be the identifier of an existing <qualitativeSpecies> object defined in the enclosing <model> object.

thresholdLevel

A multi valued species does not act the same way at every level: it acts on one target above one level and on another above a higher one. The threshold level is that level, and the identifier of the input stands for it in the math of a function term, so that a condition reads A >= theta_B_A instead of a bare number.

The report shows the threshold in the column "threshold" of the inputs of a transition and in the inspector.

Default: the threshold is written as a number in the math of the function terms.

  • 3020507 (error): The attribute 'qual:thresholdLevel' in <input> must be of the data type 'integer'.
  • 3020510 (error): The attribute 'qual:thresholdLevel' in <input> must not be negative.

transitionEffect

The effect is none, where the transition only reads the level, which is what a logical model does, or consumption, where the firing of the transition takes the level away from the species, which is what a Petri net does with the tokens of the places before a transition. The attribute is required.

The report shows the effect in the table of the inputs in the inspector of the transition.

  • 3020506 (error): The value of the attribute 'qual:transitionEffect' of an <input> object must conform to the syntax of the SBML data type 'transitionInputEffect' and may only take on the allowed values of 'transitionInputEffect' defined in SBML; that is, the value must be one of the following: 'none' or 'consumption'.
  • 3020509 (error): An <input> that refers to a <qualitativeSpecies> that has a 'qual:constant' attribute set to 'true' cannot have the attribute 'qual:transitionEffect' set to 'consumption'.

sign

The sign is positive for an activation, negative for an inhibition, dual where the species does both depending on the level of the others, and unknown where the file does not say. The specification adds it for visualisation: the mathematics of the model is in the function terms, and the sign is what lets a reader, or a drawing of the influence graph, see an arrow and a bar without reading the conditions.

The report shows the sign next to the species of the input in the column "inputs" of the transitions and in the table of the inputs in the inspector.

Default: the model says nothing about the direction of the influence.

  • 3020505 (error): The value of the attribute 'qual:sign' of an <input> object must conform to the syntax of the SBML data type 'sign' and may only take on the allowed values of 'sign' defined in SBML; that is, the value must be one of the following: 'positive', 'negative', 'dual' or 'unknown'.

Validation rules

  • 3010301 (error): (Extends validation rule #10301 in the SBML Level 3 Version 1 Core specification.) Within a <model> the values of the attributes 'id' and 'qual:id' on every instance of the following classes of objects must be unique across the set of all 'id' and 'qual:id' attribute values of all such objects in a model: the <model> itself, plus all contained <functionDefinition>, <compartment>, <species>, <reaction>, <speciesReference>, <modifierSpeciesReference>, <event>, and <parameter> objects, plus the <qualitativeSpecies>, <transition>, <input> and <output> objects defined by the Qualitative Models package.
  • 3020501 (error): An <input> 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 an <input> object.
  • 3020502 (error): An <input> 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 an <input>.
  • 3020503 (error): An <input> object must have the required attributes 'qual:qualitativeSpecies' as well as 'qual:transitionEffect' and may have the optional attributes 'qual:id', 'qual:name', 'qual:sign' and 'qual:thresholdLevel'. No other attributes from the SBML Level 3 Qualitative Models namespace are permitted on an <input> object.
  • Transition: what the level of a qualitative species becomes, and under which condition
  • QualitativeSpecies: an entity of a qualitative model, which carries a level instead of an amount
  • Output: a qualitative species a transition changes, with the effect it has on it
  • 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 3.6.1 (Chaouiya et al. 2013, BMC Syst Biol 7:135).