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"Tags" used in the SBML Test Suite

Tags are labels used to indicate properties of test cases in the SBML Test Suite. The labels are used in the NNNNN-model.m files describing every test case. Two different types of tags are used in the SBML Test Suite: component tags and test tags. For each test case, the relevant tags are listed after the componentTags: and testTags: fields, respectively, in the NNNNN-model.m file.

The following is an example of a model description file containing such tags:

(*
category:      Test
synopsis:      Basic single forward reaction with two species in one compartment
componentTags: Compartment, Species, Reaction, Parameter 
testTags:      InitialAmount, Concentration
testType:      TimeCourse
levels:        1.2, 2.1, 2.2, 2.3
generatedBy:   Analytic

The model contains one compartment called "compartment". There are two species called 
S1 and S2 and one parameter called k1. The model contains one reaction.
*)

The meaning of each possible tag is described below.

Component tags

Component tags describe the SBML elements that are present in the model. Most models are tagged with more than one component tag. (Readers may wonder whether these tags could be inferred simply by parsing the SBML content, and the answer is yes, they could. The tags are provided so that software systems can determine which components are used in each model without having to parse the model first. )

Component tags are also present for SBML Level 3 package constructs. Components from the Hierarchical Model Composition package are listed with a comp: prefix, and components from the Flux Balance Constraints package are listed with a fbc: prefix.

Tag name Level 1 Meaning Level 2 Meaning Level 3 Meaning
AlgebraicRule Model contains at least one AlgebraicRule component. Model contains at least one AlgebraicRule component. Model contains at least one AlgebraicRule component.
AssignmentRule Model contains at least one SpeciesConcentrationRule, CompartmentVolumeRule and/or ParameterRule with a type attribute value of scalar. Model contains at least one AssignmentRule component. Model contains at least one AssignmentRule component.
Compartment Model contains at least one Compartment component. Model contains at least one Compartment component. Model contains at least one Compartment component.
CSymbolAvogadro Not applicable Not applicable Model's mathematical formulas contain at least one reference to the csymbol for avogadro.
CSymbolDelay Not applicable Model's mathematical formulas contain at least one reference to the csymbol for delay. Model's mathematical formulas contain at least one reference to the csymbol for delay.
CSymbolTime Not applicable Model's mathematical formulas contain at least one reference to the csymbol for time. Model's mathematical formulas contain at least one reference to the csymbol for time.
EventNoDelay Not applicable Model contains at least one Event with no Delay subcomponent. Model contains at least one Event with no Delay subcomponent.
EventPriority Not applicable Not applicable Model contains at least one Event component with a Priority subcomponent.
EventWithDelay Not applicable Model contains at least one Event component with a Delay subcomponent. Model contains at least one Event component with a Delay subcomponent.
FunctionDefinition Not applicable Model contains at least one FunctionDefinition component. Model contains at least one FunctionDefinition component.
InitialAssignment Not applicable Model contains at least one InitialAssignment component. Model contains at least one InitialAssignment component.
Parameter Model contains at least one Parameter component. Model contains at least one Parameter component. Model contains at least one Parameter component.
RateRule Model contains at least one SpeciesConcentrationRule, CompartmentVolumeRule and/or ParameterRule with a type attribute value of rate. Model contains at least one RateRule component. Model contains at least one RateRule component.
Reaction Model contains at least one Reaction component. Model contains at least one Reaction component. Model contains at least one Reaction component.
Species Model contains at least one Species component. Model contains at least one Species component. Model contains at least one Species component.
StochiometryMath Not applicable Model contains at least one StoichiometryMath component (as a child of of a SpeciesReference element). Not applicable
comp:Deletion Not applicable Not applicable Model contains at least one Deletion component., in the 'comp' namespace
comp:ExternalModelDefinition Not applicable Not applicable Model contains at least one ExternalModelDefinition component., in the 'comp' namespace
comp:ModelDefintion Not applicable Not applicable Model contains at least one ModelDefintion component., in the 'comp' namespace
comp:Port Not applicable Not applicable Model contains at least one Port component., in the 'comp' namespace
comp:ReplacedBy Not applicable Not applicable Model contains at least one ReplacedBy component., in the 'comp' namespace
comp:ReplacedElement Not applicable Not applicable Model contains at least one ReplacedElement component., in the 'comp' namespace
comp:SBaseRef Not applicable Not applicable Model contains at least one SBaseRef component., in the 'comp' namespace
comp:Submodel Not applicable Not applicable Model contains at least one Submodel component., in the 'comp' namespace
fbc:FluxBound Not applicable Not applicable Model contains at least one FluxBound component., in the 'fbc' namespace
fbc:Objective Not applicable Not applicable Model contains at least one Objective component., in the 'fbc' namespace
fbc:FluxObjective Not applicable Not applicable Model contains at least one FluxObjective component., in the 'fbc' namespace


Test tags

Test tags may be combined in the same model. In fact, many of the SBML Test Suite test models are designed to explore escalating combinations of tests: one set of models may test a given tag, then another set of models may test that same tag plus a second tag, then a third model may test those two tags plus a third tag, in different combinations; and so on.

Some of these test tags test particular aspects of concepts introduced by a SBML Level 3 package. Tags that test aspects of the Hierarchical Model Composition package are prefixed with comp:, and tags that test aspects of the Flux Balance Constraints package are prefixed with fbc:.

Level:
Tag name 1 2 3 Meaning
0D-Compartment Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Compartment components that have a spatialDimensions attribute value of "0".
Amount Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test producing the output of Species components in terms of amounts (as opposed to concentrations or densities).
AssignedConstantStoichiometry Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of a model in which the stoichiometry for one or more SpeciesReference components is assigned a value by a stoichiometryMath element (in SBML Level 2), or by an initial assignment, assignment rule, or algebraic rule (in SBML Level 3); however, the value does not change over the course of the simulation.
AssignedVariableStoichiometry Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of a model in which the stoichiometry for one or more SpeciesReference components is assigned a value by a stoichiometryMath element (in SBML Level 2) or by a rate rule, assignment rule, algebraic rule, or event (in SBML Level 3), and the value is changed during the course of simulation.
BoundaryCondition Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Species components with values of "true" for their boundaryCondition attribute.
Concentration Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test producing the output of Species components in terms of concentrations.
ConstantSpecies Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Species components whose constant attribute value is "true".
ConversionFactors Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Species or Model components that set values for their conversionFactor attributes.
EventIsNotPersistent Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif Test interpretation of Event components that contain Trigger subcomponents whose persistent attribute value is "false" and whose mathematical formulas (i.e., the trigger conditions) revert to "false" before execution.
EventIsPersistent Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Event components that contain Trigger subcomponents whose persistent attribute value is "true" (in SBML Level 3) or whose triggers are persistent by definition (SBML Level 2), and whose mathematical formulas (i.e., the trigger conditions) revert to "false" before execution.
EventT0Firing Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Event components whose Trigger evaluates to "true" when time t = 0, and whether it fires at time t = 0 (possible in SBML Level 3; impossible in SBML Level 2) makes a difference to the output of the simulation.
EventUsesAssignmentTimeValues Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of models that contain at least one event whose useValuesFromTriggerTime attribute is set to "false", and this makes a difference in the output of the simulation.
EventUsesTriggerTimeValues Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of models that contain at least one event whose useValuesFromTriggerTime attribute is set to "true" (SBML Level 2 Version 4 and later), or which is assumed to use values from the event's trigger time by default (SBML Level 2 prior to Version 4), and it makes a difference in the output of the simulation.
FastReaction Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Reaction components whose fast attribute value is "true".
HasOnlySubstanceUnits Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Species components whose hasOnlySubstanceUnits attribute value is "true".
InitialValueReassigned Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of models where a component' initial value is set by an InitialAssignment, AssignmentRule, or AlgebraicRule.
LocalParameters Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Reaction components that have local parameter declarations within their KineticLaw subcomponents (i.e., <listofParameters> in SBML Levels 1–2 and <listOfLocalParameters> in Level 3).
MultiCompartment Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Model components with more than one Compartment component.
NonConstantCompartment Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Compartment components whose size changes during the course of simulation.
NonConstantParameter Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Parameter components whose value changes during the course of simulation.
NonUnityCompartment Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of Compartment components whose size is not numerically equal to "1.0". (Note that if the NonConstantCompartment tag is also present, then the value varies during simulation and may be equal to "1.0" at some point during simulation.)
NonUnityStoichiometry Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of SpeciesReference subcomponents in Reactions where the SpeciesReference stoichiometry is not numerically equal to "1.0" for at least part of the duration of the simulation.
RandomEventExecution Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif Test interpretation of models containing two or more events that execute at the same moment in time, and which have, at that moment, identical priorities, so that correct simulation of the model depends on randomly choosing which event to execute first.
ReversibleReaction Image:icon-checked.gif Image:icon-checked.gif Image:icon-checked.gif Test interpretation of models containing Reaction components whose reversible attribute values are "true", and whose KineticLaw evaluates to a negative value for at least part of the simulation.
SpeciesReferenceInMath Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The identifier of a SpeciesReference object is used in the <math> element of at least one SBML object elsewhere in the model.
UncommonMathML Image:icon-unchecked.gif Image:icon-checked.gif Image:icon-checked.gif The model contains at least one MathML construct that is not typically encountered in biological models, such as an unusual function, or a common function with an unusual number of arguments.
comp:ConversionFactor Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The model contains at least one replacedElement with a conversionFactor attribute, which affects the interpretation of the math in the model.
comp:ExtentConversionFactor Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The model contains at least one submodel with an extentConversionFactor attribute, which affects the interpretation of the reactions in the submodel.
comp:TimeConversionFactor Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The model contains at least one submodel with a timeConversionFactor attribute, which affects the interpretation of the math and the reactions in the submodel.
comp:SubmodelOutput Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The value of at least one non-replaced element of a submodel is requested in the output, denoted by the use of double-underscores in the requested element's ID.
fbc:BoundEqual Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The operation attribute of at least one FluxBound object is set to be equal
fbc:BoundGreaterEqual Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The operation attribute of at least one FluxBound object is set to be greaterEqual
fbc:BoundLessEqual Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The operation attribute of at least one FluxBound object is set to be lessEqual
fbc:MaximizeObjective Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The model contains at least one Objective object with a type attribute of maximize.
fbc:MinimizeObjective Image:icon-unchecked.gif Image:icon-unchecked.gif Image:icon-checked.gif The model contains at least one Objective object with a type attribute of minimize.

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This page was last modified 01:23, 18 July 2016.



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