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Error Categories

This page lists all error, warning and informational diagnostic codes and messages produced by libSBML, the software underlying the Online SBML Validator. The diagnostics whose code numbers are between 10000 and 90000 are defined in the SBML specification documents; the ones with numbers below 10000 and above 90000 are specific to libSBML or this validation system and are not defined by the SBML specifications. The groups below provide finer-grained divisions in the diagnostics, for better comprehensibility.

In the tables below, the right-hand columns titled "L1V1", "L1V2", etc. refer to Levels and Versions of the SBML specifications, and the entries in each column refer to the severity of the condition in that particular Level and Version of SBML. The codes have the following meanings:

SymbolMeaning
Warning
Error
Fatal
Not applicable

For more information about the meanings of diagnostics numbered between 10000 and 90000, please consult the SBML specification documents relevant to the particularl Level and Version combination in question.

Internal errors

This group of errors concerns problems involving the libSBML software itself, or the underlying XML parser being used. This almost certainly indicates a software defect (i.e., bug) in libSBML. Please report occurrences of these errors to the libSBML developers.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
00000XMLUnknownErrorUnknown error
00101InternalXMLParserErrorInternal XML parser error
00102UnrecognizedXMLParserCodeUnrecognized XML parser code
00103XMLTranscoderErrorTranscoder error
10000UnknownErrorEncountered unknown internal libSBML error

Operating system errors

This group of diagnostic codes refers to problems that can be reported by the operating system where libSBML is running. This indicates something that is not a libSBML error, but rather, is outside of the control of libSBML.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
00001XMLOutOfMemoryOut of memory
00002XMLFileUnreadableFile unreadable
00003XMLFileUnwritableFile unwritable
00004XMLFileOperationErrorFile operation error
00005XMLNetworkAccessErrorNetwork access error

XML errors

This group of diagnostic codes refers to problems with the XML content of the SBML file or data stream. This usually arises from malformed XML, and is detected at a very low level in the XML parsing system. Further interpretation of SBML is aborted if this type of error is encountered.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
01001MissingXMLDeclMissing XML declaration
01002MissingXMLEncodingMissing XML encoding attribute
01003BadXMLDeclBad XML declaration
01004BadXMLDOCTYPEBad XML DOCTYPE
01005InvalidCharInXMLInvalid character
01006BadlyFormedXMLBadly formed XML
01007UnclosedXMLTokenUnclosed token
01008InvalidXMLConstructInvalid XML construct
01009XMLTagMismatchXML tag mismatch
01010DuplicateXMLAttributeDuplicate attribute
01011UndefinedXMLEntityUndefined XML entity
01012BadProcessingInstructionBad XML processing instruction
01013BadXMLPrefixBad XML prefix
01014BadXMLPrefixValueBad XML prefix value
01015MissingXMLRequiredAttributeMissing required attribute
01016XMLAttributeTypeMismatchAttribute type mismatch
01017XMLBadUTF8ContentBad UTF8 content
01018MissingXMLAttributeValueMissing attribute value
01019BadXMLAttributeValueBad attribute value
01020BadXMLAttributeBad XML attribute
01021UnrecognizedXMLElementUnrecognized XML element
01022BadXMLCommentBad XML comment
01023BadXMLDeclLocationBad XML declaration location
01024XMLUnexpectedEOFUnexpected EOF
01025BadXMLIDValueBad XML ID value
01026BadXMLIDRefBad XML IDREF
01027UninterpretableXMLContentUninterpretable XML content
01028BadXMLDocumentStructureBad XML document structure
01029InvalidAfterXMLContentInvalid content after XML content
01030XMLExpectedQuotedStringExpected quoted string
01031XMLEmptyValueNotPermittedEmpty value not permitted
01032XMLBadNumberBad number
01033XMLBadColonColon character not permitted
01034MissingXMLElementsMissing XML elements
01035XMLContentEmptyEmpty XML content

Overall SBML conformance issues

This group of diagnostic codes is concerned with general and overall issues of conformance to the relevant SBML specifications.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
10101NotUTF8File does not use UTF-8 encoding
10102UnrecognizedElementEncountered unrecognized element
10103NotSchemaConformantDocument does not conform to the SBML XML schema
10104L3NotSchemaConformantDocument is not well-formed XML
10401MissingAnnotationNamespaceMissing declaration of the XML namespace for the annotation
10402DuplicateAnnotationNamespacesMultiple annotations using the same XML namespace
10403SBMLNamespaceInAnnotationThe SBML XML namespace cannot be used in an Annotation object
10404MultipleAnnotationsOnly one Annotation object is permitted under a given SBML object
10801NotesNotInXHTMLNamespaceNotes must be placed in the XHTML XML namespace
10802NotesContainsXMLDeclXML declarations are not permitted in Notes objects
10803NotesContainsDOCTYPEXML DOCTYPE elements are not permitted in Notes objects
10804InvalidNotesContentInvalid notes content found
10805OnlyOneNotesElementAllowedOnly one Notes subobject is permitted on a given SBML object
20101InvalidNamespaceOnSBMLInvalid XML namespace for the SBML container element
20102MissingOrInconsistentLevelMissing or inconsistent value for the 'level' attribute
20103MissingOrInconsistentVersionMissing or inconsistent value for the 'version' attribute
20104PackageNSMustMatchInconsistent or invalid SBML Level/Version for the package namespace declaration
20105LevelPositiveIntegerThe 'level' attribute must have a positive integer value
20106VersionPositiveIntegerThe 'version' attribute must have a positive integer value
20108AllowedAttributesOnSBMLInvalid attribute found on the SBML container element
20109L3PackageOnLowerSBMLAn L3 package ns found on the SBML container element
20201MissingModelNo model definition found
20202IncorrectOrderInModelIncorrect ordering of components within the Model object
20203EmptyListElementEmpty ListOf___ object found
20409EmptyListOfUnitsAn empty list of Unit objects is not permitted in a UnitDefinition object
21002IncorrectOrderInConstraintSubobjects inside the Constraint object are not in the prescribed order
21003ConstraintNotInXHTMLNamespaceA Constraint's Message subobject must be in the XHTML XML namespace
21004ConstraintContainsXMLDeclXML declarations are not permitted within Constraint's Message objects
21005ConstraintContainsDOCTYPEXML DOCTYPE elements are not permitted within Constraint's Message objects
21006InvalidConstraintContentInvalid content for a Constraint object's Message object
21102IncorrectOrderInReactionSubobjects inside the Reaction object are not in the prescribed order
21103EmptyListInReactionReaction components, if present, cannot be empty
21104InvalidReactantsProductsListInvalid object found in the list of reactants or products
21105InvalidModifiersListInvalid object found in the list of modifiers
21122IncorrectOrderInKineticLawIncorrect ordering of components in the KineticLaw object
21123EmptyListInKineticLawThe list of parameters, if present, cannot be empty
21205IncorrectOrderInEventIncorrect ordering of components in Event object
99101InvalidSBMLLevelVersionUnknown Level+Version combination of SBML
99104AnnotationNotesNotAllowedLevel1Annotation objects on the SBML container element are not permitted in SBML Level 1
99401RDFMissingAboutTagRDF missing the <about> tag
99402RDFEmptyAboutTagRDF empty <about> tag
99403RDFAboutTagNotMetaidRDF <about> tag is not metaid
99404RDFNotCompleteModelHistoryRDF does not contain valid ModelHistory
99405RDFNotModelHistoryRDF does not result in a ModelHistory
99406AnnotationNotElementAnnotation must contain element

General SBML consistency issues

This group of diagnostic codes concerns the correct use of SBML constructs according to the relevant SBML specifications.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
20204NeedCompartmentIfHaveSpeciesThe presence of a species requires a compartment
20205OneOfEachListOfOnly one of each kind of ListOf___ object is allowed inside a Model object
20206OnlyFuncDefsInListOfFuncDefsOnly FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions
20207OnlyUnitDefsInListOfUnitDefsOnly UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects
20208OnlyCompartmentsInListOfCompartmentsOnly Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects
20209OnlySpeciesInListOfSpeciesOnly Species, Notes and Annotation objects are allowed in ListOfSpecies objects
20210OnlyParametersInListOfParametersOnly Parameter, Notes and Annotation objects are allowed in ListOfParameters objects
20211OnlyInitAssignsInListOfInitAssignsOnly InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects
20212OnlyRulesInListOfRulesOnly Rule, Notes and Annotation objects are allowed in ListOfRules objects
20213OnlyConstraintsInListOfConstraintsOnly Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects
20214OnlyReactionsInListOfReactionsOnly Reaction, Notes and Annotation objects are allowed in ListOfReactions objects
20215OnlyEventsInListOfEventsOnly Event, Notes and Annotation objects are allowed in ListOfEvents objects
20216L3ConversionFactorOnModelA 'conversionFactor' attribute value must reference a Parameter object
20217L3TimeUnitsOnModelInvalid 'timeUnits' attribute value
20218L3VolumeUnitsOnModelInvalid 'volumeUnits' attribute value
20219L3AreaUnitsOnModelInvalid 'areaUnits' attribute value
20220L3LengthUnitsOnModelInvalid 'lengthUnits' attribute value
20221L3ExtentUnitsOnModelInvalid 'extentUnits' attribute value
20222AllowedAttributesOnModelInvalid attribute found on the Model object
20223AllowedAttributesOnListOfFuncsInvalid attribute found on the ListOfFunctionDefinitions object
20224AllowedAttributesOnListOfUnitDefsInvalid attribute found on the ListOfUnitDefinitions object
20225AllowedAttributesOnListOfCompsInvalid attribute found on the ListOfCompartments object
20226AllowedAttributesOnListOfSpeciesInvalid attribute found on the ListOfSpecies object
20227AllowedAttributesOnListOfParamsInvalid attribute found on the ListOfParameters object
20228AllowedAttributesOnListOfInitAssignInvalid attribute found on the ListOfInitialAssignments object
20229AllowedAttributesOnListOfRulesInvalid attribute found on the ListOfRules object
20230AllowedAttributesOnListOfConstraintsInvalid attribute found on the ListOfConstraints object
20231AllowedAttributesOnListOfReactionsInvalid attribute found on the ListOfReactions object
20232AllowedAttributesOnListOfEventsInvalid attribute found on the ListOfEvents object
20301FunctionDefMathNotLambdaInvalid expression found in the function definition
20302InvalidApplyCiInLambdaInvalid forward reference in the MathML <apply><ci>...</ci></apply> expression
20303RecursiveFunctionDefinitionRecursive function definitions are not permitted
20304InvalidCiInLambdaInvalid <ci> reference found inside the <lambda> mathematical formula
20305InvalidFunctionDefReturnTypeA function's return type must be either a number or a Boolean
20306OneMathElementPerFuncA FunctionDefinition object must contain one <math> element
20307AllowedAttributesOnFuncInvalid attribute found on the FunctionDefinition object
20401InvalidUnitDefIdInvalid 'id' attribute value for a UnitDefinition object
20402InvalidSubstanceRedefinitionInvalid redefinition of built-in type 'substance'
20403InvalidLengthRedefinitionInvalid redefinition of built-in type 'length'
20404InvalidAreaRedefinitionInvalid redefinition of built-in type name 'area'
20405InvalidTimeRedefinitionInvalid redefinition of built-in type name 'time'
20406InvalidVolumeRedefinitionInvalid redefinition of built-in type name 'volume'
20407VolumeLitreDefExponentNotOneMust use 'exponent'=1 when defining 'volume' in terms of litres
20408VolumeMetreDefExponentNot3Must use 'exponent'=3 when defining 'volume' in terms of metres
20410InvalidUnitKindInvalid value for the 'kind' attribute of a UnitDefinition object
20411OffsetNoLongerValidUnit attribute 'offset' is not supported in this Level+Version of SBML
20412CelsiusNoLongerValidUnit name 'Celsius' is not defined in this Level+Version of SBML
20413EmptyUnitListElementA ListOfUnits object must not be empty
20414OneListOfUnitsPerUnitDefAt most one ListOfUnits object is allowed inside a UnitDefinition object
20415OnlyUnitsInListOfUnitsOnly Unit, Notes and Annotation objects are allowed in ListOfUnits objects
20419AllowedAttributesOnUnitDefinitionInvalid attribute found on the UnitDefinition object
20420AllowedAttributesOnListOfUnitsInvalid attribute found on the ListOfUnits object
20421AllowedAttributesOnUnitInvalid attribute found on the Unit object
20501ZeroDimensionalCompartmentSizeInvalid use of the 'size' attribute for a zero-dimensional compartment
20502ZeroDimensionalCompartmentUnitsInvalid use of the 'units' attribute for a zero-dimensional compartment
20503ZeroDimensionalCompartmentConstZero-dimensional compartments must be defined to be constant
20504UndefinedOutsideCompartmentInvalid value for the 'outside' attribute of a Compartment object
20505RecursiveCompartmentContainmentRecursive nesting of compartments via the 'outside' attribute is not permitted
20506ZeroDCompartmentContainmentInvalid nesting of zero-dimensional compartments
20507Invalid1DCompartmentUnitsInvalid value for the 'units' attribute of a one-dimensional compartment
20508Invalid2DCompartmentUnitsInvalid value for the 'units' attribute of a two-dimensional compartment
20509Invalid3DCompartmentUnitsInvalid value for the 'units' attribute of a three-dimensional compartment
20510InvalidCompartmentTypeRefInvalid value for the 'compartmentType' attribute of a compartment
20517AllowedAttributesOnCompartmentInvalid attribute found on Compartment object
20601InvalidSpeciesCompartmentRefInvalid value found for Species 'compartment' attribute
20602HasOnlySubsNoSpatialUnitsAttribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true'
20603NoSpatialUnitsInZeroDAttribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional
20604NoConcentrationInZeroDAttribute 'initialConcentration' must not be set if the compartment is zero-dimensional
20605SpatialUnitsInOneDInvalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment
20606SpatialUnitsInTwoDInvalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment
20607SpatialUnitsInThreeDInvalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment
20608InvalidSpeciesSusbstanceUnitsInvalid value for a Species 'units' attribute
20609BothAmountAndConcentrationSetCannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously
20610NonBoundarySpeciesAssignedAndUsedCannot use a non-boundary species in both reactions and rules simultaneously
20611NonConstantSpeciesUsedCannot use a constant, non-boundary species as a reactant or product
20612InvalidSpeciesTypeRefInvalid value for the 'speciesType' attribute of a species
20613MultSpeciesSameTypeInCompartmentCannot have multiple species of the same species type in the same compartment
20614MissingSpeciesCompartmentMissing value for the 'compartment' attribute
20615SpatialSizeUnitsRemovedAttribute 'spatialSizeUnits' is not supported in this Level+Version of SBML
20617ConversionFactorOnSpeciesInvalid value for the 'conversionFactor' attribute
20623AllowedAttributesOnSpeciesInvalid attribute found on Species object
20701InvalidParameterUnitsInvalid value for the 'units' attribute of a Parameter object
20705ConversionFactorMustConstantA conversion factor must reference a Parameter object declared to be a constant
20706AllowedAttributesOnParameterInvalid attribute found on Parameter object
20801InvalidInitAssignSymbolInvalid value for the 'symbol' attribute of an InitialAssignment object
20802MultipleInitAssignmentsMultiple initial assignments for the same 'symbol' value are not allowed
20803InitAssignmentAndRuleForSameIdCannot set a value using both an initial assignment and an assignment rule simultaneously
20804OneMathElementPerInitialAssignAn InitialAssignment object must contain one <math> element
20805AllowedAttributesOnInitialAssignInvalid attribute found on an InitialAssignment object
20901InvalidAssignRuleVariableInvalid value for the 'variable' attribute of an AssignmentRule object
20902InvalidRateRuleVariableInvalid value for the 'variable' attribute of a RateRule object
20903AssignmentToConstantEntityAn assignment rule cannot assign an entity declared to be constant
20904RateRuleForConstantEntityA rate rule cannot assign an entity declared to be constant
20906CircularRuleDependencyCircular dependencies involving rules and reactions are not permitted
20907OneMathElementPerRuleA rule object must contain one <math> element
20908AllowedAttributesOnAssignRuleInvalid attribute found on an AssignmentRule object
20909AllowedAttributesOnRateRuleInvalid attribute found on a RateRule object
20910AllowedAttributesOnAlgRuleInvalid attribute found on an AlgebraicRule object
21001ConstraintMathNotBooleanA Constraint object's <math> must evaluate to a Boolean value
21007OneMathElementPerConstraintA Constraint object must contain one <math> element
21008OneMessageElementPerConstraintA Constraint object must contain one Message subobject
21009AllowedAttributesOnConstraintInvalid attribute found on Constraint object
21101NoReactantsOrProductsCannot have a reaction with neither reactants nor products
21106OneSubElementPerReactionA Reaction object can only contain one of each allowed type of object
21107CompartmentOnReactionInvalid value for the Reaction 'compartment' attribute
21110AllowedAttributesOnReactionInvalid attribute for a Reaction object
21111InvalidSpeciesReferenceInvalid 'species' attribute value in SpeciesReference object
21113BothStoichiometryAndMathThe 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive
21116AllowedAttributesOnSpeciesReferenceInvalid attribute found on the SpeciesReference object
21117AllowedAttributesOnModifierInvalid attribute found on the ModifierSpeciesReference object
21121UndeclaredSpeciesRefUnknown species referenced in the kinetic law <math> formula
21124NonConstantLocalParameterParameters local to a KineticLaw object must have a 'constant' attribute value of 'true'
21125SubsUnitsNoLongerValidAttribute 'substanceUnits' is not supported in this Level+Version of SBML
21126TimeUnitsNoLongerValidAttribute 'timeUnits' is not supported in this Level+Version of SBML
21127OneListOfPerKineticLawOnly one ListOfLocalParameters object is permitted within a KineticLaw object
21128OnlyLocalParamsInListOfLocalParamsOnly LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects
21129AllowedAttributesOnListOfLocalParamInvalid attribute found on the ListOfLocalParameters object
21130OneMathPerKineticLawOnly one <math> element is allowed in a KineticLaw object
21131UndeclaredSpeciesInStoichMathUnknown species referenced in the StoichiometryMath object's <math> formula
21132AllowedAttributesOnKineticLawInvalid attribute found on the KineticLaw object
21150AllowedAttributesOnListOfSpeciesRefInvalid attribute found on the ListOfSpeciesReferences object
21151AllowedAttributesOnListOfModsInvalid attribute found on the ListOfModifiers object
21172AllowedAttributesOnLocalParameterInvalid attribute found on the LocalParameter object
21201MissingTriggerInEventThe Event object is missing a Trigger subobject
21202TriggerMathNotBooleanA Trigger object's <math> expression must evaluate to a Boolean value
21203MissingEventAssignmentThe Event object is missing an EventAssignment subobject
21204TimeUnitsEventUnits referenced by 'timeUnits' attribute are not compatible with units of time
21206ValuesFromTriggerTimeNeedDelayAttribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay
21207DelayNeedsValuesFromTriggerTimeThe use of a Delay object requires the Event attribute 'useValuesFromTriggerTime'
21209OneMathPerTriggerA Trigger object must have one <math> element
21210OneMathPerDelayA Delay object must have one <math> element
21211InvalidEventAssignmentVariableInvalid 'variable' attribute value in Event object
21212EventAssignmentForConstantEntityAn EventAssignment object cannot assign to a component having attribute 'constant'='true'
21213OneMathPerEventAssignmentAn EventAssignment object must have one <math> element
21214AllowedAttributesOnEventAssignmentInvalid attribute found on the EventAssignment object
21221OnlyOneDelayPerEventAn Event object can only have one Delay subobject
21222OneListOfEventAssignmentsPerEventAn Event object can only have one ListOfEventAssignments subobject
21223OnlyEventAssignInListOfEventAssignOnly EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments
21224AllowedAttributesOnListOfEventAssignInvalid attribute found on the ListOfEventAssignments object
21225AllowedAttributesOnEventInvalid attribute found on the Event object
21226AllowedAttributesOnTriggerInvalid attribute found on the Trigger object
21227AllowedAttributesOnDelayInvalid attribute found on the Delay object
21228PersistentNotBooleanThe Trigger attribute 'persistent' must evaluate to a Boolean value
21229InitialValueNotBooleanThe Trigger attribute 'initialValue' must evaluate to a Boolean value
21230OnlyOnePriorityPerEventAn Event object can only have one Priority subobject
21231OneMathPerPriorityA Priority object must have one <math> element
21232AllowedAttributesOnPriorityInvalid attribute found on the Priority object
99106InvalidRuleOrderingInvalid ordering of rules
99107RequiredPackagePresentThe SBML document requires an SBML Level 3 package unavailable in this software
99108UnrequiredPackagePresentThe SBML document uses an SBML Level 3 package unavailable in this software
99109PackageRequiredShouldBeFalseThis package expects required to be false
99127SubsUnitsAllowedInKLDisallowed value for attribute 'substanceUnits' on KineticLaw object
99128TimeUnitsAllowedInKLDisallowed value for attribute 'timeUnits' on KineticLaw object
99129FormulaInLevel1KLOnly predefined functions are allowed in SBML Level 1 formulas
99130L3SubstanceUnitsOnModelInvalid 'substanceUnits' attribute value
99206TimeUnitsRemovedThis Level+Version of SBML does not support the 'timeUnits' attribute on Event objects
99301NoTimeSymbolInFunctionDefUse of <csymbol> for 'time' not allowed within FunctionDefinition objects
99302NoBodyInFunctionDefThere must be a <lambda> body within the <math> element of a FunctionDefinition object
Codes for SBML Level 3 package "comp"
comp-10101CompNSUndeclaredThe comp ns is not correctly declared
comp-10102CompElementNotInNsElement not in comp namespace
comp-20101CompOneListOfReplacedElementsOnly one <listOfReplacedElements> allowed.
comp-20102CompLOReplaceElementsAllowedElementsAllowed children of <listOfReplacedElements>
comp-20103CompLOReplacedElementsAllowedAttribsAllowed <listOfReplacedElements> attributes
comp-20104CompEmptyLOReplacedElements<listOfReplacedElements> must not be empty
comp-20105CompOneReplacedByElementOnly one <replacedBy> object allowed.
comp-20201CompAttributeRequiredMissingRequired comp:required attribute on <sbml>
comp-20202CompAttributeRequiredMustBeBooleanThe comp:required attribute must be Boolean
comp-20203CompRequiredTrueIfElementsRemainThe comp:required attribute must be 'true' if math changes
comp-20204CompRequiredFalseIfAllElementsReplacedThe comp:required attribute must be 'false' if math does not change
comp-20205CompOneListOfModelDefinitionsOnly one <listOfModelDefinitions> allowed.
comp-20206CompEmptyLOModelDefs<listOfModelDefinitions> and <listOfExternalModelDefinitions> must not be empty
comp-20207CompLOModelDefsAllowedElementsOnly <modelDefinitions> in <listOfModelDefinitions>
comp-20208CompLOExtModelDefsAllowedElementsOnly <externalModelDefinitions> in <listOfExternalModelDefinitions>
comp-20209CompLOModelDefsAllowedAttributesAllowed <listOfModelDefinitions> attributes
comp-20210CompLOExtModDefsAllowedAttributesAllowed <listOfExternalModelDefinitions> attributes
comp-20211CompOneListOfExtModelDefinitionsOnly one <listOfExternalModelDefinitions> allowed.
comp-20212CompAttributeRequiredMustBeTrueThe comp:required attribute must be 'true'
comp-20301CompExtModDefAllowedCoreAttributesAllowed <externalModelDefinitions> core attributes
comp-20302CompExtModDefAllowedElementsAllowed <externalModelDefinitions> elements
comp-20303CompExtModDefAllowedAttributesAllowed <externalModelDefinitions> attributes
comp-20304CompReferenceMustBeL3External models must be L3
comp-20305CompModReferenceMustIdOfModel'modelRef' must be the 'id' of a model in the 'source' document
comp-20306CompExtModMd5DoesNotMatchMD5 checksum does not match the 'source' document
comp-20307CompInvalidSourceSyntaxThe 'comp:source' attribute must be of type 'anyURI'
comp-20308CompInvalidModelRefSyntaxThe 'comp:modelRef' attribute must have the syntax of 'SId'
comp-20309CompInvalidMD5SyntaxThe 'comp:md5' attribute must have the syntax of 'string'
comp-20310CompCircularExternalModelReferenceCircular reference in <externalModelDefinition>
comp-20501CompOneListOfOnModelOnly one <listOfSubmodels> and one <listOfPorts> allowed
comp-20502CompNoEmptyListOfOnModelNo empty listOf elements allowed
comp-20503CompLOSubmodelsAllowedElementsAllowed elements on <listOfSubmodels>
comp-20504CompLOPortsAllowedElementsAllowed elements on <listOfPorts>
comp-20505CompLOSubmodelsAllowedAttributesAllowed attributes on <listOfSubmodels>
comp-20506CompLOPortsAllowedAttributesAllowed attributes on <listOfPorts>
comp-20601CompSubmodelAllowedCoreAttributesAllowed core attributes on <submodel>
comp-20602CompSubmodelAllowedElementsAllowed elements on <submodel>
comp-20603CompOneListOfDeletionOnSubmodelOnly one <listOfDeletions> on a <submodel> allowed
comp-20604CompSubmodelNoEmptyLODeletionsNo empty listOfDeletions elements allowed
comp-20605CompLODeletionsAllowedElementsAllowed elements on <listOfDeletions>
comp-20606CompLODeletionAllowedAttributesAllowed <listOfDeletions> attributes
comp-20607CompSubmodelAllowedAttributesAllowed <submodel> attributes
comp-20608CompModReferenceSyntax'comp:modelRef' must conform to SId syntax
comp-20613CompInvalidTimeConvFactorSyntax'comp:timeConversionFactor' must conform to SId syntax
comp-20614CompInvalidExtentConvFactorSyntax'comp:extentConversionFactor' must conform to SId syntax
comp-20615CompSubmodelMustReferenceModelThe 'comp:modelRef' attribute must reference a model
comp-20616CompSubmodelCannotReferenceSelfThe 'comp:modelRef' attribute cannot reference own model
comp-20617CompModCannotCircularlyReferenceSelf<model> may not reference <submodel> that references itself.
comp-20622CompTimeConversionMustBeParameterThe 'comp:timeConversionFactor' must reference a parameter
comp-20623CompExtentConversionMustBeParameterThe 'comp:extentConversionFactor' must reference a parameter
comp-20701CompPortRefMustReferencePortThe 'comp:portRef' attribute must be the 'id' of a <port>
comp-20702CompIdRefMustReferenceObjectThe 'comp:idRef' attribute must be the 'id' of a model element
comp-20703CompUnitRefMustReferenceUnitDefThe 'comp:unitRef' attribute must be the 'id' of a UnitDefinition
comp-20704CompMetaIdRefMustReferenceObjectThe 'comp:metaIdRef' attribute must be the 'metaid' of an object
comp-20705CompParentOfSBRefChildMustBeSubmodelIf <sBaseRef> has a child <sBaseRef> its parent must be a <submodel>
comp-20706CompInvalidPortRefSyntaxThe 'comp:portRef' attribute must have the syntax of an SBML SId
comp-20707CompInvalidIdRefSyntaxThe 'comp:idRef' attribute must have the syntax of an SBML SId
comp-20708CompInvalidUnitRefSyntaxThe 'comp:unitRef' attribute must have the syntax of an SBML SId
comp-20709CompInvalidMetaIdRefSyntaxThe 'comp:metaIdRef' attribute must have the syntax of an XML ID
comp-20710CompOneSBaseRefOnlyOnly one <sbaseRef>
comp-20711CompDeprecatedSBaseRefSpellingThe spelling 'sbaseRef' is deprecated
comp-20712CompSBaseRefMustReferenceObjectAn SBaseRef must reference an object.
comp-20713CompSBaseRefMustReferenceOnlyOneObjectAn SBaseRef must reference only one other object.
comp-20714CompNoMultipleReferencesObjects may not be referenced by mutiple SBaseRef constructs.
comp-20801CompPortMustReferenceObjectPort must reference an object
comp-20802CompPortMustReferenceOnlyOneObjectPort must reference only one other object.
comp-20803CompPortAllowedAttributesAllowed attributes on a Port
comp-20804CompPortReferencesUniquePort definitions must be unique.
comp-20901CompDeletionMustReferenceObjectDeletion must reference an object
comp-20902CompDeletionMustReferOnlyOneObjectDeletion must reference only one other object.
comp-20903CompDeletionAllowedAttributesAllowed attributes on a Deletion
comp-21001CompReplacedElementMustRefObjectReplacedElement must reference an object
comp-21002CompReplacedElementMustRefOnlyOneReplacedElement must reference only one other object.
comp-21003CompReplacedElementAllowedAttributesAllowed attributes on <replacedElement>
comp-21004CompReplacedElementSubModelRefThe 'comp:submodelRef' attribute must point to a <submodel>
comp-21005CompReplacedElementDeletionRefThe 'comp:deletion' attribute must point to a <deletion>
comp-21006CompReplacedElementConvFactorRefThe 'comp:conversionFactor attribute must point to a <parameter>
comp-21010CompReplacedElementSameReferenceNo <replacedElement> refer to same object
comp-21011CompReplacedElementNoDelAndConvFactNo <replacedElement> with deletion and conversionfactor
comp-21101CompReplacedByMustRefObjectReplacedBy must reference an object
comp-21102CompReplacedByMustRefOnlyOneReplacedBy must reference only one other object.
comp-21103CompReplacedByAllowedAttributesAllowed attributes on <replacedBy>
comp-21104CompReplacedBySubModelRefThe 'comp:submodelRef' attribute must point to a <submodel>
comp-21201CompMustReplaceSameClassReplaced classes must match.
comp-21202CompMustReplaceIDsReplaced IDs must be replaced with IDs.
comp-21203CompMustReplaceMetaIDsReplaced metaids must be replaced with metaids.
comp-21204CompMustReplacePackageIDsReplaced package IDs must be replaced with package IDs.
comp-90101CompUnresolvedReferenceUnresolved reference.
comp-90102CompNoModelInReferenceNo model in referenced document.
comp-90103CompExtModDefBadReferenced <externalModelDefinition> unresolvable.
comp-90104CompModelFlatteningFailedModel failed to flatten.
comp-90105CompFlatModelNotValidFlat model not valid.
comp-90106CompLineNumbersUnreliableLine numbers unreliable.
comp-90107CompFlatteningNotRecognisedReqdFlattening not implemented for required package.
comp-90108CompFlatteningNotRecognisedNotReqdFlattening not implemented for unrequired package.
comp-90109CompFlatteningNotImplementedNotReqdFlattening not implemented for unrequired package.
comp-90110CompFlatteningNotImplementedReqdFlattening not implemented for required package.
comp-90111CompFlatteningWarningFlattening reference may come from package.
comp-90112CompDeprecatedDeleteFunctionThe performDeletions functions is deprecated.
comp-90113CompDeprecatedReplaceFunctionThe performReplacementsAndConversions fuctions is deprecated.
comp-90114CompDeletedReplacementElement deleted before a subelement could be replaced.
comp-90115CompIdRefMayReferenceUnknownPackageThe 'comp:idRef' attribute must be the 'id' of a model element
comp-90116CompMetaIdRefMayReferenceUnknownPkgThe 'comp:metaIdRef' attribute must be the 'metaid' of a model element
Codes for SBML Level 3 package "fbc"
fbc-10101FbcNSUndeclaredThe fbc ns is not correctly declared
fbc-10102FbcElementNotInNsElement not in fbc namespace
fbc-20101FbcAttributeRequiredMissingRequired fbc:required attribute on <sbml>
fbc-20102FbcAttributeRequiredMustBeBooleanThe fbc:required attribute must be Boolean
fbc-20103FbcRequiredFalseThe fbc:required attribute must be 'false'
fbc-20201FbcOnlyOneEachListOfOne of each list of allowed
fbc-20202FbcNoEmptyListOfsListOf elements cannot be empty
fbc-20203FbcLOFluxBoundsAllowedElementsAllowed elements on ListOfFluxBounds
fbc-20204FbcLOObjectivesAllowedElementsAllowed elements on ListOfObjectives
fbc-20205FbcLOFluxBoundsAllowedAttributesAllowed attributes on ListOfFluxBounds
fbc-20206FbcLOObjectivesAllowedAttributesAllowed attributes on ListOfObjectives
fbc-20207FbcActiveObjectiveSyntaxType of activeObjective attribute
fbc-20208FbcActiveObjectiveRefersObjectiveActiveObjective must reference Objective
fbc-20301FbcSpeciesAllowedL3AttributesSpecies allowed attributes
fbc-20302FbcSpeciesChargeMustBeIntegerCharge must be integer
fbc-20303FbcSpeciesFormulaMustBeStringChemical formula must be string
fbc-20401FbcFluxBoundAllowedL3Attributes<fluxBound> may only have 'metaId' and 'sboTerm' from L3 namespace
fbc-20402FbcFluxBoundAllowedElements<fluxBound> may only have <notes> and <annotations> from L3 Core
fbc-20403FbcFluxBoundRequiredAttributesInvalid attribute found on <fluxBound> object
fbc-20404FbcFluxBoundRectionMustBeSIdRefDatatype for 'fbc:reaction' must be SIdRef
fbc-20405FbcFluxBoundNameMustBeStringThe attribute 'fbc:name' must be of the data type string
fbc-20406FbcFluxBoundOperationMustBeEnumThe attribute 'fbc:operation' must be of data type FbcOperation
fbc-20407FbcFluxBoundValueMustBeDoubleThe attribute 'fbc:value' must be of the data type double
fbc-20408FbcFluxBoundReactionMustExist'fbc:reaction' must refer to valid reaction
fbc-20409FbcFluxBoundsForReactionConflictConflicting set of FluxBounds for a reaction
fbc-20501FbcObjectiveAllowedL3Attributes<objective> may only have 'metaId' and 'sboTerm' from L3 namespace
fbc-20502FbcObjectiveAllowedElements<objective> may only have <notes> and <annotations> from L3 Core
fbc-20503FbcObjectiveRequiredAttributesInvalid attribute found on <objective> object
fbc-20504FbcObjectiveNameMustBeStringThe attribute 'fbc:name' must be of the data type string
fbc-20505FbcObjectiveTypeMustBeEnumThe attribute 'fbc:type' must be of data type FbcType.
fbc-20506FbcObjectiveOneListOfObjectivesAn <objective> must have one <listOfFluxObjectives>.
fbc-20507FbcObjectiveLOFluxObjMustNotBeEmpty<listOfFluxObjectives> subobject must not be empty
fbc-20508FbcObjectiveLOFluxObjOnlyFluxObjInvalid element found in <listOfFluxObjectives>
fbc-20509FbcObjectiveLOFluxObjAllowedAttribs<listOfFluxObjectives> may only have 'metaId' and 'sboTerm' from L3 core
fbc-20601FbcFluxObjectAllowedL3Attributes<fluxObjective> may only have 'metaId' and 'sboTerm' from L3 namespace
fbc-20602FbcFluxObjectAllowedElements<fluxObjective> may only have <notes> and <annotations> from L3 Core
fbc-20603FbcFluxObjectRequiredAttributesInvalid attribute found on <fluxObjective> object
fbc-20604FbcFluxObjectNameMustBeStringThe attribute 'fbc:name' must be of the data type string
fbc-20605FbcFluxObjectReactionMustBeSIdRefDatatype for 'fbc:reaction' must be SIdRef
fbc-20606FbcFluxObjectReactionMustExist'fbc:reaction' must refer to valid reaction
fbc-20607FbcFluxObjectCoefficientMustBeDoubleThe attribute 'fbc:coefficient' must be of the data type double
Codes for SBML Level 3 package "qual"
qual-10101QualNSUndeclaredThe qual ns is not correctly declared
qual-10102QualElementNotInNsElement not in qual namespace
qual-20101QualAttributeRequiredMissingRequired qual:required attribute on <sbml>
qual-20102QualAttributeRequiredMustBeBooleanThe qual:required attribute must be Boolean
qual-20103QualRequiredTrueIfTransitionsThe qual:required attribute must be 'true' if math changes
qual-20201QualOneListOfTransOrQSOnly one <listOfTransitions> or <listOfQualitativeSpecies> allowed.
qual-20202QualEmptyLONotAllowedEmpty <listOfTransitions> or <listOfQualitativeSpecies> not allowed.
qual-20203QualLOTransitiondAllowedElementsElements allowed on <listOfTransitions>.
qual-20204QualLOQualSpeciesAllowedElementsElements allowed on <listOfTransitions>.
qual-20205QualLOQualSpeciesAllowedAttributesAttributes allowed on <listOfQualitativeSpecies>.
qual-20206QualLOTransitionsAllowedAttributesAttributes allowed on <listOfTransitions>.
qual-20301QualQualSpeciesAllowedCoreAttributesCore attributes allowed on <qualitativeSpecies>.
qual-20302QualQualSpeciesAllowedElementsElements allowed on <qualitativeSpecies>.
qual-20303QualQualSpeciesAllowedAttributesAttributes allowed on <qualitativeSpecies>.
qual-20304QualConstantMustBeBoolAttribute 'constant' on <qualitativeSpecies> must be boolean.
qual-20305QualNameMustBeStringAttribute 'name' on <qualitativeSpecies> must be string.
qual-20306QualInitialLevelMustBeIntAttribute 'initialLevel' on <qualitativeSpecies> must be integer.
qual-20307QualMaxLevelMustBeIntAttribute 'maxLevel' on <qualitativeSpecies> must be integer.
qual-20308QualCompartmentMustReferExistingAttribute 'compartment' on <qualitativeSpecies> must reference compartment.
qual-20309QualInitialLevelCannotExceedMaxAttribute 'initialLevel' on <qualitativeSpecies> cannot exceed maxLevel.
qual-20310QualConstantQSCannotBeOutputConstant <qualitativeSpecies> cannot be an Output.
qual-20311QualQSAssignedOnlyOnceA <qualitativeSpecies> can only be assigned once.
qual-20312QualInitalLevelNotNegativeAttribute 'initialLevel' on <qualitativeSpecies> cannot be negative.
qual-20313QualMaxLevelNotNegativeAttribute 'maxLevel' on <qualitativeSpecies> cannot be negative.
qual-20401QualTransitionAllowedCoreAttributesCore attributes allowed on <transition>.
qual-20402QualTransitionAllowedElementsElements allowed on <transition>.
qual-20403QualTransitionAllowedAttributesAttributes allowed on <transition>.
qual-20404QualTransitionNameMustBeStringAttribute 'name' on <transition> must be string.
qual-20405QualTransitionLOElementsListOf elements on <transition>.
qual-20406QualTransitionEmptyLOElementsListOf elements on <transition> not empty.
qual-20407QualTransitionLOInputElementsElements on <listOfInputs>.
qual-20408QualTransitionLOOutputElementsElements on <listOfOutputs>.
qual-20409QualTransitionLOFuncTermElementsElements on <listOfFunctionTerms>.
qual-20410QualTransitionLOInputAttributesAttributes allowed on <listOfInputs>.
qual-20411QualTransitionLOOutputAttributesAttributes allowed on <listOfOutputs>.
qual-20412QualTransitionLOFuncTermAttributesAttributes allowed on <listOfFunctionTerms>.
qual-20413QualTransitionLOFuncTermExceedMax<listOfFunctionTerms> cannot make qualitativeSpecies exceed maxLevel.
qual-20414QualTransitionLOFuncTermNegative<listOfFunctionTerms> cannot make qualitativeSpecies negative.
qual-20501QualInputAllowedCoreAttributesCore attributes allowed on <input>.
qual-20502QualInputAllowedElementsElements allowed on <input>.
qual-20503QualInputAllowedAttributesAttributes allowed on <input>.
qual-20504QualInputNameMustBeStringAttribute 'name' on <input> must be string.
qual-20505QualInputSignMustBeSignEnumAttribute 'sign' on <input> must be enum.
qual-20506QualInputTransEffectMustBeInputEffectAttribute 'transitionEffect' on <input> must be enum.
qual-20507QualInputThreshMustBeIntegerAttribute 'thresholdLevel' on <input> must be non negative integer.
qual-20508QualInputQSMustBeExistingQSAttribute 'qualitativeSpecies' on <input> must refer to existing
qual-20509QualInputConstantCannotBeConsumedConstant <input> cannot be consumed.
qual-20510QualInputThreshMustBeNonNegativeAttribute 'thresholdLevel' on <input> must be non negative integer.
qual-20601QualOutputAllowedCoreAttributesCore attributes allowed on <output>.
qual-20602QualOutputAllowedElementsElements allowed on <output>.
qual-20603QualOutputAllowedAttributesAttributes allowed on <output>.
qual-20604QualOutputNameMustBeStringAttribute 'name' on <output> must be string.
qual-20605QualOutputTransEffectMustBeOutputAttribute 'transitionEffect' on <output> must be enum.
qual-20606QualOutputLevelMustBeIntegerAttribute 'outputLevel' on <output> must be non negative integer.
qual-20607QualOutputQSMustBeExistingQSAttribute 'qualitativeSpecies' on <output> must refer to existing
qual-20608QualOutputConstantMustBeFalseConstant 'qualitativeSpecies' cannot be <output>
qual-20609QualOutputProductionMustHaveLevel<output> being produced must have level
qual-20610QualOutputLevelMustBeNonNegativeAttribute 'outputLevel' on <output> must be non negative integer.
qual-20701QualDefaultTermAllowedCoreAttributesCore attributes allowed on <defaultTerm>.
qual-20702QualDefaultTermAllowedElementsElements allowed on <defaultTerm>.
qual-20703QualDefaultTermAllowedAttributesAttributes allowed on <defaultTerm>.
qual-20704QualDefaultTermResultMustBeIntegerAttribute 'resultLevel' on <defaultTerm> must be non negative integer.
qual-20705QualDefaultTermResultMustBeNonNegAttribute 'resultLevel' on <defaultTerm> must be non negative integer.
qual-20801QualFuncTermAllowedCoreAttributesCore attributes allowed on <functionTerm>.
qual-20802QualFuncTermAllowedElementsElements allowed on <functionTerm>.
qual-20803QualFuncTermAllowedAttributesAttributes allowed on <functionTerm>.
qual-20804QualFuncTermOnlyOneMathOnly one <math> on <functionTerm>.
qual-20805QualFuncTermResultMustBeIntegerAttribute 'resultLevel' on <functionTerm> must be non negative integer.
qual-20806QualFuncTermResultMustBeNonNegAttribute 'resultLevel' on <functionTerm> must be non negative integer.
Codes for SBML Level 3 package "layout"
layout-10101LayoutNSUndeclaredThe layout ns is not correctly declared
layout-10102LayoutElementNotInNsElement not in layout namespace
layout-20101LayoutAttributeRequiredMissingRequired layout:required attribute on <sbml>
layout-20102LayoutAttributeRequiredMustBeBooleanThe layout:required attribute must be Boolean
layout-20103LayoutRequiredFalseThe layout:required attribute must be 'false'
layout-20201LayoutOnlyOneLOLayoutsOnly one listOfLayouts on <model>
layout-20202LayoutLOLayoutsNotEmptyListOf elements cannot be empty
layout-20203LayoutLOLayoutsAllowedElementsAllowed elements on ListOfLayouts
layout-20204LayoutLOLayoutsAllowedAttributesAllowed attributes on ListOfLayouts
layout-20301LayoutLayoutAllowedElementsAllowed elements on Layout
layout-20302LayoutLayoutAllowedCoreAttributesAllowed core attributes on Layout
layout-20303LayoutOnlyOneEachListOfOnly one each listOf on <layout>
layout-20304LayoutNoEmptyListOfsListOf elements cannot be empty
layout-20305LayoutLayoutAllowedAttributes<layout> must have 'id' and may have 'name'
layout-20306LayoutLayoutNameMustBeString'name' must be string
layout-20307LayoutLOCompGlyphAllowedAttributesAttributes allowed on <listOfCompartmentGlyphs>.
layout-20308LayoutLOCompGlyphAllowedElementsElements allowed on <listOfCompartmentGlyphs>.
layout-20309LayoutLOSpeciesGlyphAllowedAttributesAttributes allowed on <listOfSpeciesGlyphs>.
layout-20310LayoutLOSpeciesGlyphAllowedElementsElements allowed on <listOfSpeciesGlyphs>.
layout-20311LayoutLORnGlyphAllowedAttributesAttributes allowed on <listOfReactionGlyphs>.
layout-20312LayoutLORnGlyphAllowedElementsElements allowed on <listOfReactionGlyphs>.
layout-20313LayoutLOAddGOAllowedAttributAttributes allowed on <listOfAdditionalGraphicalObjectGlyphs>.
layout-20314LayoutLOAddGOAllowedElementsElements allowed on <listOfAdditionalGraphicalObjectGlyphs>.
layout-20315LayoutLayoutMustHaveDimensionsLayout must have <dimensions>.
layout-20316LayoutLOTextGlyphAllowedAttributesAttributes allowed on <listOfTextGlyphs>.
layout-20317LayoutLOTextGlyphAllowedElementsElements allowed on <listOfTextGlyphs>.
layout-20401LayoutGOAllowedCoreElementsCore elements allowed on <graphicalObject>.
layout-20402LayoutGOAllowedCoreAttributesCore attributes allowed on <graphicalObject>.
layout-20403LayoutGOAllowedElementsLayout elements allowed on <graphicalObject>.
layout-20404LayoutGOAllowedAttributesLayout attributes allowed on <graphicalObject>.
layout-20405LayoutGOMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-20406LayoutGOMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-20407LayoutGOMustContainBoundingBoxA <graphicalObject> must contain a <boundingBox>.
layout-20501LayoutCGAllowedCoreElementsCore elements allowed on <compartmentGlyph>.
layout-20502LayoutCGAllowedCoreAttributesCore attributes allowed on <compartmentGlyph>.
layout-20503LayoutCGAllowedElementsLayout elements allowed on <compartmentGlyph>.
layout-20504LayoutCGAllowedAttributesLayout attributes allowed on <compartmentGlyph>.
layout-20505LayoutCGMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-20506LayoutCGMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-20507LayoutCGCompartmentSyntaxCompartmentGlyph 'compartment' must have SIdRef syntax.
layout-20508LayoutCGCompartmentMustRefCompCompartmentGlyph compartment must reference existing compartment.
layout-20509LayoutCGNoDuplicateReferencesCompartmentGlyph cannot reference two objects.
layout-20510LayoutCGOrderMustBeDoubleCompartmentGlyph order must be double.
layout-20601LayoutSGAllowedCoreElementsCore elements allowed on <speciesGlyph>.
layout-20602LayoutSGAllowedCoreAttributesCore attributes allowed on <speciesGlyph>.
layout-20603LayoutSGAllowedElementsLayout elements allowed on <speciesGlyph>.
layout-20604LayoutSGAllowedAttributesLayout attributes allowed on <speciesGlyph>.
layout-20605LayoutSGMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-20606LayoutSGMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-20607LayoutSGSpeciesSyntaxSpeciesGlyph 'species' must have SIdRef syntax.
layout-20608LayoutSGSpeciesMustRefSpeciesSpeciesGlyph species must reference existing species.
layout-20609LayoutSGNoDuplicateReferencesSpeciesGlyph cannot reference two objects.
layout-20701LayoutRGAllowedCoreElementsCore elements allowed on <reactionGlyph>.
layout-20702LayoutRGAllowedCoreAttributesCore attributes allowed on <reactionGlyph>.
layout-20703LayoutRGAllowedElementsLayout elements allowed on <reactionGlyph>.
layout-20704LayoutRGAllowedAttributesLayout attributes allowed on <reactionGlyph>.
layout-20705LayoutRGMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-20706LayoutRGMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-20707LayoutRGReactionSyntaxReactionGlyph 'reaction' must have SIdRef syntax.
layout-20708LayoutRGReactionMustRefReactionReactionGlyph reaction must reference existing reaction.
layout-20709LayoutRGNoDuplicateReferencesReactionGlyph cannot reference two objects.
layout-20710LayoutLOSpeciesRefGlyphAllowedElementsAllowed elements on ListOfSpeciesReferenceGlyphs
layout-20711LayoutLOSpeciesRefGlyphAllowedAttribsAllowed attributes on ListOfSpeciesReferenceGlyphs
layout-20712LayoutLOSpeciesRefGlyphNotEmptyListOfSpeciesReferenceGlyphs not empty
layout-20801LayoutGGAllowedCoreElementsCore elements allowed on <generalGlyph>.
layout-20802LayoutGGAllowedCoreAttributesCore attributes allowed on <generalGlyph>.
layout-20803LayoutGGAllowedElementsLayout elements allowed on <generalGlyph>.
layout-20804LayoutGGAllowedAttributesLayout attributes allowed on <generalGlyph>.
layout-20805LayoutGGMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-20806LayoutGGMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-20807LayoutGGReferenceSyntaxGeneralGlyph 'reference' must have SIdRef syntax.
layout-20808LayoutGGReferenceMustRefObjectGeneralGlyph 'reference' must reference existing element.
layout-20809LayoutGGNoDuplicateReferencesGeneralGlyph cannot reference two objects.
layout-20810LayoutLOReferenceGlyphAllowedElementsAllowed elements on ListOfReferenceGlyphs
layout-20811LayoutLOReferenceGlyphAllowedAttribsAllowed attributes on ListOfReferenceGlyphs
layout-20813LayoutLOSubGlyphAllowedAttribsAllowed attributes on ListOfSubGlyphs
layout-20901LayoutTGAllowedCoreElementsCore elements allowed on <textGlyph>.
layout-20902LayoutTGAllowedCoreAttributesCore attributes allowed on <textGlyph>.
layout-20903LayoutTGAllowedElementsLayout elements allowed on <textGlyph>.
layout-20904LayoutTGAllowedAttributesLayout attributes allowed on <textGlyph>.
layout-20905LayoutTGMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-20906LayoutTGMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-20907LayoutTGOriginOfTextSyntaxTextGlyph 'originOfText' must have SIdRef syntax.
layout-20908LayoutTGOriginOfTextMustRefObjectTextGlyph 'originOfText' must reference existing element.
layout-20909LayoutTGNoDuplicateReferencesTextGlyph cannot reference two objects.
layout-20910LayoutTGGraphicalObjectSyntaxTextGlyph 'graphicalObject' must have SIdRef syntax.
layout-20911LayoutTGGraphicalObjectMustRefObjectTextGlyph 'graphicalObject' must reference existing element.
layout-20912LayoutTGTextMustBeStringTextGlyph 'text' must be string.
layout-21001LayoutSRGAllowedCoreElementsCore elements allowed on <speciesReferenceGlyph>.
layout-21002LayoutSRGAllowedCoreAttributesCore attributes allowed on <speciesReferenceGlyph>.
layout-21003LayoutSRGAllowedElementsLayout elements allowed on <speciesReferenceGlyph>.
layout-21004LayoutSRGAllowedAttributesLayout attributes allowed on <speciesReferenceGlyph>.
layout-21005LayoutSRGMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-21006LayoutSRGMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-21007LayoutSRGSpeciesReferenceSyntaxSpeciesReferenceGlyph 'speciesReference' must have SIdRef syntax.
layout-21008LayoutSRGSpeciesRefMustRefObjectSpeciesReferenceGlyph 'speciesReference' must reference existing element.
layout-21009LayoutSRGNoDuplicateReferencesSpeciesReferenceGlyph cannot reference two objects.
layout-21010LayoutSRGSpeciesGlyphSyntaxSpeciesReferenceGlyph 'speciesGlyph' must have SIdRef syntax.
layout-21011LayoutSRGSpeciesGlyphMustRefObjectSpeciesReferenceGlyph 'speciesGlyph' must reference existing element.
layout-21012LayoutSRGRoleSyntaxSpeciesReferenceGlyph 'role' must be string from enumeration.
layout-21101LayoutREFGAllowedCoreElementsCore elements allowed on <referenceGlyph>.
layout-21102LayoutREFGAllowedCoreAttributesCore attributes allowed on <referenceGlyph>.
layout-21103LayoutREFGAllowedElementsLayout elements allowed on <referenceGlyph>.
layout-21104LayoutREFGAllowedAttributesLayout attributes allowed on <referenceGlyph>.
layout-21105LayoutREFGMetaIdRefMustBeIDREFLayout 'metIdRef' must be IDREF.
layout-21106LayoutREFGMetaIdRefMustReferenceObjectLayout 'metIdRef' must reference existing object.
layout-21107LayoutREFGReferenceSyntaxReferenceGlyph 'reference' must have SIdRef syntax.
layout-21108LayoutREFGReferenceMustRefObjectReferenceGlyph 'reference' must reference existing element.
layout-21109LayoutREFGNoDuplicateReferencesReferenceGlyph cannot reference two objects.
layout-21110LayoutREFGGlyphSyntaxReferenceGlyph 'glyph' must have SIdRef syntax.
layout-21111LayoutREFGGlyphMustRefObjectReferenceGlyph 'glyph' must reference existing element.
layout-21112LayoutREFGRoleSyntaxReferenceGlyph 'role' must be string.
layout-21201LayoutPointAllowedCoreElementsCore elements allowed on <point>.
layout-21202LayoutPointAllowedCoreAttributesCore attributes allowed on <point>.
layout-21203LayoutPointAllowedAttributesLayout attributes allowed on <point>.
layout-21204LayoutPointAttributesMustBeDoubleLayout 'x', 'y' and 'z' must be double.
layout-21301LayoutBBoxAllowedCoreElementsCore elements allowed on <boundingBox>.
layout-21302LayoutBBoxAllowedCoreAttributesCore attributes allowed on <boundingBox>.
layout-21303LayoutBBoxAllowedElementsLayout elements allowed on <boundingBox>.
layout-21304LayoutBBoxAllowedAttributesLayout attributes allowed on <boundingBox>.
layout-21305LayoutBBoxConsistent3DDefinitionLayout consistent dimensions on a <boundingBox>
layout-21401LayoutCurveAllowedCoreElementsCore elements allowed on <curve>.
layout-21402LayoutCurveAllowedCoreAttributesCore attributes allowed on <curve>.
layout-21403LayoutCurveAllowedElementsLayout elements allowed on <curve>.
layout-21404LayoutCurveAllowedAttributesLayout attributes allowed on <curve>.
layout-21405LayoutLOCurveSegsAllowedAttributesAllowed attributes on ListOfCurveSegments
layout-21406LayoutLOCurveSegsAllowedElementsAllowed elements on ListOfCurveSegments
layout-21407LayoutLOCurveSegsNotEmptyNo empty ListOfCurveSegments
layout-21501LayoutLSegAllowedCoreElementsCore elements allowed on <lineSegment>.
layout-21502LayoutLSegAllowedCoreAttributesCore attributes allowed on <lineSegment>.
layout-21503LayoutLSegAllowedElementsLayout elements allowed on <lineSegment>.
layout-21504LayoutLSegAllowedAttributesLayout attributes allowed on <lineSegment>.
layout-21601LayoutCBezAllowedCoreElementsCore elements allowed on <cubicBezier>.
layout-21602LayoutCBezAllowedCoreAttributesCore attributes allowed on <cubicBezier>.
layout-21603LayoutCBezAllowedElementsLayout elements allowed on <cubicBezier>.
layout-21604LayoutCBezAllowedAttributesLayout attributes allowed on <cubicBezier>.
layout-21701LayoutDimsAllowedCoreElementsCore elements allowed on <dimensions>.
layout-21702LayoutDimsAllowedCoreAttributesCore attributes allowed on <dimensions>.
layout-21703LayoutDimsAllowedAttributesLayout attributes allowed on <dimensions>.
layout-21704LayoutDimsAttributesMustBeDoubleLayout 'width', 'height' and 'depth' must be double.

SBML identifier consistency issues

This group of diagnostic codes concerns general SBML issues related to the identifiers used in SBML documents. For convenience and greater control during validation procedures, they are separated from the set of diagnostics for general SBML consistency.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
10301DuplicateComponentIdDuplicate 'id' attribute value
10302DuplicateUnitDefinitionIdDuplicate unit definition 'id' attribute value
10303DuplicateLocalParameterIdDuplicate local parameter 'id' attribute value
10304MultipleAssignmentOrRateRulesMultiple rules for the same variable are not allowed
10305MultipleEventAssignmentsForIdMultiple event assignments for the same variable are not allowed
10306EventAndAssignmentRuleForIdAn event assignment and an assignment rule must not have the same value for 'variable'
10307DuplicateMetaIdDuplicate 'metaid' attribute value
10308InvalidSBOTermSyntaxInvalid syntax for an 'sboTerm' attribute value
10309InvalidMetaidSyntaxInvalid syntax for a 'metaid' attribute value
10310InvalidIdSyntaxInvalid syntax for an 'id' attribute value
10311InvalidUnitIdSyntaxInvalid syntax for the identifier of a unit
10312InvalidNameSyntaxInvalid syntax for a 'name' attribute value
99303DanglingUnitSIdRefUnits must refer to valid unit or unitDefinition
Codes for SBML Level 3 package "comp"
comp-10301CompDuplicateComponentIdDuplicate 'id' attribute value
comp-10302CompUniqueModelIdsModel and ExternalModelDefinitions must have unique ids
comp-10303CompUniquePortIdsPorts must have unique ids
comp-10304CompInvalidSIdSyntaxInvalid SId syntax
comp-10308CompInvalidSubmodelRefSyntaxInvalid submodelRef syntax
comp-10309CompInvalidDeletionSyntaxInvalid deletion syntax
comp-10310CompInvalidConversionFactorSyntaxInvalid conversionFactor syntax
comp-10311CompInvalidNameSyntaxInvalid name syntax
Codes for SBML Level 3 package "fbc"
fbc-10301FbcDuplicateComponentIdDuplicate 'id' attribute value
fbc-10302FbcSBMLSIdSyntaxInvalid 'id' attribute
Codes for SBML Level 3 package "qual"
qual-10301QualDuplicateComponentIdDuplicate 'id' attribute value
Codes for SBML Level 3 package "layout"
layout-10301LayoutDuplicateComponentIdDuplicate 'id' attribute value
layout-10302LayoutSIdSyntax'id' attribute incorrect syntax
layout-10401LayoutXsiTypeAllowedLocations'xsi:type' allowed locations
layout-10402LayoutXsiTypeSyntax'xsi:type' attribute incorrect syntax

Units consistency issues

This group of diagnostic codes is concerned with the consistency of units of measurement associated with quantities specified in an SBML model. For convenience and greater control during validation procedures, they are separated from the set of diagnostics for general SBML consistency.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
10501InconsistentArgUnitsThe units of the function call's arguments are not consistent with its definition
10503InconsistentKineticLawUnitsL3The kinetic law's units are inconsistent with those of other kinetic laws in the model
10511AssignRuleCompartmentMismatchMismatched units in assignment rule for compartment
10512AssignRuleSpeciesMismatchMismatched units in assignment rule for species
10513AssignRuleParameterMismatchMismatched units in assignment rule for parameter
10514AssignRuleStoichiometryMismatchMismatched units in assignment rule for stoichiometry
10521InitAssignCompartmenMismatchMismatched units in initial assignment to compartment
10522InitAssignSpeciesMismatchMismatched units in initial assignment to species
10523InitAssignParameterMismatchMismatched units in initial assignment to parameter
10524InitAssignStoichiometryMismatchMismatched units in initial assignment to stoichiometry
10531RateRuleCompartmentMismatchMismatched units in rate rule for compartment
10532RateRuleSpeciesMismatchMismatched units in rate rule for species
10533RateRuleParameterMismatchMismatched units in rate rule for parameter
10534RateRuleStoichiometryMismatchMismatched units in rate rule for stoichiometry
10541KineticLawNotSubstancePerTimeThe units of the kinetic law are not 'substance'/'time'
10542SpeciesInvalidExtentUnitsThe species' units are not consistent with units of extent
10551DelayUnitsNotTimeThe units of the delay expression are not units of time
10561EventAssignCompartmentMismatchMismatched units in event assignment for compartment
10562EventAssignSpeciesMismatchMismatched units in event assignment for species
10563EventAssignParameterMismatchMismatched units in event assignment for parameter
10564EventAssignStoichiometryMismatchMismatched units in event assignment for stoichiometry
10565PriorityUnitsNotDimensionlessThe units of a priority expression must be 'dimensionless'
20511OneDimensionalCompartmentUnitsNo units defined for 1-D compartment
20512TwoDimensionalCompartmentUnitsNo units defined for 2-D compartment
20513ThreeDimensionalCompartmentUnitsNo units defined for 3-D Compartment object
20518NoUnitsOnCompartmentNo units defined for Compartment object
20616SubstanceUnitsOnSpeciesNo substance units defined for the species
20702ParameterUnitsNo units defined for the parameter
99505UndeclaredUnitsMissing unit declarations on parameters or literal numbers in expression
99506UndeclaredTimeUnitsL3Unable to verify consistency of units: the unit of time has not been declared
99507UndeclaredExtentUnitsL3Unable to verify consistency of units: the units of reaction extent have not been declared
99508UndeclaredObjectUnitsL3Unable to verify consistency of units: encountered a model entity with no declared units
Codes for SBML Level 3 package "comp"
comp-10501CompReplacedUnitsShouldMatchUnits of replaced elements should match replacement units.

MathML issues

This group of diagnostic codes concerns possible problems that can arise with the MathML constructs used in an SBML document.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
10201InvalidMathElementInvalid MathML
10202DisallowedMathMLSymbolDisallowed MathML symbol found
10203DisallowedMathMLEncodingUseUse of the MathML 'encoding' attribute is not allowed on this element
10204DisallowedDefinitionURLUseUse of the MathML 'definitionURL' attribute is not allowed on this element
10205BadCsymbolDefinitionURLValueInvalid <csymbol> 'definitionURL' attribute value
10206DisallowedMathTypeAttributeUseUse of the MathML 'type' attribute is not allowed on this element
10207DisallowedMathTypeAttributeValueDisallowed MathML 'type' attribute value
10208LambdaOnlyAllowedInFunctionDefUse of <lambda> not permitted outside of FunctionDefinition objects
10209BooleanOpsNeedBooleanArgsNon-Boolean argument given to Boolean operator
10210NumericOpsNeedNumericArgsNon-numerical argument given to numerical operator
10211ArgsToEqNeedSameTypeArguments to <eq> and <neq> must have the same data types
10212PiecewiseNeedsConsistentTypesTerms in a <piecewise> expression must have consistent data types
10213PieceNeedsBooleanThe second argument of a <piece> expression must yield a Boolean value
10214ApplyCiMustBeUserFunctionA <ci> element in this context must refer to a function definition
10215ApplyCiMustBeModelComponentA <ci> element in this context must refer to a model component
10216KineticLawParametersAreLocalOnlyCannot use a KineticLaw local parameter outside of its local scope
10217MathResultMustBeNumericA formula's result in this context must be a numerical value
10218OpsNeedCorrectNumberOfArgsIncorrect number of arguments given to MathML operator
10219InvalidNoArgsPassedToFunctionDefIncorrect number of arguments given to function invocation
10220DisallowedMathUnitsUseAttribute 'units' is only permitted on <cn> elements
10221InvalidUnitsValueInvalid value given for the 'units' attribute
99219BadMathMLInvalid MathML expression
99220FailedMathMLReadOfDoubleMissing or invalid floating-point number in MathML expression
99221FailedMathMLReadOfIntegerMissing or invalid integer in MathML expression
99222FailedMathMLReadOfExponentialMissing or invalid exponential expression in MathML
99223FailedMathMLReadOfRationalMissing or invalid rational expression in MathML
99224BadMathMLNodeTypeInvalid MathML element
99225InvalidMathMLAttributeInvalid MathML attribute
Codes for SBML Level 3 package "qual"
qual-10201QualFunctionTermBoolFunctionTerm should return boolean
qual-10202QualMathCSymbolDisallowedCSymbol time or delay not allowed

Systems Biology Ontology (SBO) issues

This group of diagnostic codes concerns possible problems that can arise with the MathML constructs used in an SBML document. For convenience and greater control during validation procedures, they are separated from the set of diagnostics for general SBML consistency.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
10701InvalidModelSBOTermInvalid 'sboTerm' attribute value for a Model object
10702InvalidFunctionDefSBOTermInvalid 'sboTerm' attribute value for a FunctionDefinition object
10703InvalidParameterSBOTermInvalid 'sboTerm' attribute value for a Parameter object
10704InvalidInitAssignSBOTermInvalid 'sboTerm' attribute value for an InitialAssignment object
10705InvalidRuleSBOTermInvalid 'sboTerm' attribute value for a Rule object
10706InvalidConstraintSBOTermInvalid 'sboTerm' attribute value for a Constraint object
10707InvalidReactionSBOTermInvalid 'sboTerm' attribute value for a Reaction object
10708InvalidSpeciesReferenceSBOTermInvalid 'sboTerm' attribute value for a SpeciesReference object
10709InvalidKineticLawSBOTermInvalid 'sboTerm' attribute value for a KineticLaw object
10710InvalidEventSBOTermInvalid 'sboTerm' attribute value for an Event object
10711InvalidEventAssignmentSBOTermInvalid 'sboTerm' attribute value for an EventAssignment object
10712InvalidCompartmentSBOTermInvalid 'sboTerm' attribute value for a Compartment object
10713InvalidSpeciesSBOTermInvalid 'sboTerm' attribute value for a Species object
10714InvalidCompartmentTypeSBOTermInvalid 'sboTerm' attribute value for a CompartmentType object
10715InvalidSpeciesTypeSBOTermInvalid 'sboTerm' attribute value for a SpeciesType object
10716InvalidTriggerSBOTermInvalid 'sboTerm' attribute value for an Event Trigger object
10717InvalidDelaySBOTermInvalid 'sboTerm' attribute value for an Event Delay object
99701UnrecognisedSBOTermUnrecognized 'sboTerm' attribute value
99702ObseleteSBOTermObsolete 'sboTerm' attribute value

Modeling practice issues

This group of diagnostic codes is concerned with matters of good modeling practices involving SBML and computational modeling. These are tests performed by libSBML and do not have equivalent SBML validation rules. For convenience and greater control during validation procedures, they are separated from the set of diagnostics for general SBML consistency.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
80501CompartmentShouldHaveSizeIt's best to define a size for every compartment in a model
80601SpeciesShouldHaveValueIt's best to define an initial amount or initial concentration for every species in a model
80701ParameterShouldHaveUnitsIt's best to declare units for every parameter in a model
81121LocalParameterShadowsIdLocal parameters defined within a kinetic law shadow global object symbols

Internal SBML consistency issues

This set of diagnostics is concerned with problems that can occur while validating the libSBML internal representation of SBML constructs. These are tests performed by libSBML and do not have equivalent SBML validation rules. For convenience and greater control during validation procedures, they are separated from the set of diagnostics for general SBML consistency.

Error code LibSBML name Meaning L1 V1 L1 V2 L2 V1 L2 V2 L2 V3 L2 V4 L3 V1
99901IncorrectCompartmentSpatialDimensionsIn SBML Level 1, only three-dimensional compartments are allowed
99902CompartmentTypeNotValidAttributeCompartmentType objects are not available in this Level+Version of SBML
99903ConstantNotValidAttributeThis Level+Version of SBML does not support the 'constant' attribute on this component
99904MetaIdNotValidAttributeAttribute 'metaid' is not available in SBML Level 1
99905SBOTermNotValidAttributeBeforeL2V3The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3
99906InvalidL1CompartmentUnitsInvalid units for a compartment in SBML Level 1
99907L1V1CompartmentVolumeReqdIn SBML Level 1, a compartment's volume must be specified
99908CompartmentTypeNotValidComponentCompartmentType objects are not available in this Level+Version of SBML
99909ConstraintNotValidComponentConstraint objects are not available in this Level+Version of SBML
99910EventNotValidComponentEvent objects are not available in this Level+Version of SBML
99911SBOTermNotValidAttributeBeforeL2V2The 'sboTerm' attribute is invalid for this component before Level 2 Version 2
99912FuncDefNotValidComponentFunctionDefinition objects are not available in this Level+Version of SBML
99913InitialAssignNotValidComponentInitialAssignment objects are not available in this Level+Version of SBML
99914VariableNotValidAttributeAttribute 'variable' is not available on this component in this Level+Version of SBML
99915UnitsNotValidAttributeAttribute 'units' is not available on this component in this Level+Version of SBML
99916ConstantSpeciesNotValidAttributeAttribute 'constant' is not available on Species objects in SBML Level 1
99917SpatialSizeUnitsNotValidAttributeAttribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1
99918SpeciesTypeNotValidAttributeAttribute 'speciesType' is not available on Species objects in SBML Level 1
99919HasOnlySubsUnitsNotValidAttributeAttribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1
99920IdNotValidAttributeAttribute 'id' is not available on SpeciesReference objects in SBML Level 1
99921NameNotValidAttributeAttribute 'name' is not available on SpeciesReference objects in SBML Level 1
99922SpeciesTypeNotValidComponentThe SpeciesType object is not supported in SBML Level 1
99923StoichiometryMathNotValidComponentThe StoichiometryMath object is not supported in SBML Level 1
99924MultiplierNotValidAttributeAttribute 'multiplier' on Unit objects is not supported in SBML Level 1
99925OffsetNotValidAttributeAttribute 'offset' on Unit objects is only available in SBML Level 2 Version 1
99926L3SpatialDimensionsUnsetNo value given for 'spatialDimensions' attribute; assuming a value of 3
99996PackageConversionNotSupportedConversion of SBML Level 3 package constructs is not yet supported
99997InvalidTargetLevelVersionThe requested SBML Level/Version combination is not known to exist
99998L3NotSupportedSBML Level 3 is not yet supported

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This page was last modified 16:21, 13 May 2014.



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