BioPAX Semantic Rules

Currently available (loaded) validation rules and corresponding level of error they report in each validation profile (mode).

Profile and level
Rule (class name)Description"default""notstrict"
org.biopax.validator.rules.AcyclicComplexRule Checks if a Complex Contains Itself (e.g., in its component's component) ERROR ERROR
org.biopax.validator.rules.BindingFeatureBindsToCRRule Checks BindingFeature is 'functional' property (OWL constraint) ERROR IGNORE
org.biopax.validator.rules.BindingFeatureExtraRules This 'Post Model' Rule Checks BindingFeature.bindsTo 'inverse functional' constraint ERROR WARNING
org.biopax.validator.rules.BindingFeatureSymmetricRule Checks BindingFeature.bindsTo 'symmetric' constraint (bfA.bindsTo=bfB <=> bfB.bindsTo=bfA) ERROR WARNING
org.biopax.validator.rules.BioSourceCellTypeCRRule Checks BioSource.cellType cardinality/range constraint: none or one CellVocabulary ERROR ERROR
org.biopax.validator.rules.BioSourceCellTypeCvRule BioSource.cellType - CellVocabulary, CL ontology, "cell" (CL:0000000) children terms (names) WARNING WARNING
org.biopax.validator.rules.BioSourceTaxonXrefCRRule Checks BioSource.taxonXref cardinality/range: none or one UnificationXref ERROR WARNING
org.biopax.validator.rules.BioSourceTissueCRRule Checks BioSource.tissue cardinality/range constraint: none or one TissueVocabulary ERROR IGNORE
org.biopax.validator.rules.BioSourceTissueCvRule BioSource.tissue -> TissueVocabulary, BTO ontology, children of "brenda source tissue ontology" (BTO:0000000) WARNING WARNING
org.biopax.validator.rules.BiochemReactParticipantsLocationRule BiochemicalReaction (base) participants should not change to another compartment on the other side of the reaction; otherwise, use TransportWithBiochemicalReaction. (Complexes are matched by name; other physical entities are identified using entity references) WARNING WARNING
org.biopax.validator.rules.BiochemicalPathwayStepAndCatalysisDirectionRule If a BiochemicalPathwayStep.stepDirection is not empty, then direction of Catalysis instances are either blank or equivalent; and the corresponding Conversion.conversionDirection in the stepConversion, if any, is specified as "REVERSIBLE" ERROR WARNING
org.biopax.validator.rules.BiopaxElementIdLengthRule Checks and informs whether a URI (ID) string is longer than commonly used ones WARNING WARNING
org.biopax.validator.rules.BiopaxElementIdRule BioPAX Element ID (including the namespace) Must Be a Valid URI; ERROR ERROR
org.biopax.validator.rules.CatalysisControllerCRRule Warns if a catalysis has multiple controllers (PhysicalEntity or Pathway). Normally a controller for a catalysis interaction is a single PhysicalEntity, and if you have two, they are often part of a complex. WARNING WARNING
org.biopax.validator.rules.CatalysisDirectionCRRule Checks Catalysis.catalysisDirection cardinality/range constraint: none or one CatalysisDirectionType ERROR IGNORE
org.biopax.validator.rules.CellularLocationCvRule description is not found in the messages.properties file ERROR WARNING
org.biopax.validator.rules.ClonedUtilityClassRule Warns about duplicate (semantically equivalent) utility classes (whereas, e.g., a single BioSource instance can be linked from several entities) WARNING IGNORE
org.biopax.validator.rules.ComplexAssemblyHasComplexParticipantRule Checks if either a ComplexAssembly has got a complex at least on one side, or any two or more interaction participants are bound to each other on either left or right side. ERROR WARNING
org.biopax.validator.rules.ComplexComponentsMultipleLocationRule Warns when complex components span multiple cellular compartments WARNING WARNING
org.biopax.validator.rules.ComplexComponentsSameLocationRule Checks components' cellular location is not empty if one is specified for the complex WARNING WARNING
org.biopax.validator.rules.ComplexTwoOrMoreParticipantsRule Checks complexes consist of several components, or one's stoichiometry > 1 WARNING WARNING
org.biopax.validator.rules.ControlTypeRule If set, the controlType must be "ACTIVATION" for Catalysis and either "ACTIVATION" or "INHIBITION" for TemplateReactionRegulation ERROR WARNING
org.biopax.validator.rules.ControlledVocabularyTermCRRule Checks controlled vocabulary has at least one 'term' ("best practice") WARNING WARNING
org.biopax.validator.rules.ControlledVocabularyXrefCRRule Checks controlled vocabulary has one unification xref WARNING WARNING
org.biopax.validator.rules.ConversionDirectionCRRule Checks Conversion.conversionDirection cardinality/range: 0 or 1 ConversionDirectionType value ERROR IGNORE
org.biopax.validator.rules.ConversionToComplexAssemblyRule Checks whether a Conversion should be cast as a ComplexAssembly WARNING WARNING
org.biopax.validator.rules.DanglingElementRule Checks if an object is actually referenced from other objects (except for pathways) WARNING WARNING
org.biopax.validator.rules.DataPropertyIllegalValueRule Warns about empty and potentially illegal data property values, e.g., '-1', 'NULL', 'NIL', etc. WARNING WARNING
org.biopax.validator.rules.DegradationConversionDirectionRule Checks Degradation.conversionDirection value is "LEFT_TO_RIGHT" or empty ERROR WARNING
org.biopax.validator.rules.DisplayNameRule Checks whether a short name is present (where applicable); warns if a displayName is too long WARNING WARNING
org.biopax.validator.rules.DnaEntityReferenceCRRule Checks Dna.entityReference value is a DnaReference or nothing ERROR WARNING
org.biopax.validator.rules.DnaEntityReferenceRule Checks either Dna.entityReference or Dna.memberPhysicalEntity is not empty. ERROR WARNING
org.biopax.validator.rules.DnaRegionEntityReferenceCRRule Checks DnaRegion.entityReference value is a DnaRegionReference or nothing ERROR WARNING
org.biopax.validator.rules.DnaRegionEntityReferenceRule Checks either DnaRegion.entityReference or DnaRegion.memberPhysicalEntity is not empty. ERROR WARNING
org.biopax.validator.rules.DnaRegionReferenceAbsoluteRegionCRRule DnaRegionReference.absoluteRegion property: cardinality=0,1 (functional), range = SequenceLocation ERROR ERROR
org.biopax.validator.rules.DuplicateIdCaseInsensitiveRule Checks for "duplicate" IDs - when compared ignoring case. WARNING IGNORE
org.biopax.validator.rules.EmptyModelRule Checks If a BioPAX Model Is Empty (i.e., for some reason, it has no BioPAX elements) ERROR ERROR
org.biopax.validator.rules.EntityFeatureInverseFunctionalRule Checks if an EntityFeature is owned by multiple EntityReferences ERROR ERROR
org.biopax.validator.rules.EntityReferenceSamePhysicalEntitiesRule Checks physical entities that reference the same EntityReference are different (in different states) ERROR IGNORE
org.biopax.validator.rules.EntityReferenceTypeCRRule Checks EntityReference properties cardinality/range: none or one EntityReferenceTypeVocabulary value ERROR ERROR
org.biopax.validator.rules.EntityReferenceXrefRule Checks a non-generic EntityReference has a (unification) xref ERROR ERROR
org.biopax.validator.rules.EvidenceCodeCvRule evidence.evidenceCode has valid EvidenceCodeVocabulary term: MI "interaction detection method", "participant identification method", or "feature detection method" children (names) WARNING WARNING
org.biopax.validator.rules.EvidencePropertiesUsageRule Checks Evidence properties cardinality: at least one of: 'evidenceCode' (EvidenceCodeVocabulary), 'confidence' (Score), or 'experimantalForm' (ExperimentalForm) must have value ERROR WARNING
org.biopax.validator.rules.ExperimentalFormDescriptionCRRule Checks ExperimentalForm.experimentalFormDescription has at least one ExperimentalFormVocabulary value ERROR ERROR
org.biopax.validator.rules.ExperimentalFormDescriptionCvRule experimentalForm.experimentalFormDescription: ExperimentalFormVocabulary term: MI:0002, MI:0495 or MI:0346 children (names) ERROR WARNING
org.biopax.validator.rules.GeneOrganismCRRule Checks Gene.organism has either none or one value (BioSource) ERROR ERROR
org.biopax.validator.rules.GenericEntityReferenceXrefRule Checks a generic EntityReference has a (unification) xref WARNING WARNING
org.biopax.validator.rules.GenericProteinReferenceOrganismRule Warns if organism property is not set for a generic ProteinReference. WARNING WARNING
org.biopax.validator.rules.GeneticInteractionParticipantCRRule Checks GeneticInteraction.participant property contains at least two Genes ERROR ERROR
org.biopax.validator.rules.GeneticInteractionPhenotypeCRRule Checks GeneticInteraction.phenotype has exactly one PhenotypeVocabulary value WARNING WARNING
org.biopax.validator.rules.GeneticInteractionTypeCRRule Checks GeneticInteraction.interactionType either has none or one InteractionVocabulary ERROR ERROR
org.biopax.validator.rules.InteractionParticipantsLocationRule Warns if participants of a generic interaction span multiple cellular compartments. For Transport, however, it checks separately on the left and right sides, and it does not check for TemplateReaction at all. WARNING WARNING
org.biopax.validator.rules.InteractionTypeCvRule Interaction.interactionType is InteractionTypeVocabulary valid term: MI "interaction type" children (names). WARNING WARNING
org.biopax.validator.rules.ModificationFeatureLocationCRRule Warns if ModificationFeature.featureLocation is not set WARNING WARNING
org.biopax.validator.rules.ModificationTypeCRRule Checks ModificationFeature.modificationType contains exactly one SequenceModificationVocabulary ERROR WARNING
org.biopax.validator.rules.ModulationControllerCRRule Checks Modulation.controller has at most one PhysicalEntity (or Pathway) ERROR WARNING
org.biopax.validator.rules.NextStepShareParticipantsRule PathwayStep, if listed in the nextStep property of another PathwayStep, must have not empty intersection of participants of their stepProcess-es WARNING IGNORE
org.biopax.validator.rules.NotAdvisedInstancesRule warns about using of too general BioPAX classes WARNING IGNORE
org.biopax.validator.rules.NotAllowedInstancesRule several top-level BioPAX classes are not allowed to use directly ERROR WARNING
org.biopax.validator.rules.NucleicAcidModificationFeatureCvRule Checks Dna/Rna modificationFeature.modoficationType has valid SequenceModificationVocabulary term: SO:1000132 with all its children and SO:0001059 and all children (use names) ERROR WARNING
org.biopax.validator.rules.PathwayMultiOrganismRule description is not found in the messages.properties file ERROR ERROR
org.biopax.validator.rules.PathwayOrganismCRRule Checks Pathway.organism cardinality/range: none or one BioSource value ERROR ERROR
org.biopax.validator.rules.PathwayStepProcessesArePathwayComponents PathwayStep.stepProcess (or stepConversion) must be also listed in the pathway component property WARNING IGNORE
org.biopax.validator.rules.PhenotypeCvRule GeneticInteraction.phenotype, PhenotypeVocabulary: PATO "organismal quality" all children, or "viability" ERROR WARNING
org.biopax.validator.rules.PhysicalEntityAmbiguousFeatureRule Checks if a PhysicalEntity that is both a participant of a Conversion and a component of a Complex has proper binding features WARNING WARNING
org.biopax.validator.rules.PhysicalEntityCellularLocationCRRule Checks PhysicalEntity.cellularLocation cardinality/range: either none or one CellularLocationVocabulary ERROR ERROR
org.biopax.validator.rules.ProteinEntityReferenceCRRule Checks Protein.entityReference value is a ProteinReference or nothing ERROR WARNING
org.biopax.validator.rules.ProteinEntityReferenceRule Checks either Protein.entityReference or Protein.memberPhysicalEntity is not empty. ERROR WARNING
org.biopax.validator.rules.ProteinModificationFeatureCvRule Checks Protein.modificationFeature.modoficationType has valid SequenceModificationVocabulary term: MI:0118 with all its children and MI:0120 and all children (use names) ERROR WARNING
org.biopax.validator.rules.ProteinReferenceOrganismRule Checks (non-generic) ProteinReference has organism property set (BioSource) WARNING WARNING
org.biopax.validator.rules.RelationshipTypeCvRule Checks (RelationshipXref.relationshipType) RelationshipTypeVocabulary terms: all "MI:0353" children names WARNING WARNING
org.biopax.validator.rules.RnaEntityReferenceCRRule Checks Rna.entityReference value is a RnaReference or nothing ERROR WARNING
org.biopax.validator.rules.RnaEntityReferenceRule Checks either Rna.entityReference or Rna.memberPhysicalEntity is not empty. ERROR WARNING
org.biopax.validator.rules.RnaRegionEntityReferenceCRRule Checks RnaRegion.entityReference value is a RnaRegionReference or nothing ERROR WARNING
org.biopax.validator.rules.RnaRegionEntityReferenceRule Checks either RnaRegion.entityReference or RnaRegion.memberPhysicalEntity is not empty. ERROR WARNING
org.biopax.validator.rules.RnaRegionReferenceAbsoluteRegionCRRule Checks RnaRegionReference properties cardinality/range: either one or none SequenceLocation value ERROR IGNORE
org.biopax.validator.rules.SameLeftRightRule Checks if any of the participants on one side of this conversion remained unchanged on the other side( as tested by isEquivalent method). This is a violation of chemical semantics. These participants should be listed as controllers instead ERROR WARNING
org.biopax.validator.rules.SameNameDiffKindPhysEntitiesRule Checks different physical entities having names in common (may flag about a more serious error) WARNING IGNORE
org.biopax.validator.rules.ScoreSourceCRRule Checks Score.scoreSource cardinality/range: either one or none Provenance value ERROR IGNORE
org.biopax.validator.rules.SequenceIntervalBeginCRRule Checks SequenceInterval.sequenceIntervalBegin cardinality/range: either one or none SequenceSite ERROR IGNORE
org.biopax.validator.rules.SequenceIntervalEndCRRule Checks SequenceInterval.sequenceIntervalEnd cardinality/range: either one or none SequenceSite ERROR IGNORE
org.biopax.validator.rules.SequenceRegionCvRule SequenceRegionVocabulary: SO "region" children terms (names) ERROR WARNING
org.biopax.validator.rules.SharedUnificationXrefRule Different elements have the same UnificationXrefs! This violates UnificationXref semantics, unless the objects are, in fact, equivalent (despite having different URIs) WARNING WARNING
org.biopax.validator.rules.SimplePhysicalEntityConversionRule Checks that biopolymers on one side of the conversion are those (modified and/or relocated) from the other side, and not new ones; two exceptions are: ComplexAssembly and Degradation. WARNING WARNING
org.biopax.validator.rules.SimplePhysicalEntityFeaturesRule checks if a Physical Entity Feature is also a feature of its Entity Reference. WARNING WARNING
org.biopax.validator.rules.SmallMoleculeEntityReferenceCRRule Checks SmallMolecule.entityReference value is a SmallMoleculeReference or nothing ERROR WARNING
org.biopax.validator.rules.SmallMoleculeEntityReferenceRule Checks either SmallMolecule.entityReference or SmallMolecule.memberPhysicalEntity is not empty. ERROR WARNING
org.biopax.validator.rules.SmrStructureCRRule Checks SmallMoleculeReference.structure cardinality/range: either one or none ChemicalStructure ERROR IGNORE
org.biopax.validator.rules.StoichiometricCoefficientCRRule Checks Stoichiometry.stoichiometricCoefficient range/cardinality: must have exactly one float value ERROR WARNING
org.biopax.validator.rules.StoichiometryPhysicalEntityCRRule Checks Stoichiometry.physicalEntity cardinality/range: must have exactly one PhysicalEntity value ERROR ERROR
org.biopax.validator.rules.TemplateReactionRegulationControllerCRRule Checks TemplateReactionRegulation.controller range is PhysicalEntity (multiple) ERROR ERROR
org.biopax.validator.rules.UnificationXrefDbCRRule description is not found in the messages.properties file ERROR ERROR
org.biopax.validator.rules.UnificationXrefIdCRRule description is not found in the messages.properties file ERROR ERROR
org.biopax.validator.rules.UnificationXrefLimitedRule UnificationXref external database applicability rule WARNING WARNING
org.biopax.validator.rules.XrefDbCRRule Checks 'db' property of Xref has string value ("best practice") WARNING WARNING
org.biopax.validator.rules.XrefIdCRRule Checks 'id' property of Xref has string value ("best practice") WARNING WARNING
org.biopax.validator.rules.XrefRule Validates xref (db/id). ERROR WARNING
org.biopax.validator.rules.XrefSynonymDbRule Checks for misspelled or deprecated db names. WARNING WARNING