| 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 |
WARNING |
| 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 |