• Resource: panther/Phenylethylamine_degradation.owl; different types of problem: 8
    • number of interactions : 4  number of genes : 0  number of pathways : 1  number of physical entities : 11 
    • auto-fix: true; normalize:
    • errors/warnings: 20 - not fixed: 17;  errors not fixed: 2
    • Modified BioPAX  ("escaped" RDF in HTML; choose BioPAX or XML as return if you plan to process it)
    • ERROR: cardinality.violated , category: SPECIFICATION,  cases: 1,  not fixed: 1
      Cardinality violation
      • object: STATE_TRANSITION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)

    • ERROR: no.xrefs , category: RECOMMENDATION,  cases: 1,  not fixed: 1
      EntityReference does not have any xrefs
      • object: _Phenylacetaldehyde_br_dehydrogenase_PROTEIN
        (found by: org.biopax.validator.rules.EntityReferenceXrefRule)

    • WARNING: cardinality.violated , category: SPECIFICATION,  cases: 3,  not fixed: 3
      Cardinality violation
      • object: _Phenylacetaldehyde_br_dehydrogenase_PROTEIN
        property: organism requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ProteinReferenceOrganismRule)
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=STATE_TRANSITION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=STATE_TRANSITION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 2,  not fixed: 2
      Term is not found in the recommended controlled vocabulary (- wrong name/spelling or the identifier/accession is used instead of the term)
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=STATE_TRANSITION
        Illegal term(s): [STATE_TRANSITION]; [Valid 'MI' terms: ALL children of MI:0190]
        (found by: org.biopax.validator.rules.InteractionTypeCvRule)
      • object: CELLDESIGNER_REACTION_TYPE=STATE_TRANSITION
        Illegal term(s): [STATE_TRANSITION]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)

    • WARNING: min.cardinality.violated , category: SPECIFICATION,  cases: 1,  not fixed: 1
      Minimal cardinality violation
      • object: _Phenylethylamine_br_oxidase_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)

    • WARNING: no.display.name , category: RECOMMENDATION,  cases: 3,  all fixed!
      No display name is specified. It is useful to have one for the visualization purposes
      • [FIXED!]  object: http://identifiers.org/uniprot/O75106
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P19801
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q16853
        (found by: org.biopax.validator.rules.DisplayNameRule)

    • WARNING: no.xrefs , category: RECOMMENDATION,  cases: 1,  not fixed: 1
      EntityReference does not have any xrefs
      • object: _Phenylethylamine_br_oxidase_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)

    • WARNING: too.long.display.name , category: RECOMMENDATION,  cases: 8,  not fixed: 8
      'displayName' exceeds the recommended maximum. These names should be kept short so they can easily be displayed, e.g., in a pathway diagram
      • object: _Phenylacetaldehyde_br_dehydrogenase_PROTEIN
        Phenylacetaldehyde dehydrogenase, length=32 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _Phenylacetaldehyde_dehydrogenase_s11_a12_
        Phenylacetaldehyde dehydrogenase, length=32 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/panther.pathway/P02766
        Phenylethylamine degradation, length=28 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/O75106
        Retina-specific copper amine oxidase(auto-created form other names!), length=36 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P19801
        Amiloride-sensitive amine oxidase [copper-containing](auto-created form other names!), length=53 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q16853
        Membrane primary amine oxidase(auto-created form other names!), length=30 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__O2-_phenylethylamine-_H2O-RIGHT__NH3-_phenylacetaldehyde-_H2O2-_r1
        STATE_TRANSITION_LEFT__O2-_phenylethylamine-_H2O-RIGHT__NH3-_phenylacetaldehyde-_H2O2-_r1, length=89 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__phenylacetaldehyde-_NAD-_H2O-RIGHT__NADH-_phenylacetate-_r2
        STATE_TRANSITION_LEFT__phenylacetaldehyde-_NAD-_H2O-RIGHT__NADH-_phenylacetate-_r2, length=82 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)