• Resource: panther/Beta3_adrenergic_receptor_signaling_pathway.owl; different types of problem: 9
    • number of physical entities : 24  number of pathways : 3  number of genes : 0  number of interactions : 10 
    • auto-fix: true; normalize:
    • errors/warnings: 90 - not fixed: 64;  errors not fixed: 6
    • Modified BioPAX  ("escaped" RDF in HTML; choose BioPAX or XML as return if you plan to process it)
    • ERROR: cardinality.violated , category: SPECIFICATION,  cases: 6,  not fixed: 6
      Cardinality violation
      • object: DISSOCIATION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: HETERODIMER_ASSOCIATION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: MODULATION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: STATE_TRANSITION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: TRANSPORT
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: TRIGGER
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)

    • WARNING: cardinality.violated , category: SPECIFICATION,  cases: 11,  not fixed: 11
      Cardinality violation
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=DISSOCIATION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=HETERODIMER_ASSOCIATION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=STATE_TRANSITION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=TRANSPORT
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=DISSOCIATION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=HETERODIMER_ASSOCIATION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=MODULATION
        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)
      • object: CELLDESIGNER_REACTION_TYPE=TRANSPORT
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=TRIGGER
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: PANTHER_GROUPING_10
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 10,  not fixed: 10
      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=DISSOCIATION
        Illegal term(s): [DISSOCIATION]; [Valid 'MI' terms: ALL children of MI:0190]
        (found by: org.biopax.validator.rules.InteractionTypeCvRule)
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=HETERODIMER_ASSOCIATION
        Illegal term(s): [HETERODIMER_ASSOCIATION]; [Valid 'MI' terms: ALL children of MI:0190]
        (found by: org.biopax.validator.rules.InteractionTypeCvRule)
      • 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_INTERACTION_VOCABULARY=TRANSPORT
        Illegal term(s): [TRANSPORT]; [Valid 'MI' terms: ALL children of MI:0190]
        (found by: org.biopax.validator.rules.InteractionTypeCvRule)
      • object: CELLDESIGNER_REACTION_TYPE=DISSOCIATION
        Illegal term(s): [DISSOCIATION]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: CELLDESIGNER_REACTION_TYPE=HETERODIMER_ASSOCIATION
        Illegal term(s): [HETERODIMER_ASSOCIATION]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: CELLDESIGNER_REACTION_TYPE=MODULATION
        Illegal term(s): [MODULATION]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • 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)
      • object: CELLDESIGNER_REACTION_TYPE=TRANSPORT
        Illegal term(s): [TRANSPORT]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: CELLDESIGNER_REACTION_TYPE=TRIGGER
        Illegal term(s): [TRIGGER]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)

    • WARNING: min.cardinality.violated , category: SPECIFICATION,  cases: 3,  not fixed: 3
      Minimal cardinality violation
      • object: _AC_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _G_Protein_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _SNARE_COMPLEX_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)

    • WARNING: multiple.location , category: INFORMATION,  cases: 1,  not fixed: 1
      Participants span multiple cellular locations. This may be an error e.g. if the cellular locations do not connect to each other. Check that this information makes sense
      • object: HETERODIMER_ASSOCIATION_LEFT__NE-_Complex__GDP_G_Protein__brBetasub_3_-RIGHT__Complex__GDP_G_Protein__brBetasub_3_NE_-_re18
        participants: _NE_s66_a5_, _Complex__GDP_G_Protein__brBetasub_3__s35_a45_
        (found by: org.biopax.validator.rules.InteractionParticipantsLocationRule)

    • WARNING: no.display.name , category: RECOMMENDATION,  cases: 25,  all fixed!
      No display name is specified. It is useful to have one for the visualization purposes
      • [FIXED!]  object: http://identifiers.org/uniprot/O00161
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O14610
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O14775
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O60262
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O95721
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P16520
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P23763
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P38405
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P50150
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P50151
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P51828
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P59768
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P60880
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P62873
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P62879
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P63027
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P63215
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P63218
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q08462
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q13277
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q15836
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9BV40
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9HAV0
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9UBI6
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9UK08
        (found by: org.biopax.validator.rules.DisplayNameRule)

    • WARNING: no.xref.cv.terms , category: RECOMMENDATION,  cases: 1,  all fixed!
      Controlled vocabulary(-ies) without unification xrefs for some of the (valid) terms
      • [FIXED!]  object: PANTHER_GROUPING_10
        terms: {By Homology=[OntologyTermImpl{acc='MI:2163', name='by homology'}]}; MI:2163 added!; info: [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)

    • WARNING: no.xrefs , category: RECOMMENDATION,  cases: 3,  not fixed: 3
      EntityReference does not have any xrefs
      • object: _AC_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _G_Protein_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _SNARE_COMPLEX_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)

    • WARNING: too.long.display.name , category: RECOMMENDATION,  cases: 30,  not fixed: 30
      'displayName' exceeds the recommended maximum. These names should be kept short so they can easily be displayed, e.g., in a pathway diagram
      • object: _Complex__GDP_G_Protein__brBetasub_3__s35_a45_
        Complex (GDP/G-Protein/_brBetasub_3), length=36 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _Complex__GDP_G_Protein__brBetasub_3_NE__s38_a53_
        Complex (GDP/G-Protein/_brBetasub_3/NE), length=39 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: DISSOCIATION_LEFT__GTP-_Complex__GDP_G_Protein__brBetasub_3_NE_-RIGHT__GDP-_Complex__Beta3_NE_-_Complex__GTP_G_Protein_-_re19
        DISSOCIATION_LEFT__GTP-_Complex__GDP_G_Protein__brBetasub_3_NE_-RIGHT__GDP-_Complex__Beta3_NE_-_Complex__GTP_G_Protein_-_re19, length=125 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__NE-_Complex__GDP_G_Protein__brBetasub_3_-RIGHT__Complex__GDP_G_Protein__brBetasub_3_NE_-_re18
        HETERODIMER_ASSOCIATION_LEFT__NE-_Complex__GDP_G_Protein__brBetasub_3_-RIGHT__Complex__GDP_G_Protein__brBetasub_3_NE_-_re18, length=123 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/panther.pathway/P04379
        Beta3 adrenergic receptor signaling pathway, length=43 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/O00161
        Synaptosomal-associated protein 23(auto-created form other names!), length=34 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/O14610
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-T2(auto-created form other names!), length=66 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/O14775
        Guanine nucleotide-binding protein subunit beta-5(auto-created form other names!), length=49 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/O60262
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7(auto-created form other names!), length=65 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/O95721
        Synaptosomal-associated protein 29(auto-created form other names!), length=34 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P16520
        Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3(auto-created form other names!), length=64 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P23763
        Vesicle-associated membrane protein 1(auto-created form other names!), length=37 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P38405
        Guanine nucleotide-binding protein G(olf) subunit alpha(auto-created form other names!), length=55 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P50150
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-4(auto-created form other names!), length=65 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P50151
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-10(auto-created form other names!), length=66 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P59768
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2(auto-created form other names!), length=65 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P60880
        Synaptosomal-associated protein 25(auto-created form other names!), length=34 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P62873
        Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1(auto-created form other names!), length=64 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P62879
        Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2(auto-created form other names!), length=64 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P63027
        Vesicle-associated membrane protein 2(auto-created form other names!), length=37 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P63215
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-3(auto-created form other names!), length=65 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P63218
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-5(auto-created form other names!), length=65 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q15836
        Vesicle-associated membrane protein 3(auto-created form other names!), length=37 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q9BV40
        Vesicle-associated membrane protein 8(auto-created form other names!), length=37 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q9HAV0
        Guanine nucleotide-binding protein subunit beta-4(auto-created form other names!), length=49 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q9UBI6
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-12(auto-created form other names!), length=66 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q9UK08
        Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-8(auto-created form other names!), length=65 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__AC-RIGHT__AC-_re17
        STATE_TRANSITION_LEFT__AC-RIGHT__AC-_re17, length=41 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__ATP-RIGHT__cAMP-_re9
        STATE_TRANSITION_LEFT__ATP-RIGHT__cAMP-_re9, length=43 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: TRANSPORT_LEFT__NE-RIGHT__NE-_re2
        TRANSPORT_LEFT__NE-RIGHT__NE-_re2, length=33 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)