• Resource: panther/Alpha_adrenergic_receptor_signaling_pathway.owl; different types of problem: 9
    • number of genes : 0  number of interactions : 18  number of pathways : 2  number of physical entities : 42 
    • auto-fix: true; normalize:
    • errors/warnings: 101 - not fixed: 79;  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: MODULATION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: PHYSICAL_STIMULATION
        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: 17,  not fixed: 17
      Cardinality violation
      • object: _Alpha1A_1B_1C_s16_sa13_rs1_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: _Alpha1A_1B_1C_s21_sa15_rs1_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: _Alpha1A_1B_1C_s3_sa3_rs1_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: _Alpha1A_1B_1C_s6_sa6_rs1_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: _Alpha1A_1B_1C_s9_sa9_rs1_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: _Nerve_Fiber_c5_
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: _smooth_cardiac_muscle,_or_neuron_c2_
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_INTERACTION_VOCABULARY=DISSOCIATION
        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=MODULATION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=PHYSICAL_STIMULATION
        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_9
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 9,  not fixed: 9
      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=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=MODULATION
        Illegal term(s): [MODULATION]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: CELLDESIGNER_REACTION_TYPE=PHYSICAL_STIMULATION
        Illegal term(s): [PHYSICAL_STIMULATION]; [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: 6,  not fixed: 6
      Minimal cardinality violation
      • object: _Alpha_sub_1A_1B_1C_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _Nerve_Fiber_c5_
        property: term requires at least 1 value(s).
        (found by: org.biopax.validator.rules.ControlledVocabularyTermCRRule)
      • object: _PKC_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _PLC_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _smooth_cardiac_muscle,_or_neuron_c2_
        property: term requires at least 1 value(s).
        (found by: org.biopax.validator.rules.ControlledVocabularyTermCRRule)
      • object: _SNARE_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)

    • WARNING: multiple.location , category: INFORMATION,  cases: 2,  not fixed: 2
      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: STATE_TRANSITION_LEFT__Adrenaline-_Complex__Alpha1A_1B__1C_G_Protein__GDP_-_NE-RIGHT__Complex__Alpha1A_1B__1C_Adrenaline_or_NE__G_Protein_GDP_-_r64
        participants: _Complex__Alpha1A_1B__1C_G_Protein__GDP__s68_a77_, _Adrenaline_s65_a4_
        (found by: org.biopax.validator.rules.InteractionParticipantsLocationRule)
      • object: STATE_TRANSITION_LEFT__Adrenaline-_Complex__Alpha1A_1B__1C_G_Protein__GDP_-_NE-RIGHT__Complex__Alpha1A_1B__1C_G_Protein__GDP_Adrenaline_or_NE_-_r66
        participants: _Complex__Alpha1A_1B__1C_G_Protein__GDP__s95_a94_, _NE_s66_a75_
        (found by: org.biopax.validator.rules.InteractionParticipantsLocationRule)

    • WARNING: no.display.name , category: RECOMMENDATION,  cases: 21,  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/O43752
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O60499
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P05129
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P08913
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P17252
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P18089
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P18825
        (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/P35348
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P35368
        (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/P63027
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q00722
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q01970
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q02156
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q05655
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q15147
        (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/Q9NQ66
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9P212
        (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_9
        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: 4,  not fixed: 4
      EntityReference does not have any xrefs
      • object: _Alpha_sub_1A_1B_1C_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _PKC_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _PLC_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _SNARE_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)

    • WARNING: too.long.display.name , category: RECOMMENDATION,  cases: 35,  not fixed: 35
      '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__Alpha1A_1B__1C_Adrenaline_or_NE__G_Protein_GDP__s106_a103_
        Complex (Alpha1A/1B/ 1C/Adrenaline or NE/ G-Protein/GDP), length=56 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _Complex__Alpha1A_1B__1C_Adrenaline_or_NE__s109_a109_
        Complex (Alpha1A/1B/ 1C/Adrenaline or NE), length=41 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _Complex__Alpha1A_1B__1C_G_Protein__GDP__s68_a77_
        Complex (Alpha1A/1B/ 1C/G-Protein/ GDP), length=39 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _Complex__Alpha1A_1B__1C_G_Protein__GDP__s95_a94_
        Complex (Alpha1A/1B/ 1C/G-Protein/ GDP), length=39 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _Complex__Alpha1A_1B__1C_G_Protein__GDP_Adrenaline_or_NE__s116_a118_
        Complex (Alpha1A/1B/ 1C/G-Protein/ GDP/Adrenaline or NE), length=56 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: DISSOCIATION_LEFT__GTP-_Complex__Alpha1A_1B__1C_Adrenaline_or_NE__G_Protein_GDP_-RIGHT__GDP-_Complex__GTP_G_Protein_-_Complex__Alpha1A_1B__1C_Adrenaline_or_NE_-_r65
        DISSOCIATION_LEFT__GTP-_Complex__Alpha1A_1B__1C_Adrenaline_or_NE__G_Protein_GDP_-RIGHT__GDP-_Complex__GTP_G_Protein_-_Complex__Alpha1A_1B__1C_Adrenaline_or_NE_-_r65, length=164 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: DISSOCIATION_LEFT__PIP2-RIGHT__DAG-_IP3-_r8
        DISSOCIATION_LEFT__PIP2-RIGHT__DAG-_IP3-_r8, length=43 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/panther.pathway/P00002
        Alpha 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/P05129
        Protein kinase C gamma type(auto-created form other names!), length=27 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P08913
        Alpha-2A adrenergic receptor(auto-created form other names!), length=28 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P17252
        Protein kinase C alpha type(auto-created form other names!), length=27 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P18089
        Alpha-2B adrenergic receptor(auto-created form other names!), length=28 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P18825
        Alpha-2C adrenergic receptor(auto-created form other names!), length=28 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/P35348
        Alpha-1A adrenergic receptor(auto-created form other names!), length=28 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P35368
        Alpha-1B adrenergic receptor(auto-created form other names!), length=28 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/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/Q00722
        1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2(auto-created form other names!), length=64 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q01970
        1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3(auto-created form other names!), length=64 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q02156
        Protein kinase C epsilon type(auto-created form other names!), length=29 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q05655
        Protein kinase C delta type(auto-created form other names!), length=27 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q15147
        1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4(auto-created form other names!), length=64 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/Q9NQ66
        1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1(auto-created form other names!), length=64 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q9P212
        1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1(auto-created form other names!), length=67 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Adrenaline-_Complex__Alpha1A_1B__1C_G_Protein__GDP_-_NE-RIGHT__Complex__Alpha1A_1B__1C_Adrenaline_or_NE__G_Protein_GDP_-_r64
        STATE_TRANSITION_LEFT__Adrenaline-_Complex__Alpha1A_1B__1C_G_Protein__GDP_-_NE-RIGHT__Complex__Alpha1A_1B__1C_Adrenaline_or_NE__G_Protein_GDP_-_r64, length=147 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Adrenaline-_Complex__Alpha1A_1B__1C_G_Protein__GDP_-_NE-RIGHT__Complex__Alpha1A_1B__1C_G_Protein__GDP_Adrenaline_or_NE_-_r66
        STATE_TRANSITION_LEFT__Adrenaline-_Complex__Alpha1A_1B__1C_G_Protein__GDP_-_NE-RIGHT__Complex__Alpha1A_1B__1C_G_Protein__GDP_Adrenaline_or_NE_-_r66, length=147 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__IP3R-RIGHT__IP3R-_r63
        STATE_TRANSITION_LEFT__IP3R-RIGHT__IP3R-_r63, length=44 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__PKC-RIGHT__PKC-_r52
        STATE_TRANSITION_LEFT__PKC-RIGHT__PKC-_r52, length=42 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__PLC-RIGHT__PLC-_r67
        STATE_TRANSITION_LEFT__PLC-RIGHT__PLC-_r67, length=42 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: TRANSPORT_LEFT__Adrenaline-RIGHT__Adrenaline-_r56
        TRANSPORT_LEFT__Adrenaline-RIGHT__Adrenaline-_r56, length=49 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: TRANSPORT_LEFT__Ca2_PLUS_-RIGHT__Ca2_PLUS_-_r22
        TRANSPORT_LEFT__Ca2_PLUS_-RIGHT__Ca2_PLUS_-_r22, length=47 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: TRANSPORT_LEFT__NE-RIGHT__NE-_r57
        TRANSPORT_LEFT__NE-RIGHT__NE-_r57, length=33 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)