• Resource: panther/Axon_guidance_mediated_by_Slit_Robo.owl; different types of problem: 11
    • number of pathways : 3  number of genes : 0  number of interactions : 29  number of physical entities : 45 
    • auto-fix: true; normalize:
    • errors/warnings: 75 - not fixed: 64;  errors not fixed: 8
    • 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: HETERODIMER_ASSOCIATION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: INHIBITION
        property: db requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.XrefDbCRRule)
      • object: KNOWN_TRANSITION_OMITTED
        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)

    • ERROR: no.xrefs , category: RECOMMENDATION,  cases: 2,  not fixed: 2
      EntityReference does not have any xrefs
      • object: _Mena_PROTEIN
        (found by: org.biopax.validator.rules.EntityReferenceXrefRule)
      • object: _Ptp10D_PROTEIN
        (found by: org.biopax.validator.rules.EntityReferenceXrefRule)

    • WARNING: cardinality.violated , category: SPECIFICATION,  cases: 14,  not fixed: 14
      Cardinality violation
      • object: _Mena_PROTEIN
        property: organism requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ProteinReferenceOrganismRule)
      • object: _Ptp10D_PROTEIN
        property: organism requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ProteinReferenceOrganismRule)
      • 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=HETERODIMER_ASSOCIATION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=INHIBITION
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: CELLDESIGNER_REACTION_TYPE=KNOWN_TRANSITION_OMITTED
        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: MODIFICATION_FEATURE_phosphorylated
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: PANTHER_GROUPING_7
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)
      • object: SEQUENCE_REGION_VOCABULARY__Y
        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=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=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=INHIBITION
        Illegal term(s): [INHIBITION]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: CELLDESIGNER_REACTION_TYPE=KNOWN_TRANSITION_OMITTED
        Illegal term(s): [KNOWN_TRANSITION_OMITTED]; [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)

    • WARNING: min.cardinality.violated , category: SPECIFICATION,  cases: 5,  not fixed: 5
      Minimal cardinality violation
      • object: _Netrin_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _Rac_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _Slit_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: MODIFICATION_FEATURE_phosphorylated
        property: term requires at least 1 value(s).
        (found by: org.biopax.validator.rules.ControlledVocabularyTermCRRule)
      • object: SEQUENCE_REGION_VOCABULARY__Y
        property: term requires at least 1 value(s).
        (found by: org.biopax.validator.rules.ControlledVocabularyTermCRRule)

    • WARNING: multiple.location , category: INFORMATION,  cases: 3,  not fixed: 3
      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__DCC-_Slit-RIGHT__Complex__Slit_DCC_-_r21
        participants: _Slit_s3_a3_, _Complex__Slit_DCC__s14_a14_
        (found by: org.biopax.validator.rules.InteractionParticipantsLocationRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__Sdf1-_Cxcr4-RIGHT__Complex__Sdf1_Cxcr4_-_r16
        participants: _Sdf1_s26_a30_, _Complex__Sdf1_Cxcr4__s29_a33_
        (found by: org.biopax.validator.rules.InteractionParticipantsLocationRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__SrGAP-_Slit-_Robo-RIGHT__Complex__Slit_Robo__SrGAP_-_r18
        participants: _Slit_s3_a3_, _SrGAP_s8_a36_
        (found by: org.biopax.validator.rules.InteractionParticipantsLocationRule)

    • WARNING: no.display.name , category: RECOMMENDATION,  cases: 10,  all fixed!
      No display name is specified. It is useful to have one for the visualization purposes
      • [FIXED!]  object: http://identifiers.org/uniprot/O00634
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O75093
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O75094
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O94813
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O95631
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P15153
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P63000
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q96CW9
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9HB63
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9Y2I2
        (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_7
        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: _Netrin_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _Rac_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _Slit_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)

    • WARNING: null.entity.reference , category: RECOMMENDATION,  cases: 3,  not fixed: 3
      A Protein, SmallMolecule, etc. (but not a complex) has neither 'entityReference' (highly recommended) nor 'memberPhysicalEntity' values set
      • object: _Comm_s34_sa16_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)
      • object: _Comm_s37_a42_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)
      • object: _Comm_s54_sa11_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)

    • WARNING: too.long.display.name , category: RECOMMENDATION,  cases: 19,  not fixed: 19
      '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__Slit_Robo__SrGAP__s19_a22_
        Complex (Slit/Robo/ SrGAP), length=26 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__DCC-_Complex__Slit_Robo__SrGAP_-RIGHT__SrGAP-_Complex__Slit_Robo__DCC_-_r25
        HETERODIMER_ASSOCIATION_LEFT__DCC-_Complex__Slit_Robo__SrGAP_-RIGHT__SrGAP-_Complex__Slit_Robo__DCC_-_r25, length=105 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__DCC-_Slit-RIGHT__Complex__Slit_DCC_-_r21
        HETERODIMER_ASSOCIATION_LEFT__DCC-_Slit-RIGHT__Complex__Slit_DCC_-_r21, length=70 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__Robo-_Comm-RIGHT__Complex__Robo_Comm_-_re26
        HETERODIMER_ASSOCIATION_LEFT__Robo-_Comm-RIGHT__Complex__Robo_Comm_-_re26, length=73 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__Sdf1-_Cxcr4-RIGHT__Complex__Sdf1_Cxcr4_-_r16
        HETERODIMER_ASSOCIATION_LEFT__Sdf1-_Cxcr4-RIGHT__Complex__Sdf1_Cxcr4_-_r16, length=74 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: HETERODIMER_ASSOCIATION_LEFT__SrGAP-_Slit-_Robo-RIGHT__Complex__Slit_Robo__SrGAP_-_r18
        HETERODIMER_ASSOCIATION_LEFT__SrGAP-_Slit-_Robo-RIGHT__Complex__Slit_Robo__SrGAP_-_r18, length=86 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/panther.pathway/P00008
        Axon guidance mediated by Slit/Robo, length=35 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P15153
        Ras-related C3 botulinum toxin substrate 2(auto-created form other names!), length=42 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P63000
        Ras-related C3 botulinum toxin substrate 1(auto-created form other names!), length=42 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: KNOWN_TRANSITION_OMITTED_LEFT__Cytoskeletal_dynamics-RIGHT__Axonal_plasticity-_r11
        KNOWN_TRANSITION_OMITTED_LEFT__Cytoskeletal_dynamics-RIGHT__Axonal_plasticity-_r11, length=82 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: r27
        STATE_TRANSITION_LEFT__Complex__Robo_Comm_-RIGHT__a59_degraded-_r27, length=67 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Abl-RIGHT__Abl-_r5
        STATE_TRANSITION_LEFT__Abl-RIGHT__Abl-_r5, length=41 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Cdc42-RIGHT__Cdc42-_re23
        STATE_TRANSITION_LEFT__Cdc42-RIGHT__Cdc42-_re23, length=47 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Complex__Netrin_DCC_-RIGHT__Complex__Netrin_DCC_-_re25
        STATE_TRANSITION_LEFT__Complex__Netrin_DCC_-RIGHT__Complex__Netrin_DCC_-_re25, length=77 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Mena-RIGHT__Mena-_r3
        STATE_TRANSITION_LEFT__Mena-RIGHT__Mena-_r3, length=43 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Mena-RIGHT__Mena-_r4
        STATE_TRANSITION_LEFT__Mena-RIGHT__Mena-_r4, length=43 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Rac-RIGHT__Rac-_r28
        STATE_TRANSITION_LEFT__Rac-RIGHT__Rac-_r28, length=42 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Rho-RIGHT__Rho-_re24
        STATE_TRANSITION_LEFT__Rho-RIGHT__Rho-_re24, length=43 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: TRANSPORT_LEFT__Complex__Robo_Comm_-RIGHT__Complex__Robo_Comm_-_r26
        TRANSPORT_LEFT__Complex__Robo_Comm_-RIGHT__Complex__Robo_Comm_-_r26, length=67 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)