• Resource: panther/5-Hydroxytryptamine_degredation.owl; different types of problem: 9
    • number of interactions : 4  number of physical entities : 7  number of genes : 0  number of pathways : 1 
    • auto-fix: true; normalize:
    • errors/warnings: 53 - not fixed: 34;  errors not fixed: 1
    • 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)

    • WARNING: cardinality.violated , category: SPECIFICATION,  cases: 3,  not fixed: 3
      Cardinality violation
      • 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)
      • 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: 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: 2,  not fixed: 2
      Minimal cardinality violation
      • object: _Aldehyde_Dehydrogenase_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)
      • object: _Monoamine_Oxidase_PROTEIN
        property: organism requires at least 1 value(s).
        (found by: org.biopax.validator.rules.GenericProteinReferenceOrganismRule)

    • WARNING: no.display.name , category: RECOMMENDATION,  cases: 18,  all fixed!
      No display name is specified. It is useful to have one for the visualization purposes
      • [FIXED!]  object: http://identifiers.org/uniprot/O75891
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/O94788
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P00352
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P05091
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P21397
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P27338
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P30038
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P30837
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P30838
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P47895
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P48448
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P49189
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P49419
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P51648
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q3SY69
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q8IZ83
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q96RQ9
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q9H2A2
        (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: 2,  not fixed: 2
      EntityReference does not have any xrefs
      • object: _Aldehyde_Dehydrogenase_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)
      • object: _Monoamine_Oxidase_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)

    • WARNING: null.entity.reference , category: RECOMMENDATION,  cases: 1,  not fixed: 1
      A Protein, SmallMolecule, etc. (but not a complex) has neither 'entityReference' (highly recommended) nor 'memberPhysicalEntity' values set
      • object: _5_Hydroxyindoleacetaldhyde_s2_a2_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)

    • WARNING: too.long.display.name , category: RECOMMENDATION,  cases: 23,  not fixed: 23
      'displayName' exceeds the recommended maximum. These names should be kept short so they can easily be displayed, e.g., in a pathway diagram
      • object: _5_Hydroxyindoleacetaldhyde_s2_a2_
        5-Hydroxyindoleacetaldhyde, length=26 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _5_Hydroxyindoleacetic_Acid_s3_a3_
        5-Hydroxyindoleacetic Acid, length=26 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _5_Hydroxytryptamine__serotonin__s1_a1_
        5-Hydroxytryptamine (serotonin), length=31 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: CHEBI:27823
        5-Hydroxyindoleacetic Acid, length=26 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: CHEBI:28790
        5-Hydroxytryptamine (serotonin), length=31 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/panther.pathway/P04372
        5-Hydroxytryptamine degredation, length=32 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/O75891
        Cytosolic 10-formyltetrahydrofolate dehydrogenase(auto-created form other names!), length=49 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P05091
        Aldehyde dehydrogenase, mitochondrial(auto-created form other names!), length=37 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P21397
        Amine oxidase [flavin-containing] A(auto-created form other names!), length=35 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P27338
        Amine oxidase [flavin-containing] B(auto-created form other names!), length=35 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P30038
        Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial(auto-created form other names!), length=60 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P30837
        Aldehyde dehydrogenase X, mitochondrial(auto-created form other names!), length=39 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P30838
        Aldehyde dehydrogenase, dimeric NADP-preferring(auto-created form other names!), length=47 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P47895
        Aldehyde dehydrogenase family 1 member A3(auto-created form other names!), length=41 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P48448
        Aldehyde dehydrogenase family 3 member B2(auto-created form other names!), length=41 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P49189
        4-trimethylaminobutyraldehyde dehydrogenase(auto-created form other names!), length=43 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P49419
        Alpha-aminoadipic semialdehyde dehydrogenase(auto-created form other names!), length=44 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/P51648
        Fatty aldehyde dehydrogenase(auto-created form other names!), length=28 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q3SY69
        Mitochondrial 10-formyltetrahydrofolate dehydrogenase(auto-created form other names!), length=53 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q8IZ83
        Aldehyde dehydrogenase family 16 member A1(auto-created form other names!), length=42 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: http://identifiers.org/uniprot/Q9H2A2
        Aldehyde dehydrogenase family 8 member A1(auto-created form other names!), length=41 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__5_Hydroxyindoleacetaldhyde-_H2O-_NAD_PLUS_-RIGHT__5_Hydroxyindoleacetic_Acid-_re2
        STATE_TRANSITION_LEFT__5_Hydroxyindoleacetaldhyde-_H2O-_NAD_PLUS_-RIGHT__5_Hydroxyindoleacetic_Acid-_re2, length=104 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__5_Hydroxytryptamine__serotonin_-RIGHT__5_Hydroxyindoleacetaldhyde-_re1
        STATE_TRANSITION_LEFT__5_Hydroxytryptamine__serotonin_-RIGHT__5_Hydroxyindoleacetaldhyde-_re1, length=93 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)