• Resource: panther/Pentose_phosphate_pathway.owl; different types of problem: 10
    • number of genes : 0  number of interactions : 34  number of pathways : 1  number of physical entities : 34 
    • auto-fix: true; normalize:
    • errors/warnings: 52 - not fixed: 48;  errors not fixed: 3
    • 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: 2,  not fixed: 2
      EntityReference does not have any xrefs
      • object: _D_Ribulo_br_Kinase_PROTEIN
        (found by: org.biopax.validator.rules.EntityReferenceXrefRule)
      • object: _Ribitol_br_Dehydrogenase_PROTEIN
        (found by: org.biopax.validator.rules.EntityReferenceXrefRule)

    • WARNING: cardinality.violated , category: SPECIFICATION,  cases: 5,  not fixed: 5
      Cardinality violation
      • object: _D_Ribulo_br_Kinase_PROTEIN
        property: organism requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ProteinReferenceOrganismRule)
      • object: _Ribitol_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)
      • object: PANTHER_GROUPING_5
        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: _Hexokinase_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/P19367
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/P52789
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://identifiers.org/uniprot/Q2TB90
        (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_5
        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: 1,  not fixed: 1
      EntityReference does not have any xrefs
      • object: _Hexokinase_PROTEIN
        (found by: org.biopax.validator.rules.GenericEntityReferenceXrefRule)

    • WARNING: null.entity.reference , category: RECOMMENDATION,  cases: 16,  not fixed: 16
      A Protein, SmallMolecule, etc. (but not a complex) has neither 'entityReference' (highly recommended) nor 'memberPhysicalEntity' values set
      • object: _6_P_Glucono_Lactonase_s47_a45_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)
      • object: _Alpha__D_5_P_Ribosyl_PP_s62_a65_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _BetaD_Fructose_6_phosphate_s6_a4_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_6_P_Gluconate_s46_a44_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_6_P_Glucono_1,5_Lactone_s45_a40_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_Erythrose_4_P_s68_a73_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_Glyceraldehyde_3_P_s59_a62_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_Ribose_5_P_s63_a66_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_Ribulose_5_P_s51_a47_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_SedoHeptulose_7_P_s67_a72_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _D_Xylulose_5_P_s58_a61_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _Glucose_6_P_Dehydrogenase_s40_a41_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)
      • object: _NADPH__PLUS__H_PLUS__s43_a43_
        entityReference (range: SmallMoleculeReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.SmallMoleculeEntityReferenceRule)
      • object: _Ribo_Kinase_s64_a67_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)
      • object: _Ribose_P_Pyrophospho_Kinase_s65_a68_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)
      • object: _Ribulose_P_3_Epimerase_s60_a63_
        entityReference (range: ProteinReference) is null, and memberPhysicalEntity is empty
        (found by: org.biopax.validator.rules.ProteinEntityReferenceRule)

    • WARNING: too.long.display.name , category: RECOMMENDATION,  cases: 20,  not fixed: 20
      'displayName' exceeds the recommended maximum. These names should be kept short so they can easily be displayed, e.g., in a pathway diagram
      • object: _BetaD_Fructose_6_phosphate_s6_a4_
        BetaD-Fructose 6-phosphate, length=26 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: _Ribose_P_Pyrophospho_Kinase_s65_a68_
        Ribose-P Pyrophospho Kinase, length=27 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__ATP-_D_Ribulose-RIGHT__D_Ribulose_5_P-_ADP-_r25
        STATE_TRANSITION_LEFT__ATP-_D_Ribulose-RIGHT__D_Ribulose_5_P-_ADP-_r25, length=70 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__ATP-_Glucose-RIGHT__ADP-_Glucose_6_phosphate-_r5
        STATE_TRANSITION_LEFT__ATP-_Glucose-RIGHT__ADP-_Glucose_6_phosphate-_r5, length=71 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__BetaD_Fructose_6_phosphate-RIGHT__D_Erythrose_4_P-_r37
        STATE_TRANSITION_LEFT__BetaD_Fructose_6_phosphate-RIGHT__D_Erythrose_4_P-_r37, length=77 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__BetaD_Fructose_6_phosphate-RIGHT__Glucose_6_phosphate-_r36
        STATE_TRANSITION_LEFT__BetaD_Fructose_6_phosphate-RIGHT__Glucose_6_phosphate-_r36, length=81 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Glyceraldehyde_3_P-RIGHT__D_Erythrose_4_P-_r34
        STATE_TRANSITION_LEFT__D_Glyceraldehyde_3_P-RIGHT__D_Erythrose_4_P-_r34, length=71 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Ribitol-_NADP_PLUS_-RIGHT__NADPH__PLUS__H_PLUS_-_D_Ribulose-_r24
        STATE_TRANSITION_LEFT__D_Ribitol-_NADP_PLUS_-RIGHT__NADPH__PLUS__H_PLUS_-_D_Ribulose-_r24, length=89 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Ribose-RIGHT__D_Ribose_5_P-_r29
        STATE_TRANSITION_LEFT__D_Ribose-RIGHT__D_Ribose_5_P-_r29, length=56 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Ribose_5_P-_ATP-RIGHT__ADP-_Alpha__D_5_P_Ribosyl_PP-_r30
        STATE_TRANSITION_LEFT__D_Ribose_5_P-_ATP-RIGHT__ADP-_Alpha__D_5_P_Ribosyl_PP-_r30, length=81 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Ribose_5_P-RIGHT__D_SedoHeptulose_7_P-_r32
        STATE_TRANSITION_LEFT__D_Ribose_5_P-RIGHT__D_SedoHeptulose_7_P-_r32, length=67 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Ribulose_5_P-RIGHT__D_Ribose_5_P-_r31
        STATE_TRANSITION_LEFT__D_Ribulose_5_P-RIGHT__D_Ribose_5_P-_r31, length=62 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Ribulose_5_P-RIGHT__D_Xylulose_5_P-_r26
        STATE_TRANSITION_LEFT__D_Ribulose_5_P-RIGHT__D_Xylulose_5_P-_r26, length=64 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_SedoHeptulose_7_P-RIGHT__BetaD_Fructose_6_phosphate-_r35
        STATE_TRANSITION_LEFT__D_SedoHeptulose_7_P-RIGHT__BetaD_Fructose_6_phosphate-_r35, length=81 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_SedoHeptulose_7_P-RIGHT__D_Erythrose_4_P-_r33
        STATE_TRANSITION_LEFT__D_SedoHeptulose_7_P-RIGHT__D_Erythrose_4_P-_r33, length=70 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__D_Xylulose_5_P-RIGHT__D_Glyceraldehyde_3_P-_r27
        STATE_TRANSITION_LEFT__D_Xylulose_5_P-RIGHT__D_Glyceraldehyde_3_P-_r27, length=70 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Glucose_6_phosphate-_NADP_PLUS_-RIGHT__D_6_P_Glucono_1,5_Lactone-_NADPH__PLUS__H_PLUS_-_r21
        STATE_TRANSITION_LEFT__Glucose_6_phosphate-_NADP_PLUS_-RIGHT__D_6_P_Glucono_1,5_Lactone-_NADPH__PLUS__H_PLUS_-_r21, length=114 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__Glucose_6_phosphate-RIGHT__BetaD_Fructose_6_phosphate-_r6
        STATE_TRANSITION_LEFT__Glucose_6_phosphate-RIGHT__BetaD_Fructose_6_phosphate-_r6, length=80 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__H2O-_D_6_P_Glucono_1,5_Lactone-RIGHT__D_6_P_Gluconate-_r22
        STATE_TRANSITION_LEFT__H2O-_D_6_P_Glucono_1,5_Lactone-RIGHT__D_6_P_Gluconate-_r22, length=81 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • object: STATE_TRANSITION_LEFT__NADP_PLUS_-_D_6_P_Gluconate-RIGHT__D_Ribulose_5_P-_NADPH__PLUS__H_PLUS_-_CO2-_r23
        STATE_TRANSITION_LEFT__NADP_PLUS_-_D_6_P_Gluconate-RIGHT__D_Ribulose_5_P-_NADPH__PLUS__H_PLUS_-_CO2-_r23, length=104 exceeds 25
        (found by: org.biopax.validator.rules.DisplayNameRule)