• Resource: intact_complex/Saccharomyces_cerevisiae_curi_yeast-1.xml; different types of problem: 7
    • number of physical entities : 8  number of genes : 0  number of pathways : 0  number of interactions : 0 
    • auto-fix: true; normalize:
    • errors/warnings: 50 - not fixed: 49;  errors not fixed: 0
    • Modified BioPAX  ("escaped" RDF in HTML; choose BioPAX or XML as return if you plan to process it)
    • WARNING: cardinality.violated , category: SPECIFICATION,  cases: 16,  not fixed: 16
      Cardinality violation
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_0062d08a-7ca2-46ea-a55c-66ffdafee024__28854_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_23afa7b5-2ffc-403a-a1d9-07b0f4841c2c__28860_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_318b6caa-d3af-4b61-878e-03fbac84c89b__28843_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_3470a9e7-bbf9-48b6-85d9-750c02fc570c__28864_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_3d166003-b49c-4cf2-89a1-6564d62b648a__28845_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_3e0c47a2-ea1b-4b31-bce3-84dca74d5cf9__28849_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_4b78b08b-6eca-49b7-a943-ffb3c68afec5__28858_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_4d27bff2-ea6f-46b0-b43b-932bd767c7a1__28851_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_521ee79b-040a-4d4f-a60e-891d7f2b0b20__28856_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_564af81d-f625-4a21-86ca-78be269a3e8d__28847_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_77085dac-6eb3-4910-bfdf-258428c5b675__28848_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_77fa6400-6b80-4661-9dbf-235130847d2e__28862_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_b3f13377-8164-4356-8be5-9f145e3c859c__28857_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_cd5364c4-4698-4b9f-9e6c-b720e0e9c3e7__28853_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_d38013bc-2651-45cd-a2c2-ea8651c8d3e3__28844_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_e1c5c48b-e9d8-4a22-9e3f-b6ef5d654cec__28863_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 8,  not fixed: 8
      Term is not found in the recommended controlled vocabulary (- wrong name/spelling or the identifier/accession is used instead of the term)
      • object: http://identifiers.org/psimi/MI:2282
        Illegal term(s): [complex-primary]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_cka1_binding_region
        Illegal term(s): [cka1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_cka2_binding_region
        Illegal term(s): [cka2 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ckb1_binding_region
        Illegal term(s): [ckb1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ckb2_binding_region
        Illegal term(s): [ckb2 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ifh1_binding_region
        Illegal term(s): [ifh1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rrp7_binding_region
        Illegal term(s): [rrp7 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_utp22_binding_region
        Illegal term(s): [utp22 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: illegal.cv.xref , category: SPECIFICATION,  cases: 8,  not fixed: 8
      Unification xref cannot be resolved to a recommended term for the controlled vocabulary
      • object: http://identifiers.org/psimi/MI:2282
        Illegal xref(s): [MOLECULAR INTERACTIONS ONTOLOGY:MI:2282]; info: [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_cka1_binding_region
        Illegal xref(s): [intact:EBI-16591245]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_cka2_binding_region
        Illegal xref(s): [intact:EBI-16591226]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ckb1_binding_region
        Illegal xref(s): [intact:EBI-16591228]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ckb2_binding_region
        Illegal xref(s): [intact:EBI-16591230]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ifh1_binding_region
        Illegal xref(s): [intact:EBI-16591280]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rrp7_binding_region
        Illegal xref(s): [intact:EBI-16591278]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_utp22_binding_region
        Illegal xref(s): [intact:EBI-16591282]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: invalid.id.format , category: RECOMMENDATION,  cases: 7,  not fixed: 7
      Xref 'id' value does not match the standard pattern for this type of db identifier. If this is due to the version of the object is embedded into the id, please use the idVersion property instead. If the database was not properly recognized (and the pattern is wrong), consider using a standard, more specific, db name (or contact the MIRIAM or identifiers.org team).
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P15790
        db: mint (recognized as: MINT), id: P15790, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P19454
        db: mint (recognized as: MINT), id: P19454, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P25368
        db: mint (recognized as: MINT), id: P25368, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P38930
        db: mint (recognized as: MINT), id: P38930, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P39520
        db: mint (recognized as: MINT), id: P39520, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P43639
        db: mint (recognized as: MINT), id: P43639, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P53254
        db: mint (recognized as: MINT), id: P53254, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)

    • WARNING: no.display.name , category: RECOMMENDATION,  cases: 1,  all fixed!
      No display name is specified. It is useful to have one for the visualization purposes
      • [FIXED!]  object: http://pathwaycommons.org/yeast1/BioSource_taxonomy_559292
        (found by: org.biopax.validator.rules.DisplayNameRule)

    • WARNING: not.allowed.xref , category: RECOMMENDATION,  cases: 9,  not fixed: 9
      Database name in the UnificationXref (of a BioPAX element), probably, does not make sense for this type of element
      • object: http://pathwaycommons.org/yeast1/UnificationXref_intact_EBI-16591226
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_cka2_binding_region, xref.db: intact (unification xrefs of: SequenceRegionVocabulary are limited to: [so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_intact_EBI-16591228
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ckb1_binding_region, xref.db: intact (unification xrefs of: SequenceRegionVocabulary are limited to: [so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_intact_EBI-16591230
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ckb2_binding_region, xref.db: intact (unification xrefs of: SequenceRegionVocabulary are limited to: [so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_intact_EBI-16591245
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_cka1_binding_region, xref.db: intact (unification xrefs of: SequenceRegionVocabulary are limited to: [so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_intact_EBI-16591278
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rrp7_binding_region, xref.db: intact (unification xrefs of: SequenceRegionVocabulary are limited to: [so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_intact_EBI-16591280
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_ifh1_binding_region, xref.db: intact (unification xrefs of: SequenceRegionVocabulary are limited to: [so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_intact_EBI-16591282
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_utp22_binding_region, xref.db: intact (unification xrefs of: SequenceRegionVocabulary are limited to: [so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_psi-mi_MI_0117
        element: http://pathwaycommons.org/yeast1/SequenceModificationVocabulary_binding_region, xref.db: psi-mi (unification xrefs of: SequenceModificationVocabulary are limited to: [mod, MOD, PSI-MOD, PROTEIN MODIFICATION ONTOLOGY, so, SO, SEQUENCE ONTOLOGY, SEQUENCE TYPES AND FEATURES])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_psi-mi_MI_0469
        element: http://pathwaycommons.org/yeast1/Provenance_IntAct, xref.db: psi-mi (unification xrefs of: Provenance are limited to: [miriam, MIRIAM RESOURCES, MIRIAM REGISTRY COLLECTION, MIRIAM])
        (found by: org.biopax.validator.rules.UnificationXrefLimitedRule)

    • WARNING: unknown.db , category: RECOMMENDATION,  cases: 1,  not fixed: 1
      Unknown database identifier. For Xref 'db' property and Provenance standard/display name properties, please use the official database names from MIRIAM. PSI-MI "database citation" and child terms are also allowed but they are deprecated. Please use MIRIAM when possible
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_complex_portal_CPX-774_complex-primary
        db name: complex portal
        (found by: org.biopax.validator.rules.XrefRule)