• Resource: intact_complex/Saccharomyces_cerevisiae_argr_yeast.xml; different types of problem: 7
    • number of genes : 0  number of pathways : 0  number of physical entities : 5  number of interactions : 0 
    • auto-fix: true; normalize:
    • errors/warnings: 29 - not fixed: 28;  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: 8,  not fixed: 8
      Cardinality violation
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_1f0f0aef-2b64-447a-96ac-200bc2a2ab8f__29874_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_382eedc4-3ad1-4766-91d8-238fc57c9da4__29869_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_4d694c3b-f905-4a37-a3ba-2cac83d299a6__29871_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_4fc64857-7ed3-4d93-a4c8-f19f4414f11f__29875_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_89d96285-dacc-4569-9f92-5d746b9c8d04__29866_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_a2d300da-050f-4d82-bf15-8d98f0d4b0fc__29868_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_bc0d436f-5f8b-442b-ab66-951ffe93388a__29865_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_d55013c3-c34d-4079-a4c3-edf99a6f6cf7__29872_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 5,  not fixed: 5
      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_arg80_binding_region
        Illegal term(s): [arg80 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg81_binding_region
        Illegal term(s): [arg81 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg82_binding_region
        Illegal term(s): [arg82 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_mcm1_binding_region
        Illegal term(s): [mcm1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: illegal.cv.xref , category: SPECIFICATION,  cases: 5,  not fixed: 5
      Unification xref cannot be resolved to a recommended term for the controlled vocabulary
      • object: http://identifiers.org/psimi/MI:2282
        Illegal xref(s): [PSI-MI:MI:2282]; info: [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg80_binding_region
        Illegal xref(s): [intact:EBI-15101355]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg81_binding_region
        Illegal xref(s): [intact:EBI-15101411]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg82_binding_region
        Illegal xref(s): [intact:EBI-15101407]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_mcm1_binding_region
        Illegal xref(s): [intact:EBI-15101409]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: invalid.id.format , category: RECOMMENDATION,  cases: 3,  not fixed: 3
      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_P05085
        db: mint (recognized as: MINT), id: P05085, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P07250
        db: mint (recognized as: MINT), id: P07250, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P11746
        db: mint (recognized as: MINT), id: P11746, 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: 6,  not fixed: 6
      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-15101355
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg80_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-15101407
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg82_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-15101409
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_mcm1_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-15101411
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_arg81_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-1152_complex-primary
        db name: complex portal
        (found by: org.biopax.validator.rules.XrefRule)