• Resource: intact_complex/Saccharomyces_cerevisiae_cul8-esc2_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: 32 - not fixed: 31;  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_01434525-4cb2-4ed8-8ef0-98f58d4f1cee__29981_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_07b611de-4d22-4021-912e-5a4087cb546a__29986_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_2487b57a-6fc8-43ed-9dcd-9e5ff63cc65c__29988_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_25d1aca3-d39e-43cc-b8c5-911cf15fa8ea__29979_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_36a1735e-c4cd-4b7e-9307-c2d35ba08644__29983_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_5bf404fe-a4bf-4fbc-9402-ca18132b20fe__29987_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_9b044453-0782-41a7-b447-365e9a027273__29984_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_b88f9ec1-e0ca-4221-9381-00d89e08ba2b__29978_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 6,  not fixed: 6
      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_esc2_binding_region
        Illegal term(s): [esc2 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_hrt1_binding_region
        Illegal term(s): [hrt1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_mms1_binding_region
        Illegal term(s): [mms1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rtt101_binding_region
        Illegal term(s): [rtt101 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rtt101_bnding_region
        Illegal term(s): [rtt101 bnding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: illegal.cv.xref , category: SPECIFICATION,  cases: 6,  not fixed: 6
      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_esc2_binding_region
        Illegal xref(s): [intact:EBI-15483301]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_hrt1_binding_region
        Illegal xref(s): [intact:EBI-15483296]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_mms1_binding_region
        Illegal xref(s): [intact:EBI-15483309]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rtt101_binding_region
        Illegal xref(s): [intact:EBI-15483311]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rtt101_bnding_region
        Illegal xref(s): [intact:EBI-15483303]; 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_P47050
        db: mint (recognized as: MINT), id: P47050, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_Q06211
        db: mint (recognized as: MINT), id: Q06211, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_Q08273
        db: mint (recognized as: MINT), id: Q08273, 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: 7,  not fixed: 7
      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-15483296
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_hrt1_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-15483301
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_esc2_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-15483303
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rtt101_bnding_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-15483309
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_mms1_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-15483311
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_rtt101_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-1166_complex-primary
        db name: complex portal
        (found by: org.biopax.validator.rules.XrefRule)