• Resource: intact_complex/Saccharomyces_cerevisiae_nucleosome_yeast-1-3.xml; different types of problem: 7
    • number of physical entities : 6  number of genes : 0  number of pathways : 0  number of interactions : 0 
    • auto-fix: true; normalize:
    • errors/warnings: 20 - not fixed: 18;  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: 2,  not fixed: 2
      Cardinality violation
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_543d5187-744d-4fc4-ab73-dfd90b85094c__31684_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_721bff97-203b-4966-a3ea-0ac784823073__31682_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 3,  not fixed: 3
      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_hhf1_binding_region
        Illegal term(s): [hhf1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_hht1_binding_region
        Illegal term(s): [hht1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: illegal.cv.xref , category: SPECIFICATION,  cases: 3,  not fixed: 3
      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_hhf1_binding_region
        Illegal xref(s): [intact:EBI-16746630]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_hht1_binding_region
        Illegal xref(s): [intact:EBI-16746635]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: invalid.id.format , category: RECOMMENDATION,  cases: 5,  not fixed: 5
      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_P02293
        db: mint (recognized as: MINT), id: P02293, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P02309
        db: mint (recognized as: MINT), id: P02309, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P04912
        db: mint (recognized as: MINT), id: P04912, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P61830
        db: mint (recognized as: MINT), id: P61830, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_taxonomy_-2
        db: Taxonomy (recognized as: TAXONOMY), id: -2, pattern: ^\d+$
        (found by: org.biopax.validator.rules.XrefRule)

    • WARNING: no.display.name , category: RECOMMENDATION,  cases: 2,  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_-2
        (found by: org.biopax.validator.rules.DisplayNameRule)
      • [FIXED!]  object: http://pathwaycommons.org/yeast1/BioSource_taxonomy_559292
        (found by: org.biopax.validator.rules.DisplayNameRule)

    • WARNING: not.allowed.xref , category: RECOMMENDATION,  cases: 4,  not fixed: 4
      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-16746630
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_hhf1_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-16746635
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_hht1_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-1611_complex-primary
        db name: complex portal
        (found by: org.biopax.validator.rules.XrefRule)