• Resource: intact_complex/Saccharomyces_cerevisiae_bub1-bub3_yeast.xml; different types of problem: 7
    • number of genes : 0  number of pathways : 0  number of interactions : 0  number of physical entities : 3 
    • auto-fix: true; normalize:
    • errors/warnings: 18 - not fixed: 17;  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: 3,  not fixed: 3
      Cardinality violation
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_36f444dd-adf3-48a8-8ce6-aabcac9c3bdb__27340_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_f1192007-5912-4e17-8763-2ea2460b3215__27338_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/RTV_exp-evidence
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 4,  not fixed: 4
      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/RTV_exp-evidence
        Illegal term(s): [exp-evidence]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_bub1_binding_region
        Illegal term(s): [bub1 binding region]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_bub3_binding_region
        Illegal term(s): [bub3 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): [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_bub1_binding_region
        Illegal xref(s): [intact:EBI-10890974]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_bub3_binding_region
        Illegal xref(s): [interpro:IPR012572]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: invalid.id.format , category: RECOMMENDATION,  cases: 2,  not fixed: 2
      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_P26449
        db: mint (recognized as: MINT), id: P26449, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P41695
        db: mint (recognized as: MINT), id: P41695, 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: 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-10890974
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_bub1_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_interpro_IPR012572
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_bub3_binding_region, xref.db: interpro (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_0442
        element: http://pathwaycommons.org/yeast1/SequenceModificationVocabulary_sufficient_to_bind, 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-154_complex-primary
        db name: complex portal
        (found by: org.biopax.validator.rules.XrefRule)