• Resource: intact/yeast_02_negative.xml; different types of problem: 6
    • number of physical entities : 6  number of interactions : 3  number of genes : 0  number of pathways : 0 
    • auto-fix: true; normalize:
    • errors/warnings: 16 - not fixed: 14;  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: 4,  not fixed: 4
      Cardinality violation
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_126b2e38-53bd-4425-9d32-32bb9416a5be__145401_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_48734d52-87f9-4326-82ad-598821a6baf2__145397_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/ModificationFeature_a2f9e950-c31e-4768-bfb0-679da10d9653__145406_
        property: featureLocation requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ModificationFeatureLocationCRRule)
      • object: http://pathwaycommons.org/yeast1/RTV_intact-secondary
        property: xref requires exactly 1 value(s)
        (found by: org.biopax.validator.rules.ControlledVocabularyXrefCRRule)

    • WARNING: illegal.cv.term , category: SPECIFICATION,  cases: 2,  not fixed: 2
      Term is not found in the recommended controlled vocabulary (- wrong name/spelling or the identifier/accession is used instead of the term)
      • object: http://pathwaycommons.org/yeast1/RTV_intact-secondary
        Illegal term(s): [intact-secondary]; [Valid 'MI' terms: ALL children of MI:0353]
        (found by: org.biopax.validator.rules.RelationshipTypeCvRule)
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_tagged_molecule
        Illegal term(s): [tagged molecule]; [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: illegal.cv.xref , category: SPECIFICATION,  cases: 1,  not fixed: 1
      Unification xref cannot be resolved to a recommended term for the controlled vocabulary
      • object: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_tagged_molecule
        Illegal xref(s): [mint:MINT-468334]; info: [Valid 'SO' terms: DIRECT children of SO:0000001]
        (found by: org.biopax.validator.rules.SequenceRegionCvRule)

    • WARNING: invalid.id.format , category: RECOMMENDATION,  cases: 4,  not fixed: 4
      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_intact_MINT-468312_intact-secondary
        db: intact (recognized as: INTACT), id: MINT-468312, pattern: ^EBI\-[0-9]+$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P25604
        db: mint (recognized as: MINT), id: P25604, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P36095
        db: mint (recognized as: MINT), id: P36095, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P52917
        db: mint (recognized as: MINT), id: P52917, pattern: ^MINT\-\d{1,7}$
        (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_284812
        (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: 3,  not fixed: 3
      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_mint_MINT-468334
        element: http://pathwaycommons.org/yeast1/SequenceRegionVocabulary_tagged_molecule, xref.db: mint (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_0471
        element: http://pathwaycommons.org/yeast1/Provenance_MINT, 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)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_psi-mi_MI_0507
        element: http://pathwaycommons.org/yeast1/SequenceModificationVocabulary_tag, 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)