• Resource: intact_complex/Saccharomyces_cerevisiae_cytc_oxidase_yeast-2.xml; different types of problem: 7
    • number of genes : 0  number of pathways : 0  number of interactions : 0  number of physical entities : 12 
    • auto-fix: true; normalize:
    • errors/warnings: 24 - not fixed: 23;  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: 1,  not fixed: 1
      Cardinality violation
      • 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: 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://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)

    • 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://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)

    • WARNING: invalid.id.format , category: RECOMMENDATION,  cases: 17,  not fixed: 17
      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_P00401
        db: mint (recognized as: MINT), id: P00401, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P00420
        db: mint (recognized as: MINT), id: P00420, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_mint_P10174
        db: mint (recognized as: MINT), id: P10174, pattern: ^MINT\-\d{1,7}$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_uniprotkb_P00410-PRO_0000006048_identity
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P00410-PRO_0000006048, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_uniprotkb_P00425-PRO_0000006098_identity
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P00425-PRO_0000006098, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_uniprotkb_P00427-PRO_0000006108_identity
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P00427-PRO_0000006108, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_uniprotkb_P04037-PRO_0000006114_identity
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P04037-PRO_0000006114, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_uniprotkb_P04039-PRO_0000006173_identity
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P04039-PRO_0000006173, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_uniprotkb_P07255-PRO_0000006076_identity
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P07255-PRO_0000006076, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/RelationshipXref_uniprotkb_P32799-PRO_0000006127_identity
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P32799-PRO_0000006127, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_uniprotkb_P00410-PRO_0000006048
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P00410-PRO_0000006048, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_uniprotkb_P00425-PRO_0000006098
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P00425-PRO_0000006098, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_uniprotkb_P00427-PRO_0000006108
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P00427-PRO_0000006108, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_uniprotkb_P04037-PRO_0000006114
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P04037-PRO_0000006114, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_uniprotkb_P04039-PRO_0000006173
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P04039-PRO_0000006173, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_uniprotkb_P07255-PRO_0000006076
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P07255-PRO_0000006076, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (found by: org.biopax.validator.rules.XrefRule)
      • object: http://pathwaycommons.org/yeast1/UnificationXref_uniprotkb_P32799-PRO_0000006127
        db: UNIPROT KNOWLEDGEBASE (recognized as: UNIPROT KNOWLEDGEBASE), id: P32799-PRO_0000006127, pattern: ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$
        (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: 1,  not fixed: 1
      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_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-1722_complex-primary
        db name: complex portal
        (found by: org.biopax.validator.rules.XrefRule)