wikipathways-collection

WikiPathways WP4313

• WikiPathways: WP4313 (classic)
• Species: Homo sapiens
• Scholia: WP4313

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 1
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 5 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 4
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 6
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests
  • ChEBIIDsNotMarkedAsMetabolite: .. all OK!
  • HMDBIDsNotMarkedAsMetabolite: .. all OK!
  • KEGGIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotNumbers: .. all OK!
  • PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemSubstanceIDsNotNumbers: .. all OK!
  • achiralAminoAcids: .x we found 1 problem(s):
    • Metabolites with ChEBI identifiers of achiral amino acids: 1
  • casNumbersNotMarkedAsMetabolite: .. all OK!
  • chemspiderIDsNotMarkedAsMetabolite: .. all OK!
  • metaboliteAlsoOtherType: .. all OK!
  • metabolitesWithAnEnsembleID: .. all OK!
  • metabolitesWithAnEntrezGeneID: .. all OK!
  • metabolitesWithDbButNoIdentifier: .. all OK!
  • metabolitesWithIdentifierButNoDb: .. all OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 8 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 20
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 1

• http://classic.wikipathways.org/instance/WP4313_r137936 http://rdf.wikipathways.org/Pathway/WP4313_r137936/DataNode/a2804 (Terpenoid backbone biosynthesis)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

Interactions with Labels

Interactions found that involve Labels: 4

• http://classic.wikipathways.org/instance/WP4313_r137936 “Transsulfuration Pathway” with graphId fddb0
• http://classic.wikipathways.org/instance/WP4313_r137936 “Ferroptosis” with graphId bac11
• http://classic.wikipathways.org/instance/WP4313_r137936 “Ferritin degradation Released iron” with graphId fbb8b
• http://classic.wikipathways.org/instance/WP4313_r137936 “Fenton reaction” with graphId b3035

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels

Possible MIM translocation

Interactions between identical nodes: 6

• http://classic.wikipathways.org/instance/WP4313_r137936 http://rdf.wikipathways.org/Pathway/WP4313_r137936/WP/Interaction/id8fbd5c05 “Fe2+” (https://identifiers.org/chebi/CHEBI:29033) and Fe2+” (https://identifiers.org/chebi/CHEBI:29033)
• http://classic.wikipathways.org/instance/WP4313_r137936 http://rdf.wikipathways.org/Pathway/WP4313_r137936/WP/Interaction/idfd73c27c “Fe2+” (https://identifiers.org/chebi/CHEBI:29033) and Fe2+” (https://identifiers.org/chebi/CHEBI:29033)
• http://classic.wikipathways.org/instance/WP4313_r137936 http://rdf.wikipathways.org/Pathway/WP4313_r137936/WP/Interaction/id3f71117d “Fe2+” (https://identifiers.org/chebi/CHEBI:29033) and Fe2+” (https://identifiers.org/chebi/CHEBI:29033)
• http://classic.wikipathways.org/instance/WP4313_r137936 http://rdf.wikipathways.org/Pathway/WP4313_r137936/WP/Interaction/id37f0d1d8 “Fe2+” (https://identifiers.org/chebi/CHEBI:29033) and Fe2+” (https://identifiers.org/chebi/CHEBI:29033)
• http://classic.wikipathways.org/instance/WP4313_r137936 http://rdf.wikipathways.org/Pathway/WP4313_r137936/WP/Interaction/id42a83318 “Fe2+” (https://identifiers.org/chebi/CHEBI:29033) and Fe2+” (https://identifiers.org/chebi/CHEBI:29033)
• http://classic.wikipathways.org/instance/WP4313_r137936 http://rdf.wikipathways.org/Pathway/WP4313_r137936/WP/Interaction/idda9e5f1c “Fe2+” (https://identifiers.org/chebi/CHEBI:29033) and Fe2+” (https://identifiers.org/chebi/CHEBI:29033)

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations

Identifier used of a amino acid with undefined stereochemistry

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP4313_r137936 cysteine  (Cys) CHEBI:15356

More details at https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/achiralAminoAcids