wikipathways-collection

WikiPathways WP5312

• WikiPathways: WP5312 (classic)
• Species: Homo sapiens
• Scholia: WP5312

  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: 3
  • 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: 2
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 5
  • 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 7 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: 119
• Number of assertions: 239
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 3

• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/DataNode/aceb6 (Preprocollagen)
• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/DataNode/d8ab5 (Procollagen)
• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/DataNode/abb71 (Tropocollagen)

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

Interactions with Labels

Interactions found that involve Labels: 2

• http://classic.wikipathways.org/instance/WP5312_r125794 “PDC” with graphId b41ba
• http://classic.wikipathways.org/instance/WP5312_r125794 “Cell proliferation, survival, migration” with graphId be27b

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

Possible MIM translocation

Interactions between identical nodes: 5

• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/WP/Interaction/id17272ae9 “Glucose” (https://identifiers.org/hmdb/HMDB0000122) and Glucose” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/WP/Interaction/idf0323a6d “Lactic acid” (https://identifiers.org/hmdb/HMDB0000190) and Lactic acid” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/WP/Interaction/iddde970a6 “Glutamine” (https://identifiers.org/chebi/CHEBI:18050) and Glutamine” (https://identifiers.org/chebi/CHEBI:18050)
• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/WP/Interaction/ida0d3364a “Glutamine” (https://identifiers.org/chebi/CHEBI:18050) and Glutamine” (https://identifiers.org/chebi/CHEBI:18050)
• http://classic.wikipathways.org/instance/WP5312_r125794 http://rdf.wikipathways.org/Pathway/WP5312_r125794/WP/Interaction/id6b696830 “Fatty acid” (https://identifiers.org/chebi/CHEBI:35366) and Fatty acid” (https://identifiers.org/chebi/CHEBI:35366)

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

MetabolitesTests.achiralAminoAcids

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP5312_r125794 Serine CHEBI:17822