wikipathways-collection

WikiPathways WP3992

• WikiPathways: WP3992 (classic)
• Species: Danio rerio

  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: 2
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: …. all OK!
  • nonNumericHGNCAccessionNumbers: .. all OK!
  • genesWithoutEnsemblMapping: .x we found 1 problem(s):
    • The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .. all OK!
  • 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: all 14 tests 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: 118
• Number of assertions: 237
• Number of fails: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/DataNode/e488d (Peroxisomal β-oxidation)
• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/DataNode/e70c6 (β-oxidation)

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

Genes with identifier but no Ensembl identifier mapping

The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1

http://classic.wikipathways.org/instance/WP3992_r123369 pk with datasource ZFIN

More details at https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping

Possible MIM translocation

Interactions between identical nodes: 6

• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/WP/Interaction/id826746e6 “Carnitine” (https://identifiers.org/chebi/CHEBI:3424) and Carnitine” (https://identifiers.org/chebi/CHEBI:3424)
• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/WP/Interaction/idf83b046a “Acetyl-CoA” (https://identifiers.org/chebi/CHEBI:15351) and Acetyl-CoA” (https://identifiers.org/chebi/CHEBI:15351)
• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/WP/Interaction/ide3a93cb3 “Carnitine” (https://identifiers.org/chebi/CHEBI:3424) and Carnitine” (https://identifiers.org/chebi/CHEBI:3424)
• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/WP/Interaction/c7057 “L-malate” (https://identifiers.org/chebi/CHEBI:15589) and L-malate” (https://identifiers.org/chebi/CHEBI:15589)
• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/WP/Interaction/id82457aa0 “Acyl carnitine C16:2” (https://identifiers.org/chebi/CHEBI:89745) and Acyl carnitine C16:2” (https://identifiers.org/chebi/CHEBI:89745)
• http://classic.wikipathways.org/instance/WP3992_r123369 http://rdf.wikipathways.org/Pathway/WP3992_r123369/WP/Interaction/id9a2e0d94 “pyruvate” (https://identifiers.org/chebi/CHEBI:15361) and pyruvate” (https://identifiers.org/chebi/CHEBI:15361)

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