wikipathways-collection

WikiPathways WP5219

• WikiPathways: WP5219 (classic)
• Species: Homo sapiens
• Scholia: WP5219

  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: 7
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 1
  • 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: 2
  • 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: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 7

• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/fcecf (BBU)
• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/d55d9 (Betaine exporter)
• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/acf06 (CaIT)
• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/fdf29 (CutC (and CutD))
• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/cd1bc (Decarboxylation)
• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/d0033 (Process Mediated by Bacterial Metabolism)
• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/b0edf (R07228)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 1

• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/DataNode/d55d9 (Betaine exporter)

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

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/WP5219_r126795 Transmethylase with datasource KEGG Genes

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/WP/Interaction/idd4794418 “BET” (https://identifiers.org/kegg.compound/C00719) and BET” (https://identifiers.org/kegg.compound/C00719)
• http://classic.wikipathways.org/instance/WP5219_r126795 http://rdf.wikipathways.org/Pathway/WP5219_r126795/WP/Interaction/id4f32c2db “Choline” (https://identifiers.org/kegg.compound/C00114) and Choline” (https://identifiers.org/kegg.compound/C00114)

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