wikipathways-collection

WikiPathways WP4628

• WikiPathways: WP4628 (classic)
• Species: Homo sapiens
• Scholia: WP4628

  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: 14
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 2
  • 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: 51
  • 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: 14

• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/cca15 (ALT)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/ff293 (ASP)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/e55fb (ATPase)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/fa2b1 (GPHOS)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/b1484 (GPS)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/c7ada (GRPDH)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/cd89d (GSYN)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/daa73 (MAL)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/be553 (MAS)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/b4253 (OXPHOS)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/eb61b (PDH)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/c4f35 (PHGDH)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/a279b (SPT)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/bb18c (Serine biosynthesis)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 2

• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/be553 (MAS)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/DataNode/b4253 (OXPHOS)

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/WP4628_r134298 G6PDH with datasource HGNC Accession number

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

Possible MIM translocation

Interactions between identical nodes: 51

• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_1 “SER” (https://identifiers.org/hmdb/HMDB0000187) and SER” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_1 “SER” (https://identifiers.org/hmdb/HMDB0000187) and GLY” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_1 “GLY” (https://identifiers.org/hmdb/HMDB0000187) and SER” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_1 “GLY” (https://identifiers.org/hmdb/HMDB0000187) and GLY” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “O2” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “O2” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “O2” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “O2e” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “O2e” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “O2e” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “H2O” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “H2O” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_1 “H2O” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “O2” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “O2” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “O2” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “O2e” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “O2e” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “O2e” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “H2O” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “H2O” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id99a2604b “H2O” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_1 “GLUe” (https://identifiers.org/hmdb/HMDB0000122) and GLUe” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_1 “GLUe” (https://identifiers.org/hmdb/HMDB0000122) and GLU” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_1 “GLU” (https://identifiers.org/hmdb/HMDB0000122) and GLUe” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_1 “GLU” (https://identifiers.org/hmdb/HMDB0000122) and GLU” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_2 “LACe” (https://identifiers.org/hmdb/HMDB0000190) and LACe” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_2 “LACe” (https://identifiers.org/hmdb/HMDB0000190) and LAC” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_2 “LAC” (https://identifiers.org/hmdb/HMDB0000190) and LACe” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_2 “LAC” (https://identifiers.org/hmdb/HMDB0000190) and LAC” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_2 “SER” (https://identifiers.org/hmdb/HMDB0000187) and SER” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_2 “SER” (https://identifiers.org/hmdb/HMDB0000187) and GLY” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_2 “GLY” (https://identifiers.org/hmdb/HMDB0000187) and SER” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id7a6c03b4_2 “GLY” (https://identifiers.org/hmdb/HMDB0000187) and GLY” (https://identifiers.org/hmdb/HMDB0000187)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “O2” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “O2” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “O2” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “O2e” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “O2e” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “O2e” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “H2O” (https://identifiers.org/chebi/CHEBI:26689) and O2” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “H2O” (https://identifiers.org/chebi/CHEBI:26689) and O2e” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id38db71f5_2 “H2O” (https://identifiers.org/chebi/CHEBI:26689) and H2O” (https://identifiers.org/chebi/CHEBI:26689)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_1 “LACe” (https://identifiers.org/hmdb/HMDB0000190) and LACe” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_1 “LACe” (https://identifiers.org/hmdb/HMDB0000190) and LAC” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_1 “LAC” (https://identifiers.org/hmdb/HMDB0000190) and LACe” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/id4492be65_1 “LAC” (https://identifiers.org/hmdb/HMDB0000190) and LAC” (https://identifiers.org/hmdb/HMDB0000190)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_2 “GLUe” (https://identifiers.org/hmdb/HMDB0000122) and GLUe” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_2 “GLUe” (https://identifiers.org/hmdb/HMDB0000122) and GLU” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_2 “GLU” (https://identifiers.org/hmdb/HMDB0000122) and GLUe” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP4628_r134298 http://rdf.wikipathways.org/Pathway/WP4628_r134298/WP/Interaction/ea8dd_2 “GLU” (https://identifiers.org/hmdb/HMDB0000122) and GLU” (https://identifiers.org/hmdb/HMDB0000122)

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