wikipathways-collection

WikiPathways WP5237

• WikiPathways: WP5237 (classic)
• Species: Daphnia magna

  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: 17
  • 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: 7
• 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 17

• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/a5d9b ()
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/d1f43 ()
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/d7ac4 ()
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/da29a ()
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/f8f1e (ATPC)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/c302a (GlcT-1)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/feb2c (Glycolysis)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/a5620 (Glycospingolipids biosynthesis)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/cda48 (Lipid metabolism)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/edb3b (Metabolite)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/fef83 (Sphingolipids biogenesis)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/f7527 (Starch and sucrose metabolism)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/d25eb (Tryptophan metabolism)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/c71fa (cDASE)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/ceedd (lace)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/cfea1 (ldh)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/DataNode/df5c2 (ldh)

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: 7

http://classic.wikipathways.org/instance/WP5237_r124088 Ddc with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5237_r124088 Pfk with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5237_r124088 UGP with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5237_r124088 Acon with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5237_r124088 Fbp with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5237_r124088 GlyP with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5237_r124088 thiolase with datasource Entrez Gene

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/WP/Interaction/a533e “tryptamine” (https://identifiers.org/chebi/CHEBI:16765) and tryptamine” (https://identifiers.org/chebi/CHEBI:16765)
• http://classic.wikipathways.org/instance/WP5237_r124088 http://rdf.wikipathways.org/Pathway/WP5237_r124088/WP/Interaction/id5ff1117f “tryptamine” (https://identifiers.org/chebi/CHEBI:16765) and tryptamine” (https://identifiers.org/chebi/CHEBI:16765)

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