wikipathways-collection

WikiPathways WP4342

• WikiPathways: WP4342 (classic)
• Species: Homo sapiens
• Scholia: WP4342

  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: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 3
  • 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: 1
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 4
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 15 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 8 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: 120
• Number of assertions: 241
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/DataNode/b3d9c (Vitamin D rich diet)
• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/DataNode/ec0fb (Vitamin D rich diet)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 3

• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/DataNode/bbc8d (UV-B light)
• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/DataNode/b3d9c (Vitamin D rich diet)
• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/DataNode/ec0fb (Vitamin D rich diet)

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP4342_r136783 “Retinoic acid” with graphId cb2b6

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

Possible MIM translocation

Interactions between identical nodes: 4

• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/WP/Interaction/id3b60e567 “9-cis-Retinoic acid” (https://identifiers.org/hmdb/HMDB0002369) and ATRA” (https://identifiers.org/chebi/CHEBI:50648)
• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/WP/Interaction/id95b27a2a “25(OH)D3” (https://identifiers.org/chebi/CHEBI:17933) and 25(OH)D3” (https://identifiers.org/chebi/CHEBI:17933)
• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/WP/Interaction/idd3d33d9e “1,25(OH)2D3” (https://identifiers.org/hmdb/HMDB0000969) and 1,25(OH)2D3” (https://identifiers.org/hmdb/HMDB0000969)
• http://classic.wikipathways.org/instance/WP4342_r136783 http://rdf.wikipathways.org/Pathway/WP4342_r136783/WP/Interaction/id10f4bf73 “ATRA” (https://identifiers.org/chebi/CHEBI:50648) and 9-cis-Retinoic acid” (https://identifiers.org/hmdb/HMDB0002369)

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