wikipathways-collection

WikiPathways WP4020

• WikiPathways: WP4020 (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: 1
  • 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: .x we found 1 problem(s):
    • Interactions found that involve Labels: 4
  • 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: 1

• http://classic.wikipathways.org/instance/WP4020_r123454 http://rdf.wikipathways.org/Pathway/WP4020_r123454/DataNode/af9c2 (Adipocyokine signaling pathway)

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/WP4020_r123454 acs16 with datasource ZFIN

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

Interactions with Labels

Interactions found that involve Labels: 4

• http://classic.wikipathways.org/instance/WP4020_r123454 “Ubiquitination” with graphId cb5ef
• http://classic.wikipathways.org/instance/WP4020_r123454 “Lipid metabolism” with graphId cd016
• http://classic.wikipathways.org/instance/WP4020_r123454 “Adipocyte differentiation” with graphId b5924
• http://classic.wikipathways.org/instance/WP4020_r123454 “Cell survival” with graphId f6563

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP4020_r123454 http://rdf.wikipathways.org/Pathway/WP4020_r123454/WP/Interaction/d80d5 “VLDL Chylomicron” (https://identifiers.org/chebi/CHEBI:6495) and VLDL Chylomicron” (https://identifiers.org/chebi/CHEBI:6495)
• http://classic.wikipathways.org/instance/WP4020_r123454 http://rdf.wikipathways.org/Pathway/WP4020_r123454/WP/Interaction/idcee81e0f “VLDL Chylomicron” (https://identifiers.org/chebi/CHEBI:6495) and VLDL Chylomicron” (https://identifiers.org/chebi/CHEBI:6495)

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