wikipathways-collection

WikiPathways WP4331

• WikiPathways: WP4331 (classic)
• Species: Homo sapiens
• Scholia: WP4331

  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: 18
  • 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: 5
• 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: 4
  • 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: 18

• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/d4a72 (Apoptosis)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/ce82e (Arteriolar specification)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/d8066 (Cell differentiation)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/cda4d (Cell recruitment)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/e7903 (DLL2)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/c388a (De novo arteriogenesis)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/f98f0 (Integrins)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/f52c7 (Matrix and collagen deposition)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/b037b (Migration)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/ff221 (NO)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/c80a0 (Proliferation)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/af3e8 (Remodeling arteriogenesis)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/c532b (Shear stress)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/a4731 (Sprouting angiogenesis)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/cf120 (Tube formation)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/b77db (VEGF)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/dd43d (Vasculogenesis)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/DataNode/d1906 (Vessel maturation)

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: 5

http://classic.wikipathways.org/instance/WP4331_r135060 FAK with datasource InterPro
http://classic.wikipathways.org/instance/WP4331_r135060 PDGF-BB with datasource InterPro
http://classic.wikipathways.org/instance/WP4331_r135060 VEGF with datasource InterPro
http://classic.wikipathways.org/instance/WP4331_r135060 VEGFR with datasource UniProtKB
http://classic.wikipathways.org/instance/WP4331_r135060 PI3K with datasource InterPro

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

Possible MIM translocation

Interactions between identical nodes: 4

• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/WP/Interaction/id959f9a3b “sKitL” (https://identifiers.org/ensembl/ENSG00000049130) and sKitL” (https://identifiers.org/ensembl/ENSG00000049130)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/WP/Interaction/id959f9a3b “sKitL” (https://identifiers.org/ensembl/ENSG00000049130) and mKitL” (https://identifiers.org/ensembl/ENSG00000049130)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/WP/Interaction/id959f9a3b “mKitL” (https://identifiers.org/ensembl/ENSG00000049130) and sKitL” (https://identifiers.org/ensembl/ENSG00000049130)
• http://classic.wikipathways.org/instance/WP4331_r135060 http://rdf.wikipathways.org/Pathway/WP4331_r135060/WP/Interaction/id959f9a3b “mKitL” (https://identifiers.org/ensembl/ENSG00000049130) and mKitL” (https://identifiers.org/ensembl/ENSG00000049130)

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