wikipathways-collection

WikiPathways WP4949

• WikiPathways: WP4949 (classic)
• Species: Homo sapiens
• Scholia: WP4949

  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: 2
• 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: 11
  • possibleTranslocations: .. all OK!
  • 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 1

• http://classic.wikipathways.org/instance/WP4949_r134719 http://rdf.wikipathways.org/Pathway/WP4949_r134719/DataNode/c5a76 (Phosphoprotein Phosphatase 4 complex)

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: 2

http://classic.wikipathways.org/instance/WP4949_r134719 Actin with datasource Pfam
http://classic.wikipathways.org/instance/WP4949_r134719 Histone with datasource Pfam

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

Interactions with Labels

Interactions found that involve Labels: 11

• http://classic.wikipathways.org/instance/WP4949_r134719 “excitotoxic to neurons” with graphId a67e4
• http://classic.wikipathways.org/instance/WP4949_r134719 “mitosis” with graphId f2b2f
• http://classic.wikipathways.org/instance/WP4949_r134719 “Lymphocyte trafficking Lympthocyte polarization” with graphId f324c
• http://classic.wikipathways.org/instance/WP4949_r134719 “exact function unknown but involved in movement disorders in genetic epilepsies “ with graphId f9384
• http://classic.wikipathways.org/instance/WP4949_r134719 “Function unclear Enzymatic activity dioxygenase activity” with graphId f78ac
• http://classic.wikipathways.org/instance/WP4949_r134719 “involved in sperm and egg fusion” with graphId c4f3a
• http://classic.wikipathways.org/instance/WP4949_r134719 “unknown function” with graphId e8c8e
• http://classic.wikipathways.org/instance/WP4949_r134719 “Function unclear involved in neuronal ER trafficking” with graphId fa69f
• http://classic.wikipathways.org/instance/WP4949_r134719 “Transcription factor regulating mesoderm specification mesoderm segmentation (in zebrafish)” with graphId a66f2
• http://classic.wikipathways.org/instance/WP4949_r134719 “KCTD13 deficient mice
• synaptic formation
• mature spine density in hippocampus” with graphId aeb74
• http://classic.wikipathways.org/instance/WP4949_r134719 “Stress” with graphId b4e8e

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