wikipathways-collection

WikiPathways WP4172

• WikiPathways: WP4172 (classic)
• Species: Homo sapiens
• Scholia: WP4172

  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: 5
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 1
  • 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: 10
  • 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 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: 5

• http://classic.wikipathways.org/instance/WP4172_r134839 http://rdf.wikipathways.org/Pathway/WP4172_r134839/DataNode/f6f49 (Cell proliferation)
• http://classic.wikipathways.org/instance/WP4172_r134839 http://rdf.wikipathways.org/Pathway/WP4172_r134839/DataNode/d0656 (FoxO signaling pathway)
• http://classic.wikipathways.org/instance/WP4172_r134839 http://rdf.wikipathways.org/Pathway/WP4172_r134839/DataNode/a806f (Kik1b4)
• http://classic.wikipathways.org/instance/WP4172_r134839 http://rdf.wikipathways.org/Pathway/WP4172_r134839/DataNode/e8864 (Mtcp1)
• http://classic.wikipathways.org/instance/WP4172_r134839 http://rdf.wikipathways.org/Pathway/WP4172_r134839/DataNode/aa6aa (mTOR signaling pathway)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 1

• http://classic.wikipathways.org/instance/WP4172_r134839 http://rdf.wikipathways.org/Pathway/WP4172_r134839/DataNode/b03b3 (Hypoxia)

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

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/WP4172_r134839 BCR with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 10

• http://classic.wikipathways.org/instance/WP4172_r134839 “Metabolism” with graphId b7abd
• http://classic.wikipathways.org/instance/WP4172_r134839 “Cell cycle progression” with graphId e7f49
• http://classic.wikipathways.org/instance/WP4172_r134839 “Actin reorganization” with graphId b4de4
• http://classic.wikipathways.org/instance/WP4172_r134839 “Pathogen-associated molecular patterns (PAMPS)” with graphId d7ce1
• http://classic.wikipathways.org/instance/WP4172_r134839 “Antigen” with graphId c7b46
• http://classic.wikipathways.org/instance/WP4172_r134839 “Protein synthesis” with graphId f8076
• http://classic.wikipathways.org/instance/WP4172_r134839 “Cell survival” with graphId fce69
• http://classic.wikipathways.org/instance/WP4172_r134839 “Glucose uptake Vesicle transport” with graphId eb17a
• http://classic.wikipathways.org/instance/WP4172_r134839 “Chemokines, hormones, neurotransmitters” with graphId c3505
• http://classic.wikipathways.org/instance/WP4172_r134839 “Survival signal, Growth and proliferation” with graphId f1c4a

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