wikipathways-collection

WikiPathways WP5115

• WikiPathways: WP5115 (classic)
• Species: Homo sapiens
• Scholia: WP5115

  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: .. 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: 27
• 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: .. 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP5115_r134657 http://rdf.wikipathways.org/Pathway/WP5115_r134657/DataNode/fdf13 (TLRs)
• http://classic.wikipathways.org/instance/WP5115_r134657 http://rdf.wikipathways.org/Pathway/WP5115_r134657/DataNode/1268066861 (VEGFA)

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: 27

http://classic.wikipathways.org/instance/WP5115_r134657 IL8 with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 IFNA with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 HLA-DRB4 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 TANK with datasource EMBL
http://classic.wikipathways.org/instance/WP5115_r134657 IGHE with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 IRF27 with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 ISG56 with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 IGHG1 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 MCP1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 TRAC with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 LDH with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 PDGF with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 MIP1A with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 IL1RA with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 IGHG4 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 IL2B with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 IL23 with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 IL2R with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 CALC1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 MIP1B with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 ISRE with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 GCSF with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 IGHG2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 TRBC1 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 IGLC2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP5115_r134657 CXCR7 with datasource HGNC
http://classic.wikipathways.org/instance/WP5115_r134657 GMCSF with datasource HGNC

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP5115_r134657 “Apoptosis” with graphId d7fd1

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