wikipathways-collection

WikiPathways WP4585

• WikiPathways: WP4585 (classic)
• Species: Homo sapiens
• Scholia: WP4585

  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: 3
  • 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: 1
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • 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: 3

• http://classic.wikipathways.org/instance/WP4585_r134735 http://rdf.wikipathways.org/Pathway/WP4585_r134735/DataNode/fb550 (AMP-224)
• http://classic.wikipathways.org/instance/WP4585_r134735 http://rdf.wikipathways.org/Pathway/WP4585_r134735/DataNode/f897c (MDX-1105)
• http://classic.wikipathways.org/instance/WP4585_r134735 http://rdf.wikipathways.org/Pathway/WP4585_r134735/DataNode/a8e9d (Tumor-associated antigen)

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/WP4585_r134735 TRB with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP4585_r134735 TRA with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP4585_r134735 “T cell activation Growth Proliferation Survival” with graphId d7a36

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

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP4585_r134735 http://rdf.wikipathways.org/Pathway/WP4585_r134735/WP/Interaction/idfbed420c “BATF” (https://identifiers.org/ensembl/ENSG00000156127) and BATF” (https://identifiers.org/ensembl/ENSG00000156127)

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