wikipathways-collection

WikiPathways WP2583

• WikiPathways: WP2583 (classic)
• Species: Homo sapiens
• Scholia: WP2583

  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: 10
  • 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: 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: 2
  • 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: 10

• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/dc90a (AP-1 )
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/a8ece (B7-1/ B7-2)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/f7b20 (B7-1/ B7-2)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/eeb8e (Bcl-xL)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/cf1d5 (Erk)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/ff54e (LAT / SLP-76 scaffold complex)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/da6cd (MHC peptide)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/c951f (PD-L1)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/e35aa (Ras-GDP)
• http://classic.wikipathways.org/instance/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/f002d (Ras-GTP)

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/WP2583_r135033 http://rdf.wikipathways.org/Pathway/WP2583_r135033/DataNode/f2340 (PI3K)

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: 2

http://classic.wikipathways.org/instance/WP2583_r135033 TCRB with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2583_r135033 TCRA with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 2

• http://classic.wikipathways.org/instance/WP2583_r135033 “Survival” with graphId d8ce7
• http://classic.wikipathways.org/instance/WP2583_r135033 “Proliferation” with graphId bdd9d

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