wikipathways-collection

WikiPathways WP4217

• WikiPathways: WP4217 (classic)
• Species: Homo sapiens
• Scholia: WP4217

  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: 4
  • 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: 5
• 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: 23
  • 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: 4

• http://classic.wikipathways.org/instance/WP4217_r134288 http://rdf.wikipathways.org/Pathway/WP4217_r134288/DataNode/fe112 (ERK)
• http://classic.wikipathways.org/instance/WP4217_r134288 http://rdf.wikipathways.org/Pathway/WP4217_r134288/DataNode/d4f9e (FILAMIN)
• http://classic.wikipathways.org/instance/WP4217_r134288 http://rdf.wikipathways.org/Pathway/WP4217_r134288/DataNode/e8d69 (MHC1)
• http://classic.wikipathways.org/instance/WP4217_r134288 http://rdf.wikipathways.org/Pathway/WP4217_r134288/DataNode/fa83a (MHC2)

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: 5

http://classic.wikipathways.org/instance/WP4217_r134288 HLA-DRB4 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP4217_r134288 HLA-DRB3 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP4217_r134288 CAVEOLIN with datasource InterPro
http://classic.wikipathways.org/instance/WP4217_r134288 ACTIN with datasource InterPro
http://classic.wikipathways.org/instance/WP4217_r134288 LC8 with datasource NCBI Protein

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

Interactions with Labels

Interactions found that involve Labels: 23

• http://classic.wikipathways.org/instance/WP4217_r134288 “VP40” with graphId fd60b
• http://classic.wikipathways.org/instance/WP4217_r134288 “Exit of Secreted GP” with graphId ced7e
• http://classic.wikipathways.org/instance/WP4217_r134288 “GP1,2” with graphId ceed9
• http://classic.wikipathways.org/instance/WP4217_r134288 “Interferon Response” with graphId ead0c
• http://classic.wikipathways.org/instance/WP4217_r134288 “GP” with graphId f641c
• http://classic.wikipathways.org/instance/WP4217_r134288 “Transcription, Translation and Replication” with graphId b08bc
• http://classic.wikipathways.org/instance/WP4217_r134288 “NP” with graphId dd9ee
• http://classic.wikipathways.org/instance/WP4217_r134288 “Trans-Infection” with graphId c4b2d
• http://classic.wikipathways.org/instance/WP4217_r134288 “VP35” with graphId b7577
• http://classic.wikipathways.org/instance/WP4217_r134288 “PtdSer” with graphId b9fc7
• http://classic.wikipathways.org/instance/WP4217_r134288 “Lysosome” with graphId c0def
• http://classic.wikipathways.org/instance/WP4217_r134288 “VP30” with graphId d96ac
• http://classic.wikipathways.org/instance/WP4217_r134288 “Assembly and Budding” with graphId b8b34
• http://classic.wikipathways.org/instance/WP4217_r134288 “Cell Adhesion Immune Surveillance “ with graphId a5634
• http://classic.wikipathways.org/instance/WP4217_r134288 “L” with graphId f1080
• http://classic.wikipathways.org/instance/WP4217_r134288 “EBOLA” with graphId ca190
• http://classic.wikipathways.org/instance/WP4217_r134288 “ssGP” with graphId f742b
• http://classic.wikipathways.org/instance/WP4217_r134288 “VIRUS’ RNA” with graphId ca18b
• http://classic.wikipathways.org/instance/WP4217_r134288 “Cytokine Signal” with graphId f4161
• http://classic.wikipathways.org/instance/WP4217_r134288 “VP24” with graphId c190d
• http://classic.wikipathways.org/instance/WP4217_r134288 “GP” with graphId a23e0
• http://classic.wikipathways.org/instance/WP4217_r134288 “Endosome” with graphId a02b4
• http://classic.wikipathways.org/instance/WP4217_r134288 “sGP” with graphId c2f57

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