wikipathways-collection

WikiPathways WP5318

• WikiPathways: WP5318 (classic)
• Species: Homo sapiens
• Scholia: WP5318

  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: 13
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 7
  • 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: 8
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .x we found 1 problem(s):
    • Unexpected non-metabolite to metabolite conversions: 1
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .. all OK!
  • possibleTranslocations: .. all OK!
  • noProteinProteinConversions: .x we found 1 problem(s):
    • Unexpected protein-protein conversions: 1
  • 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: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 13

• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/a19a6 (AMPK-stimulated GLUT-4)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/b2a6b (CoA)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/b98d2 (Estrogen response element)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/ba872 (Fructose 1, 6-biphosphate)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/d0ee5 (GLUT4)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/ef524 (H20)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/cb651 (Hydrogen peroxide)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/c15a5 (Increased risk of carcinogenesis)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/c8418 (K+)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/cdaff (O2)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/bcd18 (PI3K)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/a1ca1 (RAF/KSR family kinases)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/e9dbb (TF)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 7

• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/d8aa8 (11B-HSD1)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/c7a78 (Cortisol)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/f4673 (Cortisol)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/bb14d (Glucocoticoid receptor)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/e2ecd (Glucocoticoid response elements )
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/c15a5 (Increased risk of carcinogenesis)
• http://classic.wikipathways.org/instance/WP5318_r134651 http://rdf.wikipathways.org/Pathway/WP5318_r134651/DataNode/f246b (Inhibition of IL1-B)

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: 8

http://classic.wikipathways.org/instance/WP5318_r134651 cTNL with datasource KEGG Genes
http://classic.wikipathways.org/instance/WP5318_r134651 Troponin with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5318_r134651 Elk-1 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5318_r134651 MYH6 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5318_r134651 FoxO1 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5318_r134651 Inhibition of TNF-a with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5318_r134651 ROS with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5318_r134651 MEF2 with datasource UniProtKB

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

No non-metabolite to metabolite conversions

Unexpected non-metabolite to metabolite conversions: 1

• Homo sapiens http://classic.wikipathways.org/instance/WP5318_r134651 → https://identifiers.org/uniprot/P11474 https://identifiers.org/reactome/R-HSA-194002 http://rdf.wikipathways.org/Pathway/WP5318_r134651/WP/Interaction/id1ff5f428

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

Protein converted into another protein

Unexpected protein-protein conversions: 1

• Homo sapiens http://classic.wikipathways.org/instance/WP5318_r134651 -> https://identifiers.org/uniprot/P11474 https://identifiers.org/reactome/R-HSA-194002 http://rdf.wikipathways.org/Pathway/WP5318_r134651/WP/Interaction/id1ff5f428

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