wikipathways-collection

WikiPathways WP5088

• WikiPathways: WP5088 (classic)
• Species: Homo sapiens
• Scholia: WP5088

  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: 6
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 2
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 13 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: 9
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 4
  • 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 8 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: 99
• Number of assertions: 200
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 6

http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/ac39d ()
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/b946c ()
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/c776b ()
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/c794d ()
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/bfe24 (COX2)
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/c10b1 (COX2)

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

DataNodesTests.unknownTypes

The following DataNodes have Unknown @Type: 2

http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/b946c ()
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/DataNode/c794d ()

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 9

http://classic.wikipathways.org/instance/WP5088_r128022 "Decreased platelet 
activation" with graphId fab80
http://classic.wikipathways.org/instance/WP5088_r128022 "NK cell migration
" with graphId d2946
http://classic.wikipathways.org/instance/WP5088_r128022 "Inflammatory Th17 
cell expansion" with graphId bf8e0
http://classic.wikipathways.org/instance/WP5088_r128022 "Protection against 
viral infection" with graphId fd670
http://classic.wikipathways.org/instance/WP5088_r128022 "NK and CD8+ T cell 
cytolytic activity" with graphId bef69
http://classic.wikipathways.org/instance/WP5088_r128022 "NET formation" with graphId bd9b6
http://classic.wikipathways.org/instance/WP5088_r128022 "Cytokine storm, hyperinflammation 
(postive feedback loop)" with graphId f3d1c
http://classic.wikipathways.org/instance/WP5088_r128022 "Decreased recruitment 
of CCR2 expressing 
monocytes and macrophages" with graphId a4238
http://classic.wikipathways.org/instance/WP5088_r128022 "T cell activation 
and proliferation" with graphId f7daa

Possible MIM translocation

Interactions between identical nodes: 4

http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/WP/Interaction/idf7ae457b "IL1B" (https://identifiers.org/ensembl/ENSG00000125538) and 
IL1B" (https://identifiers.org/ensembl/ENSG00000125538)
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/WP/Interaction/idf7ae457b "IL1B" (https://identifiers.org/ensembl/ENSG00000125538) and 
pro-IL1B" (https://identifiers.org/ensembl/ENSG00000125538)
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/WP/Interaction/idf7ae457b "pro-IL1B" (https://identifiers.org/ensembl/ENSG00000125538) and 
IL1B" (https://identifiers.org/ensembl/ENSG00000125538)
http://classic.wikipathways.org/instance/WP5088_r128022 http://rdf.wikipathways.org/Pathway/WP5088_r128022/WP/Interaction/idf7ae457b "pro-IL1B" (https://identifiers.org/ensembl/ENSG00000125538) and 
pro-IL1B" (https://identifiers.org/ensembl/ENSG00000125538)

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