wikipathways-collection

WikiPathways WP5356

• WikiPathways: WP5356 (classic)
• Species: Homo sapiens
• Scholia: WP5356

  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: 12
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 tests OK!
• 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: 6
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 10
  • 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: 117
• Number of assertions: 235
• Number of fails: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 12

• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/ab994 (Fibrosis)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/cc8c0 (Fibrosis)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/f7a3f (Inflammatory pathway)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/a70b5 (Inflammatory pathways )
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/aefe8 (Inflammatory pathways )
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/faa00 (Inflammatory response)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/ce34b (Leukotrienes)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/f3228 (Oxidative stress)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/b418b (Prostaglandins)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/ade48 (ROS)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/a2197 (SOCE)
• http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/DataNode/e52cc (Sodium regulators)

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

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 6

http://classic.wikipathways.org/instance/WP5356_r134500 "Fibroblast Activation" with graphId df2c7
http://classic.wikipathways.org/instance/WP5356_r134500 "
Membrane Tear" with graphId ad1b9
http://classic.wikipathways.org/instance/WP5356_r134500 "Loss of mitochondria" with graphId c7ba4
http://classic.wikipathways.org/instance/WP5356_r134500 "Sustained  Muscle Contraction" with graphId db650
http://classic.wikipathways.org/instance/WP5356_r134500 "DAMPs" with graphId feb3b
http://classic.wikipathways.org/instance/WP5356_r134500 "Muscle Stiffness " with graphId a3ed1

Possible MIM translocation

Interactions between identical nodes: 10

http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/e876f "Ca2+" (https://identifiers.org/hmdb/HMDB0000464) and 
Ca2+" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/e876f "Ca2+" (https://identifiers.org/hmdb/HMDB0000464) and 
[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/e876f "[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464) and 
Ca2+" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/e876f "[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464) and 
[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/aba4f "HOCl" (https://identifiers.org/hmdb/HMDB0001050) and 
HOCl" (https://identifiers.org/hmdb/HMDB0001050)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/f8a08 "Na+" (https://identifiers.org/hmdb/HMDB0000588) and 
Na+" (https://identifiers.org/hmdb/HMDB0000588)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/a489d "Ca2+" (https://identifiers.org/hmdb/HMDB0000464) and 
Ca2+" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/a489d "Ca2+" (https://identifiers.org/hmdb/HMDB0000464) and 
[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/a489d "[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464) and 
Ca2+" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5356_r134500 http://rdf.wikipathways.org/Pathway/WP5356_r134500/WP/Interaction/a489d "[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464) and 
[Ca2+]mito" (https://identifiers.org/hmdb/HMDB0000464)

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