wikipathways-collection

WikiPathways WP5104

• WikiPathways: WP5104 (classic)
• Species: Homo sapiens
• Scholia: WP5104

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .. all OK!
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 3
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 5 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: 5
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 18
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests
  • ChEBIIDsNotMarkedAsMetabolite: .. all OK!
  • HMDBIDsNotMarkedAsMetabolite: .. all OK!
  • KEGGIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotNumbers: .. all OK!
  • PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemSubstanceIDsNotNumbers: .. all OK!
  • achiralAminoAcids: .x we found 1 problem(s):
    • Metabolites with ChEBI identifiers of achiral amino acids: 1
  • casNumbersNotMarkedAsMetabolite: .. all OK!
  • chemspiderIDsNotMarkedAsMetabolite: .. all OK!
  • metaboliteAlsoOtherType: .. all OK!
  • metabolitesWithAnEnsembleID: .. all OK!
  • metabolitesWithAnEntrezGeneID: .. all OK!
  • metabolitesWithDbButNoIdentifier: .. all OK!
  • metabolitesWithIdentifierButNoDb: .. all 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: 119
• Number of assertions: 239
• Number of fails: 4

Fails

Datanodes of unknown type

The following DataNodes have Unknown @Type: 3

• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/DataNode/cdde8 (Autoimmune disease)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/DataNode/ed628 (Barraquer-Simons syndrome)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/DataNode/c7ca1 (Membranoproliferative glomerulonephritis)

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

Interactions with Labels

Interactions found that involve Labels: 5

• http://classic.wikipathways.org/instance/WP5104_r128462 “Hydrolysis” with graphId ef858
• http://classic.wikipathways.org/instance/WP5104_r128462 “Nuclear lamina” with graphId f56d5
• http://classic.wikipathways.org/instance/WP5104_r128462 “DNA replication RNA transcription Cell cycle regulation Mechanical support etc.” with graphId e99b5
• http://classic.wikipathways.org/instance/WP5104_r128462 “Adipocyte lysis” with graphId c2596
• http://classic.wikipathways.org/instance/WP5104_r128462 “Excess amount of membrane attack complex” with graphId f07fd

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

Possible MIM translocation

Interactions between identical nodes: 18

• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3” (https://identifiers.org/ensembl/ENSG00000125730) and C3” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3” (https://identifiers.org/ensembl/ENSG00000125730) and C3b” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3” (https://identifiers.org/ensembl/ENSG00000125730) and C3a” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3b” (https://identifiers.org/ensembl/ENSG00000125730) and C3” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3b” (https://identifiers.org/ensembl/ENSG00000125730) and C3b” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3b” (https://identifiers.org/ensembl/ENSG00000125730) and C3a” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3a” (https://identifiers.org/ensembl/ENSG00000125730) and C3” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3a” (https://identifiers.org/ensembl/ENSG00000125730) and C3b” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/c9f4a “C3a” (https://identifiers.org/ensembl/ENSG00000125730) and C3a” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3” (https://identifiers.org/ensembl/ENSG00000125730) and C3” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3” (https://identifiers.org/ensembl/ENSG00000125730) and C3b” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3” (https://identifiers.org/ensembl/ENSG00000125730) and C3a” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3b” (https://identifiers.org/ensembl/ENSG00000125730) and C3” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3b” (https://identifiers.org/ensembl/ENSG00000125730) and C3b” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3b” (https://identifiers.org/ensembl/ENSG00000125730) and C3a” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3a” (https://identifiers.org/ensembl/ENSG00000125730) and C3” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3a” (https://identifiers.org/ensembl/ENSG00000125730) and C3b” (https://identifiers.org/ensembl/ENSG00000125730)
• http://classic.wikipathways.org/instance/WP5104_r128462 http://rdf.wikipathways.org/Pathway/WP5104_r128462/WP/Interaction/id33f792da “C3a” (https://identifiers.org/ensembl/ENSG00000125730) and C3a” (https://identifiers.org/ensembl/ENSG00000125730)

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

MetabolitesTests.achiralAminoAcids

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP5104_r128462 CAAX CHEBI:15356