wikipathways-collection

WikiPathways WP5103

• WikiPathways: WP5103 (classic)
• Species: Homo sapiens
• Scholia: WP5103

  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: 8
  • 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: 2
  • 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
  • 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 8 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: 120
• Number of assertions: 241
• Number of fails: 3

Fails

Datanodes of unknown type

The following DataNodes have Unknown @Type: 8

• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/d6538 (Hutchinson-Gilford Progeria Syndrome)
• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/e440d (Keppen-Lubinsky syndrome)
• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/efb22 (MDP syndrome)
• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/f4495 (Mandibuloacral dysplasia)
• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/f626b (Marfan syndrome)
• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/e12e0 (Nestor-Guillermo progeria syndrome)
• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/d7ddc (Progeroid features-hepatocellular carcinoma predisposition syndrome )
• http://classic.wikipathways.org/instance/WP5103_r119170 http://rdf.wikipathways.org/Pathway/WP5103_r119170/DataNode/eb3f8 (Werner syndrome)

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

Interactions with Labels

Interactions found that involve Labels: 2

• http://classic.wikipathways.org/instance/WP5103_r119170 “Progeria Associated Lipodystrophy” with graphId e8fb3
• http://classic.wikipathways.org/instance/WP5103_r119170 “K+ influx” with graphId ac0c0

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

Identifier used of a amino acid with undefined stereochemistry

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP5103_r119170 CAAX CHEBI:15356

More details at https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/achiralAminoAcids