wikipathways-collection

WikiPathways WP4290

• WikiPathways: WP4290 (classic)
• Species: Homo sapiens
• Scholia: WP4290

  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: 4
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • 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: 1
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 2
  • 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: 3
  • 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

Data nodes without an identifier

The following DataNodes have no identifier: 4

• http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/b2ba1 (Amino acid synthesis)
• http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/c28b6 (Cell cycle Proliferation)
• http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/ded28 (Nucleotide synthesis)
• http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/bd312 (Purine synthesis)

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP4290_r136156 “pH balance Nitrogen source” with graphId f0da4

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/WP/Interaction/id35c246c6 “glutamine” (https://identifiers.org/chebi/CHEBI:28300) and glutamine” (https://identifiers.org/chebi/CHEBI:28300)
• http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/WP/Interaction/idd3a00f33 “Lactate” (https://identifiers.org/hmdb/HMDB0000190) and Lactate” (https://identifiers.org/hmdb/HMDB0000190)

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

MetabolitesTests.achiralAminoAcids

Metabolites with ChEBI identifiers of achiral amino acids: 3

http://classic.wikipathways.org/instance/WP4290_r136156 glutamine CHEBI:28300
http://classic.wikipathways.org/instance/WP4290_r136156 Proline CHEBI:26271
http://classic.wikipathways.org/instance/WP4290_r136156 serine CHEBI:17822