wikipathways-collection

WikiPathways WP5314

• WikiPathways: WP5314 (classic)
• Species: Homo sapiens
• Scholia: WP5314

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 6 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: .. all OK!
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 9
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 6
  • 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 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• Sec2PriProjectTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• UnicodeTests
  • water: .. all OK!
  • calcium: .. all OK!
  • hydron: .. all OK!
  • sodium: .. all OK!
  • potassium: .. all OK!
  • oxygen: .. all OK!
  • carbondioxide: .. all OK!
  • iron2: .. all OK!
  • iron3: .. all OK!
  • copper: .. all OK!
  • copper2: .. all OK!
  • manganese: .. all OK!
  • magnesium: .. all OK!
  • ammonia: .. all OK!
  • chloride: .. all OK!
  • bicarbonate: .x we found 1 problem(s):
    • Metabolite can use HCO₃⁻ instead of HCO3-: 1
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 147
• Number of assertions: 293
• Number of fails: 4

Fails

Interactions with unconnected points

Interactions with unconnected points: 9

• http://classic.wikipathways.org/instance/WP5314_r140445

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

Possible MIM translocation

Interactions between identical nodes: 6

• http://classic.wikipathways.org/instance/WP5314_r140445 http://rdf.wikipathways.org/Pathway/WP5314_r140445/WP/Interaction/idfbad38df “Glutamate” (https://identifiers.org/chebi/CHEBI:14321) and Glutamate” (https://identifiers.org/chebi/CHEBI:14321)
• http://classic.wikipathways.org/instance/WP5314_r140445 http://rdf.wikipathways.org/Pathway/WP5314_r140445/WP/Interaction/id5ca97d16 “Glutamate” (https://identifiers.org/chebi/CHEBI:14321) and Glutamate” (https://identifiers.org/chebi/CHEBI:14321)
• http://classic.wikipathways.org/instance/WP5314_r140445 http://rdf.wikipathways.org/Pathway/WP5314_r140445/WP/Interaction/ida4c7d417 “Lactate” (https://identifiers.org/chebi/CHEBI:24996) and Lactate” (https://identifiers.org/chebi/CHEBI:24996)
• http://classic.wikipathways.org/instance/WP5314_r140445 http://rdf.wikipathways.org/Pathway/WP5314_r140445/WP/Interaction/id53b50a6e “Glucose” (https://identifiers.org/chebi/CHEBI:17234) and Glucose” (https://identifiers.org/chebi/CHEBI:17234)
• http://classic.wikipathways.org/instance/WP5314_r140445 http://rdf.wikipathways.org/Pathway/WP5314_r140445/WP/Interaction/id4c1ca33 “Glucose” (https://identifiers.org/chebi/CHEBI:17234) and Glucose” (https://identifiers.org/chebi/CHEBI:17234)
• http://classic.wikipathways.org/instance/WP5314_r140445 http://rdf.wikipathways.org/Pathway/WP5314_r140445/WP/Interaction/id24d75b25 “HCO3-“ (https://identifiers.org/chebi/CHEBI:17544) and HCO3-“ (https://identifiers.org/chebi/CHEBI:17544)

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

Identifier used of a amino acid with undefined stereochemistry

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP5314_r140445 Glutamine CHEBI:28300

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

The bicarbonate ion formula can use Unicode

Metabolite can use HCO₃⁻ instead of HCO3-: 1

• http://classic.wikipathways.org/instance/WP5314_r140445

More details at https://www.wikipathways.org/WikiPathwaysCurator/UnicodeTests/bicarbonate