wikipathways-collection

WikiPathways WP5355

• WikiPathways: WP5355 (classic)
• Species: Homo sapiens
• Scholia: WP5355

  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: 2
  • 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: 13
  • 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

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/DataNode/a7bf7 (Metabolite)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/DataNode/ea794 (Metabolite)

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP5355_r129474 “Glutamine deprivation “ with graphId a1ebd

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

Possible MIM translocation

Interactions between identical nodes: 13

• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/id2821b8bd “Aspartate” (https://identifiers.org/hmdb/HMDB0000191) and Aspartate” (https://identifiers.org/hmdb/HMDB0000191)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/id97d3f5a6 “L-Glutamine” (https://identifiers.org/hmdb/HMDB0000641) and L-Glutamine” (https://identifiers.org/hmdb/HMDB0000641)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/f43f0 “Malate” (https://identifiers.org/hmdb/HMDB0000744) and Malate” (https://identifiers.org/hmdb/HMDB0000744)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/c4561 “Glucose” (https://identifiers.org/hmdb/HMDB0000122) and Glucose” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/a8fa1 “Pyruvate” (https://identifiers.org/hmdb/HMDB0000243) and Pyruvate” (https://identifiers.org/hmdb/HMDB0000243)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/idb3470e70 “Ornithine” (https://identifiers.org/hmdb/HMDB0000214) and Ornithine” (https://identifiers.org/hmdb/HMDB0000214)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/a3a75 “Malate” (https://identifiers.org/hmdb/HMDB0000744) and Malate” (https://identifiers.org/hmdb/HMDB0000744)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/id76a579f0 “Biocytin” (https://identifiers.org/hmdb/HMDB0003134) and Biocytin” (https://identifiers.org/hmdb/HMDB0003134)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/a5f40 “Glucose” (https://identifiers.org/hmdb/HMDB0000122) and Glucose” (https://identifiers.org/hmdb/HMDB0000122)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/d1bc6 “L-serine” (https://identifiers.org/chebi/CHEBI:33384) and L-serine” (https://identifiers.org/chebi/CHEBI:33384)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/id7601a3df “Biotin” (https://identifiers.org/hmdb/HMDB0000030) and Biotin” (https://identifiers.org/hmdb/HMDB0000030)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/id8003bd1 “Allysine” (https://identifiers.org/hmdb/HMDB0001263) and Allysine” (https://identifiers.org/hmdb/HMDB0001263)
• http://classic.wikipathways.org/instance/WP5355_r129474 http://rdf.wikipathways.org/Pathway/WP5355_r129474/WP/Interaction/id3aad3d61 “Citrulline” (https://identifiers.org/hmdb/HMDB0000904) and Citrulline” (https://identifiers.org/hmdb/HMDB0000904)

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/WP5355_r129474 Cysteine CHEBI:15356