wikipathways-collection

WikiPathways WP5488

• WikiPathways: WP5488 (classic)
• Species: Homo sapiens
• Scholia: WP5488

  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: 3
  • 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: .. all OK!
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 40
  • 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 3

• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/DataNode/c164e (SLC?)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/DataNode/f2d05 (SLC?)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/DataNode/d5335 (vitamin B12)

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

Possible MIM translocation

Interactions between identical nodes: 40

• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/e3b67 “PL” (https://identifiers.org/chebi/CHEBI:17310) and PL” (https://identifiers.org/chebi/CHEBI:17310)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/idc32f66a9 “B9” (https://identifiers.org/chebi/CHEBI:27470) and B9” (https://identifiers.org/chebi/CHEBI:27470)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/aa385 “PM” (https://identifiers.org/chebi/CHEBI:57761) and PM” (https://identifiers.org/chebi/CHEBI:57761)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/id32e912ac “B2” (https://identifiers.org/chebi/CHEBI:17015) and B2” (https://identifiers.org/chebi/CHEBI:17015)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/bb088 “PLP” (https://identifiers.org/chebi/CHEBI:597326) and PLP” (https://identifiers.org/chebi/CHEBI:597326)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ab51b “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ab51b “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ab51b “PN” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ab51b “PN” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/eccfe “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/eccfe “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/eccfe “PN” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/eccfe “PN” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/id2453f95c “5-MTHF” (https://identifiers.org/chebi/CHEBI:15641) and 5-MTHF” (https://identifiers.org/chebi/CHEBI:15641)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/fbdfd “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/fbdfd “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/fbdfd “PN” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/fbdfd “PN” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/cfe07 “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/cfe07 “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/cfe07 “PN” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/cfe07 “PN” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/a42c0 “PM” (https://identifiers.org/chebi/CHEBI:57761) and PM” (https://identifiers.org/chebi/CHEBI:57761)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/id902a858d “B2” (https://identifiers.org/chebi/CHEBI:17015) and B2” (https://identifiers.org/chebi/CHEBI:17015)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/idde3ff607 “cob(II)alamin” (https://identifiers.org/chebi/CHEBI:16304) and cob(II)alamin” (https://identifiers.org/chebi/CHEBI:16304)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/b1030 “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/b1030 “PNP” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/b1030 “PN” (https://identifiers.org/chebi/CHEBI:28803) and PNP” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/b1030 “PN” (https://identifiers.org/chebi/CHEBI:28803) and PN” (https://identifiers.org/chebi/CHEBI:28803)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/id3ef6cbb4 “5-MTHF” (https://identifiers.org/chebi/CHEBI:15641) and 5-MTHF” (https://identifiers.org/chebi/CHEBI:15641)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ida6e4b985 “Cbl” (https://identifiers.org/chebi/CHEBI:23334) and Cbl” (https://identifiers.org/chebi/CHEBI:23334)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ida6e4b985 “Cbl” (https://identifiers.org/chebi/CHEBI:23334) and cobalamins” (https://identifiers.org/chebi/CHEBI:23334)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ida6e4b985 “cobalamins” (https://identifiers.org/chebi/CHEBI:23334) and Cbl” (https://identifiers.org/chebi/CHEBI:23334)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ida6e4b985 “cobalamins” (https://identifiers.org/chebi/CHEBI:23334) and cobalamins” (https://identifiers.org/chebi/CHEBI:23334)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/af87c “PL” (https://identifiers.org/chebi/CHEBI:17310) and PL” (https://identifiers.org/chebi/CHEBI:17310)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/idb476947d “B9” (https://identifiers.org/chebi/CHEBI:27470) and B9” (https://identifiers.org/chebi/CHEBI:27470)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/idb3ddf4dd “cob(II)alamin” (https://identifiers.org/chebi/CHEBI:16304) and cob(II)alamin” (https://identifiers.org/chebi/CHEBI:16304)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/idbd55f5ab “B2” (https://identifiers.org/chebi/CHEBI:17015) and B2” (https://identifiers.org/chebi/CHEBI:17015)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/f517b “PLP” (https://identifiers.org/chebi/CHEBI:597326) and PLP” (https://identifiers.org/chebi/CHEBI:597326)
• http://classic.wikipathways.org/instance/WP5488_r135731 http://rdf.wikipathways.org/Pathway/WP5488_r135731/WP/Interaction/ad04c “PL” (https://identifiers.org/chebi/CHEBI:17310) and PL” (https://identifiers.org/chebi/CHEBI:17310)

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/WP5488_r135731 Met CHEBI:16811