wikipathways-collection

WikiPathways WP3953

• WikiPathways: WP3953 (classic)
• Species: Homo sapiens
• Scholia: WP3953

  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: 5
  • 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: 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 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: 5

• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/DataNode/cd3ad (glutamate cysteine ligase catalytic subunit)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/DataNode/c4831 (glutamate cysteine ligase modifier subunit)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/DataNode/e4432 (glutamate cysteine ligase modifier subunit)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/DataNode/eea31 (glutamate cysteine ligase modifier subunit)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/DataNode/a6312 (glutathione reductase)

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

Possible MIM translocation

Interactions between identical nodes: 6

• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/WP/Interaction/id65fa99f2 “SLC1A5” (https://identifiers.org/ensembl/ENSG00000105281) and SLC1A5” (https://identifiers.org/ensembl/ENSG00000105281)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/WP/Interaction/iddb549c07 “SLC7A11” (https://identifiers.org/ensembl/ENSG00000151012) and SLC7A11” (https://identifiers.org/ensembl/ENSG00000151012)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/WP/Interaction/id87c72705 “SLC7A5” (https://identifiers.org/ensembl/ENSG00000103257) and SLC7A5” (https://identifiers.org/ensembl/ENSG00000103257)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/WP/Interaction/id40853d5e “SLC3A2” (https://identifiers.org/ensembl/ENSG00000168003) and SLC3A2” (https://identifiers.org/ensembl/ENSG00000168003)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/WP/Interaction/idadb3e53e “KEAP1” (https://identifiers.org/ensembl/ENSG00000079999) and KEAP1” (https://identifiers.org/ensembl/ENSG00000079999)
• http://classic.wikipathways.org/instance/WP3953_r106206 http://rdf.wikipathways.org/Pathway/WP3953_r106206/WP/Interaction/id4a6208ff “SLC3A2” (https://identifiers.org/ensembl/ENSG00000168003) and SLC3A2” (https://identifiers.org/ensembl/ENSG00000168003)

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/WP3953_r106206 cysteine CHEBI:15356