wikipathways-collection

WikiPathways WP4159

• WikiPathways: WP4159 (classic)
• Species: Homo sapiens
• Scholia: WP4159

  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
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: …. all OK!
  • nonNumericHGNCAccessionNumbers: .. all OK!
  • genesWithoutEnsemblMapping: .x we found 1 problem(s):
    • The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1
• 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: 12
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 4
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 7 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests
  • nonNumericPubMedIDs: .. all OK!
  • unexpectedPubMedIdentifier: .. all OK!
  • zeroPubMedIDs: .. all OK!
  • atLeastOneReference: .x we found 1 problem(s):
    • Found 1 pathways with zero (PubMed) references
  • citesRetractedArticle: .. all OK!
  • outdatedPubMedIdentifiers: .. all OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 20
• Number of tests: 118
• Number of assertions: 237
• Number of fails: 4

Fails

Genes with identifier but no Ensembl identifier mapping

The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1

http://classic.wikipathways.org/instance/WP4159_r128692 NSF with datasource Wikidata

More details at https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping

Interactions with Labels

Interactions found that involve Labels: 12

• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId b9880
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId b4e4c
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId a7640
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId db3f9
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId c3c5d
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId c8283
• http://classic.wikipathways.org/instance/WP4159_r128692 “Translocation/Transport” with graphId a0452
• http://classic.wikipathways.org/instance/WP4159_r128692 “” with graphId a2493
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId ccfd2
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId a4555
• http://classic.wikipathways.org/instance/WP4159_r128692 “AP2” with graphId f8897
• http://classic.wikipathways.org/instance/WP4159_r128692 “GABA-A-receptor” with graphId b2182

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

Possible MIM translocation

Interactions between identical nodes: 4

• http://classic.wikipathways.org/instance/WP4159_r128692 http://rdf.wikipathways.org/Pathway/WP4159_r128692/WP/Interaction/id498b252a “release of GABA” (https://identifiers.org/wikidata/Q210021) and release of GABA” (https://identifiers.org/wikidata/Q210021)
• http://classic.wikipathways.org/instance/WP4159_r128692 http://rdf.wikipathways.org/Pathway/WP4159_r128692/WP/Interaction/id498b252a “release of GABA” (https://identifiers.org/wikidata/Q210021) and GABA” (https://identifiers.org/wikidata/Q210021)
• http://classic.wikipathways.org/instance/WP4159_r128692 http://rdf.wikipathways.org/Pathway/WP4159_r128692/WP/Interaction/id498b252a “GABA” (https://identifiers.org/wikidata/Q210021) and release of GABA” (https://identifiers.org/wikidata/Q210021)
• http://classic.wikipathways.org/instance/WP4159_r128692 http://rdf.wikipathways.org/Pathway/WP4159_r128692/WP/Interaction/id498b252a “GABA” (https://identifiers.org/wikidata/Q210021) and GABA” (https://identifiers.org/wikidata/Q210021)

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP4159_r128692 ‘GABA receptor signaling’ in Homo sapiens has zero references;

More details at https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference