wikipathways-collection

WikiPathways WP5446

• WikiPathways: WP5446 (classic)
• Species: Homo sapiens
• Scholia: WP5446

  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: 4
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 4
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all 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: 8
• 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: 1
  • 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: all 6 tests 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

Data nodes without an identifier

The following DataNodes have no identifier: 4

• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/ba809 ()
• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/d57c6 ()
• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/d1a49 (Parasympathetic nervous system)
• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/f182e (Sympathetic nervous system)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 4

• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/ba809 ()
• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/d57c6 ()
• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/d1a49 (Parasympathetic nervous system)
• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/DataNode/f182e (Sympathetic nervous system)

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

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: 8

http://classic.wikipathways.org/instance/WP5446_r129189 GPCR with datasource Wikidata
http://classic.wikipathways.org/instance/WP5446_r129189 G-beta with datasource InterPro
http://classic.wikipathways.org/instance/WP5446_r129189 mAChR with datasource Wikidata
http://classic.wikipathways.org/instance/WP5446_r129189 G-gamma with datasource InterPro
http://classic.wikipathways.org/instance/WP5446_r129189 Ca+ channel with datasource Wikidata
http://classic.wikipathways.org/instance/WP5446_r129189 KATP channel with datasource Wikidata
http://classic.wikipathways.org/instance/WP5446_r129189 Na+ channel with datasource Wikidata
http://classic.wikipathways.org/instance/WP5446_r129189 Alpha AR with datasource Wikidata

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

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP5446_r129189 http://rdf.wikipathways.org/Pathway/WP5446_r129189/WP/Interaction/id8cac31c7 “GLP-1” (https://identifiers.org/wikidata/Q424611) and GLP-1” (https://identifiers.org/wikidata/Q424611)

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