wikipathways-collection

WikiPathways WP1293

• WikiPathways: WP1293 (classic)
• Species: Rattus norvegicus

  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: 14
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: .. all OK!
  • numericHGNCIDs: .. 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: 9
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests: all 9 tests OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 15 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• Sec2PriProjectTests
  • outdatedHGNCSymbol: .. all OK!
  • outdatedHGNCAccessionNumber: .. all OK!
  • outdatedNCBIIdentifiers: .. all OK!
  • outdatedChEBIIdentifiers: .. all OK!
  • outdatedHMDBIdentifiers: .x we found 1 problem(s):
    • Old HMDB identifiers detected: 1
  • outdatedUniProtKBIdentifiers2: .. all OK!
• UniProtTests: all 5 tests OK!
• UnicodeTests: all 17 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 148
• Number of assertions: 295
• Number of fails: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 14

• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/bb7 (Cystathionine g-lyase)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/d176f (H2Se)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/e231d (MethylSelenol MeSeH)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/ce9 (Pouf2f1)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/a0d (Pstk)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/a0e (SBP2)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/ab2 (SBP2)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/e0a (SBP2)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/cf9 (SelH)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/c5a95 (Selenate)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/d646e (Selenate)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/e7bbe (Selenite)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/f9c6f (Selenite)
• http://classic.wikipathways.org/instance/WP1293_r116447 http://rdf.wikipathways.org/Pathway/WP1293_r116447/DataNode/d33 (UGA)

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

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: 9

http://classic.wikipathways.org/instance/WP1293_r116447 Sp1 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Sla with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Selo with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Scly with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Gpx4 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Txnrd1 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Dio2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Gpx2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP1293_r116447 Selenbp1 with datasource Entrez Gene

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

HMDB identifier has been retracted

Old HMDB identifiers detected: 1

• http://classic.wikipathways.org/instance/WP1293_r116447 Selenophosphate has HMDB ID HMDB0006407 but has been replaced by HMDB0003840

More details at https://www.wikipathways.org/WikiPathwaysCurator/Sec2PriProjectTests/outdatedHMDBIdentifiers