wikipathways-collection

WikiPathways WP5562

• WikiPathways: WP5562 (classic)
• Species: Homo sapiens
• Scholia: WP5562

  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: 17
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 2
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests
  • wrongEnsemblIDForCowSpecies: .. all OK!
  • wrongEnsemblIDForHumanSpecies: .x we found 1 problem(s):
    • Ensembl identifiers for wrong species for a human pathway: 1
  • wrongEnsemblIDForMouseSpecies: .. all OK!
  • wrongEnsemblIDForRatSpecies: .. all 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: .. all OK!
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 2
  • possibleTranslocations: .. all OK!
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all 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 10 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• UnicodeTests: all 2 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 21
• Number of tests: 125
• Number of assertions: 251
• Number of fails: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 17

• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/e7442 (AGY)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/b62e1 (CALY-002)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/a71ad (GSK3915393)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/c20b6 (HLA-DQA1)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/e18ed (HLA-DQA1)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/bdfd3 (HLA-DQB1)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/dac01 (HLA-DQB1)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/a4ed0 (Inflammation)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/f36f8 (KAN-101)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/b7803 (Loss of tolerance)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/a7454 (PRV-015)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/bfc82 (PTG-100)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/c3669 (Pyrimidine synthesis)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/ac239 (TAK-062)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/f8f55 (TAK-101)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/c17b2 (Tolerase G)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/ef393 (ZED1227)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 2

• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/a4ed0 (Inflammation)
• http://classic.wikipathways.org/instance/WP5562_r139728 http://rdf.wikipathways.org/Pathway/WP5562_r139728/DataNode/b7803 (Loss of tolerance)

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

EnsemblTests.wrongEnsemblIDForHumanSpecies

Ensembl identifiers for wrong species for a human pathway: 1

http://classic.wikipathways.org/instance/WP5562_r139728 -> TGM2, TGM2

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/WP5562_r139728 TRA with datasource Entrez Gene

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

Interactions with unconnected points

Interactions with unconnected points: 2

• http://classic.wikipathways.org/instance/WP5562_r139728

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