wikipathways-collection

WikiPathways WP3998

• WikiPathways: WP3998 (classic)
• Species: Homo sapiens
• Scholia: WP3998

  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: 10
  • 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!
  • 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: 3
• 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: 13
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 2
  • 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: 10

• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/e7315 (Exon I)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/c41f7 (G2/M arrest)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/ab293 (Gamma-tubulin ring complex)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/fa659 (II)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/c7b99 (III)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/d1d5f (IV)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/f1eb1 (Metabolite)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/e7ff2 (VI)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/a0a43 (Va)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/DataNode/a5c7a (Vb)

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: 3

http://classic.wikipathways.org/instance/WP3998_r134606 IPW with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP3998_r134606 SNORD116@ with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP3998_r134606 SNORD115@ with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 13

• http://classic.wikipathways.org/instance/WP3998_r134606 “Transcription of INK4/ARF locus” with graphId a5914
• http://classic.wikipathways.org/instance/WP3998_r134606 “Formation of centrosomal microtubule organising centre” with graphId d326a
• http://classic.wikipathways.org/instance/WP3998_r134606 “Dynein microtubule based molecular motor” with graphId b6905
• http://classic.wikipathways.org/instance/WP3998_r134606 “Adenosine-to-inosine RNA-editing” with graphId a75fd
• http://classic.wikipathways.org/instance/WP3998_r134606 “Neurite outgrowth” with graphId df708
• http://classic.wikipathways.org/instance/WP3998_r134606 “unknown function” with graphId b9d10
• http://classic.wikipathways.org/instance/WP3998_r134606 “Neurite/axonal outgrowth” with graphId dcc7e
• http://classic.wikipathways.org/instance/WP3998_r134606 “Molecular motor kinesin” with graphId ca959
• http://classic.wikipathways.org/instance/WP3998_r134606 “Axonal transport” with graphId b930a
• http://classic.wikipathways.org/instance/WP3998_r134606 “Stem cell differentiation” with graphId a4cd6
• http://classic.wikipathways.org/instance/WP3998_r134606 “unknown function” with graphId deea3
• http://classic.wikipathways.org/instance/WP3998_r134606 “Alternate splicing” with graphId b38b3
• http://classic.wikipathways.org/instance/WP3998_r134606 “Melanocytes” with graphId e6301

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/WP/Interaction/db738 “MAGEL2” (https://identifiers.org/ensembl/ENSG00000254585) and MAGEL2” (https://identifiers.org/ensembl/ENSG00000254585)
• http://classic.wikipathways.org/instance/WP3998_r134606 http://rdf.wikipathways.org/Pathway/WP3998_r134606/WP/Interaction/c4bc2 “NDN” (https://identifiers.org/ensembl/ENSG00000182636) and NDN” (https://identifiers.org/ensembl/ENSG00000182636)

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