wikipathways-collection

WikiPathways WP2901

• WikiPathways: WP2901 (classic)
• Species: Bos taurus

  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: 8
  • 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: 4
• 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: 1
  • 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 8 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: 120
• Number of assertions: 241
• Number of fails: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 8

• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/ca1e3 (Calcium signaling pathway)
• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/bda5e (Cytokine-cytokine receptor interaction pathway)
• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/b7986 (DNA)
• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/c6769 (DNA)
• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/cd4a6 (DNA)
• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/d85e3 (MEKK)
• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/c4be3 (Neuroactive ligand-receptor interactionPathway)
• http://classic.wikipathways.org/instance/WP2901_r123067 http://rdf.wikipathways.org/Pathway/WP2901_r123067/DataNode/abbc1 (PKC)

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: 4

http://classic.wikipathways.org/instance/WP2901_r123067 LH-β with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2901_r123067 GNRH2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2901_r123067 PLCB3 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2901_r123067 CALML6 with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP2901_r123067 “Gonadothropins gene expression & Secration” with graphId c13d8

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