wikipathways-collection

WikiPathways WP5343

• WikiPathways: WP5343 (classic)
• Species: Homo sapiens
• Scholia: WP5343

  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: 6
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 3
  • 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: 14
• 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: 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 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: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 6

• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/f1785 (Absence of Dystrophin)
• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/dea40 (Inflammatory pathways )
• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/b08f7 (Mutation in DMD gene)
• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/e733c (Myopathy )
• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/e4953 (Pathway)
• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/bd126 (ROS production)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 3

• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/f1785 (Absence of Dystrophin)
• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/b08f7 (Mutation in DMD gene)
• http://classic.wikipathways.org/instance/WP5343_r126461 http://rdf.wikipathways.org/Pathway/WP5343_r126461/DataNode/bd126 (ROS production)

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: 14

http://classic.wikipathways.org/instance/WP5343_r126461 Phospholipase A2 with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Triadin with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Voltage gated  Ca2+ channel with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Troponin C with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 RyR 1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Dystroglycan 1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Dystrophin with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 SERCA 1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 alpha sarcoglycan with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Syntrophin beta-1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Dystrobrevin alpha with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Calpain 3 with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 CASQ 1 with datasource HGNC
http://classic.wikipathways.org/instance/WP5343_r126461 Sarcospan with datasource HGNC

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

Interactions with Labels

Interactions found that involve Labels: 2

• http://classic.wikipathways.org/instance/WP5343_r126461 “Alteration in Ca2+ handling” with graphId f0972
• http://classic.wikipathways.org/instance/WP5343_r126461 “Reduced force generation during muscle contraction” with graphId c0094

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