wikipathways-collection

WikiPathways WP5060

• WikiPathways: WP5060 (classic)
• Species: Escherichia coli

  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: 2
  • 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: 27
• 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!
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP5060_r123880 http://rdf.wikipathways.org/Pathway/WP5060_r123880/DataNode/e8315 (TonB-dependent uptake?)
• http://classic.wikipathways.org/instance/WP5060_r123880 http://rdf.wikipathways.org/Pathway/WP5060_r123880/DataNode/a45c7 (anhMurNAc-L-Ala-gamma-D-Glu-meso-DAP-D-Ala)

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: 27

http://classic.wikipathways.org/instance/WP5060_r123880 murE with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murB with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murC with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 nagK with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 ftsW with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murQ with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 ampG with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murA with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 mpl with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 nagA with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 ddlB with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murI with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 nagZ with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 anmK with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murD with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murJ with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murF with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 mraY with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 mtgA with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 glmM with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 glmU with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 nagB with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 dadX with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murP with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 alr with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 murG with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5060_r123880 glmS with datasource UniProtKB

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

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP5060_r123880 http://rdf.wikipathways.org/Pathway/WP5060_r123880/WP/Interaction/b5af5 “GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-meso-DAP-D-Ala” (https://identifiers.org/pubchem.compound/163626) and GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-meso-DAP-D-Ala” (https://identifiers.org/pubchem.compound/163626)

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