wikipathways-collection

WikiPathways WP347

• WikiPathways: WP347 (classic)
• Species: Rattus norvegicus

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests 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: 9
• 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: 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
  • nonNumericPubMedIDs: .. all OK!
  • unexpectedPubMedIdentifier: .. all OK!
  • zeroPubMedIDs: .. all OK!
  • atLeastOneReference: .x we found 1 problem(s):
    • Found 1 pathways with zero (PubMed) references
  • citesRetractedArticle: .. all OK!
  • outdatedPubMedIdentifiers: .. all 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

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: 9

http://classic.wikipathways.org/instance/WP347_r124581 Idh3g with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Pdha2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Cs with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Idh2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Sdhd with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Dlat with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Idh3a with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Aco2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP347_r124581 Pdhx with datasource Entrez Gene

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP347_r124581 http://rdf.wikipathways.org/Pathway/WP347_r124581/WP/Interaction/b9834_1 “Malate” (https://identifiers.org/chebi/CHEBI:30797) and Malate” (https://identifiers.org/chebi/CHEBI:30797)
• http://classic.wikipathways.org/instance/WP347_r124581 http://rdf.wikipathways.org/Pathway/WP347_r124581/WP/Interaction/b9834_2 “Malate” (https://identifiers.org/chebi/CHEBI:30797) and Malate” (https://identifiers.org/chebi/CHEBI:30797)

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP347_r124581 ‘TCA cycle’ in Rattus norvegicus has zero references;

More details at https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference