wikipathways-collection

WikiPathways WP2624

• WikiPathways: WP2624 (classic)
• Species: Arabidopsis thaliana

  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: 3
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 tests OK!
• 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: 117
• Number of assertions: 235
• Number of fails: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 3

• http://classic.wikipathways.org/instance/WP2624_r123106 http://rdf.wikipathways.org/Pathway/WP2624_r123106/DataNode/d2948 (Glutamate Biosynthesis)
• http://classic.wikipathways.org/instance/WP2624_r123106 http://rdf.wikipathways.org/Pathway/WP2624_r123106/DataNode/f8a83 (H2O)
• http://classic.wikipathways.org/instance/WP2624_r123106 http://rdf.wikipathways.org/Pathway/WP2624_r123106/DataNode/b1650 (Pi)

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

Possible MIM translocation

Interactions between identical nodes: 2

http://classic.wikipathways.org/instance/WP2624_r123106 http://rdf.wikipathways.org/Pathway/WP2624_r123106/WP/Interaction/id3e0cb2a8 "isocitrate" (https://identifiers.org/kegg.compound/C00311) and 
isocitrate" (https://identifiers.org/kegg.compound/C00311)
http://classic.wikipathways.org/instance/WP2624_r123106 http://rdf.wikipathways.org/Pathway/WP2624_r123106/WP/Interaction/id98e31c38 "2-oxoglutarate" (https://identifiers.org/kegg.compound/C00026) and 
2-oxoglutarate" (https://identifiers.org/kegg.compound/C00026)

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/WP2624_r123106 ‘TCA cycle (Krebs cycle)’ in Arabidopsis thaliana has zero references;

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