wikipathways-collection

WikiPathways WP2212

• WikiPathways: WP2212 (classic)
• Species: Oryza sativa

  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: 4
  • 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: 4

• http://classic.wikipathways.org/instance/WP2212_r123064 http://rdf.wikipathways.org/Pathway/WP2212_r123064/DataNode/a87f7 (phytyl-PP biosynthesis)
• http://classic.wikipathways.org/instance/WP2212_r123064 http://rdf.wikipathways.org/Pathway/WP2212_r123064/DataNode/f70cf (polyisoprenoid biosynthesis)
• http://classic.wikipathways.org/instance/WP2212_r123064 http://rdf.wikipathways.org/Pathway/WP2212_r123064/DataNode/ef2bd (protein disulfide)
• http://classic.wikipathways.org/instance/WP2212_r123064 http://rdf.wikipathways.org/Pathway/WP2212_r123064/DataNode/e3766 (protein dithiol)

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

Possible MIM translocation

Interactions between identical nodes: 2

http://classic.wikipathways.org/instance/WP2212_r123064 http://rdf.wikipathways.org/Pathway/WP2212_r123064/WP/Interaction/idaf0dfa46 "Δ3-isopentenyl-PP" (https://identifiers.org/kegg.compound/C00129) and 
dimethylallyl-PP" (https://identifiers.org/cas/358-71-4)
http://classic.wikipathways.org/instance/WP2212_r123064 http://rdf.wikipathways.org/Pathway/WP2212_r123064/WP/Interaction/idd6efa0e8 "dimethylallyl-PP" (https://identifiers.org/cas/358-71-4) and 
Δ3-isopentenyl-PP" (https://identifiers.org/kegg.compound/C00129)

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/WP2212_r123064 ‘Methylerythritol phosphate pathway’ in Oryza sativa has zero references;

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