wikipathways-collection

WikiPathways WP2207

• WikiPathways: WP2207 (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: 9
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 5 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!
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 16
  • 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
  • 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!
• UnicodeTests
  • water: .x we found 1 problem(s):
    • Metabolite can use H₂O instead of H2O: 1
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 21
• Number of tests: 122
• Number of assertions: 245
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 9

• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/b845d (Spermidine biosynthesis)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/e5fdd (Spermine biosynthesis)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/b1107 (Spontaneous)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/d74ad (Spontaneous)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/f3208 (Spontaneous)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/a7491 (oxidized electron acceptor)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/acea2 (pantothenate biosynthesis II)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/b2a30 (pantothenate biosynthesis III)
• http://classic.wikipathways.org/instance/WP2207_r117414 http://rdf.wikipathways.org/Pathway/WP2207_r117414/DataNode/ce6bd (reduced electron acceptor)

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

Interactions with unconnected points

Interactions with unconnected points: 16

• http://classic.wikipathways.org/instance/WP2207_r117414

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP2207_r117414 ‘Beta-alanine biosynthesis’ in Oryza sativa has zero references;

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

Water chemical formula can use Unicode

Metabolite can use H₂O instead of H2O: 1

* [http://classic.wikipathways.org/instance/WP2207_r117414](http://classic.wikipathways.org/instance/WP2207_r117414)

More details at https://www.wikipathways.org/WikiPathwaysCurator/UnicodeTests/water