sr24-curation

WikiPathways WP4396

• WikiPathways: WP4396 (classic)
• Species: Homo sapiens
• Scholia: WP4396

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• CovidDiseaseMapsTests
  • interactionsWithoutReferences: .x we found 1 problem(s):
    • Interactions without literature references: 44
  • missingHGNC: .. all OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 5
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 5 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 2 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests
  • allMetabolitesInteract: .x we found 1 problem(s):
    • Found metabolites without interaction: 2
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .. all OK!
  • metabolicConversionIdentifiersCommon: .. all OK!
  • diseasesHaveIdentifiers: .. all OK!
  • omimIdentifiers: .. all OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 6
  • 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 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 15 tests OK!

Summary

• Number of test classes: 23
• Number of tests: 140
• Number of assertions: 281
• Number of fails: 4

Fails

Interactions without references

Interactions without literature references: 44

• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idd36a3184
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/eddef
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id1d92c355
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/e4b4f
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idf4012931
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id30d6884d
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id451103b0
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/c1abd
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idbe4e36d1
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id401f274b
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/f19c9
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/be0f1
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idc3e89f30
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id1d3a8068
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id4acdf96d
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id571f48f2
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idf6ce2762
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/b0bf9
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idd68bf87b
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idb3cd5f1f
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id1cf3ff7f
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/dfd59
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id830edab0
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id7d8f7441
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/ida5ab6872
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id32579e10
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id7e59fd56
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id3986654b
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/e179a
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/ComplexBinding/e4d95
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/ida9fec7d8
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id66fa8f78
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id45b2f622
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idf20847ec
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id53d756bb
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id38b689df
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idce61d08c
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/idbdba71ff
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id4e2d468d
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id4fbae4af
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id7b2dfba3
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id73187b8
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id5cf8731b
• http://classic.wikipathways.org/instance/WP4396_r135137 -> http://rdf.wikipathways.org/Pathway/WP4396_r135137/WP/Interaction/id7a3ac1ff

More details at https://www.wikipathways.org/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences

Data nodes without an identifier

The following DataNodes have no identifier: 5

• http://classic.wikipathways.org/instance/WP4396_r135137 http://rdf.wikipathways.org/Pathway/WP4396_r135137/DataNode/d6e96 (CxI)
• http://classic.wikipathways.org/instance/WP4396_r135137 http://rdf.wikipathways.org/Pathway/WP4396_r135137/DataNode/f0d67 (CxII)
• http://classic.wikipathways.org/instance/WP4396_r135137 http://rdf.wikipathways.org/Pathway/WP4396_r135137/DataNode/d4e51 (CxIII)
• http://classic.wikipathways.org/instance/WP4396_r135137 http://rdf.wikipathways.org/Pathway/WP4396_r135137/DataNode/adc10 (CxIV)
• http://classic.wikipathways.org/instance/WP4396_r135137 http://rdf.wikipathways.org/Pathway/WP4396_r135137/DataNode/cd4b7 (Lipogenic enzymes)

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

All metabolites are involved in interactions

Found metabolites without interaction: 2

• https://identifiers.org/wikipathways/WP4396 has an metabolite not linked to an interaction: D-glucose
• https://identifiers.org/wikipathways/WP4396 has an metabolite not linked to an interaction: Fatty acids

More details at https://www.wikipathways.org/WikiPathwaysCurator/IEMPathwayTests/allMetabolitesInteract

Interactions with Labels

Interactions found that involve Labels: 6

• http://classic.wikipathways.org/instance/WP4396_r135137 “Fatty acid oxidation” with graphId e6f89
• http://classic.wikipathways.org/instance/WP4396_r135137 “Development of NAFLD” with graphId dc678
• http://classic.wikipathways.org/instance/WP4396_r135137 “NASH Fibrogenesis” with graphId ef1c9
• http://classic.wikipathways.org/instance/WP4396_r135137 “Hepatocyte injury” with graphId a206d
• http://classic.wikipathways.org/instance/WP4396_r135137 “Glucose uptake” with graphId c79ea
• http://classic.wikipathways.org/instance/WP4396_r135137 “Insulin resistance” with graphId f75a6

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