sr24-curation

WikiPathways WP4018

• WikiPathways: WP4018 (classic)
• Species: Homo sapiens
• Scholia: WP4018

  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: 8
  • missingHGNC: .. all OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 8
  • 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: all 6 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: 1
  • 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: 3

Fails

Interactions without references

Interactions without literature references: 8

• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/ComplexBinding/c476b
• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/ComplexBinding/efdba
• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/WP/Interaction/ida67f7091
• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/ComplexBinding/c3f28
• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/ComplexBinding/b7dfd
• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/WP/Interaction/idf75c1c60
• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/WP/Interaction/id9cc40d42
• http://classic.wikipathways.org/instance/WP4018_r135127 -> http://rdf.wikipathways.org/Pathway/WP4018_r135127/WP/Interaction/ide308fea3

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

Data nodes without an identifier

The following DataNodes have no identifier: 8

• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/dc837 (AMPK)
• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/e2cf4 (Cell proliferation)
• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/ca20e (H2)
• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/fc670 (H2)
• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/ab0a6 (H3)
• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/e2943 (H3)
• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/ce0d9 (PI3K)
• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/DataNode/e9ef2 (RTK)

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

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP4018_r135127 http://rdf.wikipathways.org/Pathway/WP4018_r135127/WP/Interaction/idf75c1c60 “HIF1B” (https://identifiers.org/ensembl/ENSG00000143437) and HIF1B” (https://identifiers.org/ensembl/ENSG00000143437)

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