sr24-curation

WikiPathways WP4341

• WikiPathways: WP4341 (classic)
• Species: Homo sapiens
• Scholia: WP4341

  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: 26
  • missingHGNC: .. all OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 1
  • 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: 5
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 11
  • 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: 5

Fails

Interactions without references

Interactions without literature references: 26

• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/idad76ceb5
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/b3929
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/db1b4
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/ida0fc622e
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id14d5294b
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/ae4ff
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id9f6127db
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/idbd396ec
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/e99cc
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/bf5d4
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id2d65842d
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/cbcc1
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/d917a
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id4aee4cd7
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/ca0e9
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/d40be
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/b3649
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id8018d559
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/fb2a2
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/e0232
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/ide241ec12
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id8155bdbf
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id1a217e9d
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/df3b9
• http://classic.wikipathways.org/instance/WP4341_r134957 -> http://rdf.wikipathways.org/Pathway/WP4341_r134957/ComplexBinding/d3f28

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

Data nodes without an identifier

The following DataNodes have no identifier: 1

• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/DataNode/ce3fe (VSE)

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/WP4341 has an metabolite not linked to an interaction: PMA
• https://identifiers.org/wikipathways/WP4341 has an metabolite not linked to an interaction: DAG

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

Interactions with Labels

Interactions found that involve Labels: 5

• http://classic.wikipathways.org/instance/WP4341_r134957 “Stress” with graphId a70e0
• http://classic.wikipathways.org/instance/WP4341_r134957 “TLR2/4/8 ligands” with graphId b4453
• http://classic.wikipathways.org/instance/WP4341_r134957 “Cell death” with graphId eebf1
• http://classic.wikipathways.org/instance/WP4341_r134957 “?” with graphId b53b9
• http://classic.wikipathways.org/instance/WP4341_r134957 “VDR transcription” with graphId da643

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

Possible MIM translocation

Interactions between identical nodes: 11

• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRn” (https://identifiers.org/ensembl/ENSG00000111424) and VDRn” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRn” (https://identifiers.org/ensembl/ENSG00000111424) and VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRn” (https://identifiers.org/ensembl/ENSG00000111424) and VDR” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424) and VDRn” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424) and VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424) and VDR” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDR” (https://identifiers.org/ensembl/ENSG00000111424) and VDRn” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDR” (https://identifiers.org/ensembl/ENSG00000111424) and VDRm/n” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/c5e4d “VDR” (https://identifiers.org/ensembl/ENSG00000111424) and VDR” (https://identifiers.org/ensembl/ENSG00000111424)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/ide241ec12 “25D” (https://identifiers.org/hmdb/HMDB0003550) and 25D” (https://identifiers.org/hmdb/HMDB0003550)
• http://classic.wikipathways.org/instance/WP4341_r134957 http://rdf.wikipathways.org/Pathway/WP4341_r134957/WP/Interaction/id8155bdbf “CYP27B1” (https://identifiers.org/ensembl/ENSG00000111012) and CYP27B1” (https://identifiers.org/ensembl/ENSG00000111012)

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