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: all 5 tests 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: 4

Fails

CovidDiseaseMapsTests.interactionsWithoutReferences

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

IEMPathwayTests.allMetabolitesInteract

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

InteractionTests.interactionsWithLabels

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

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