sr24-curation

WikiPathways WP5176

• WikiPathways: WP5176 (classic)
• Species: Homo sapiens
• Scholia: WP5176

  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: 36
  • 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 5 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: 22
  • 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: 23
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 10
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 18
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 16 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• UnicodeTests: all 2 tests OK!
• WikidataTests: all 15 tests OK!

Summary

• Number of test classes: 24
• Number of tests: 149
• Number of assertions: 299
• Number of fails: 6

Fails

Interactions without references

Interactions without literature references: 36

• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idd35e240a
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/f79f6
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id1d5900d8
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/iddca38220
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idbbfdd88e
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id96a4f2d4
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7bb1b1e
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id208b5bc7
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idb2b8e9c2
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id65daa818
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/fa787
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id57a6c794
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id614ebc
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idb319f660
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id2452e40d
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/iddd131e99
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/ida7fdfba6
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/c0013
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id9b1e8d5e
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id74ac6806
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/d2fc6
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc113f090
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idb48f7124
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/ide7aec33e
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc140a77b
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id16ef543
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idd570d3dd
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id7163f5cd
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id7dc4b6b3
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id5146a5f2
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/b1016
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/d6e0a
• http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf6fc40c0

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/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/DataNode/a89f4 (Bilirubin disposal)

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

All metabolites are involved in interactions

Found metabolites without interaction: 22

• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3α,7α,12α-trihydroxy-24-oxo-5β-cholestan-26-oyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: (25S)-3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 7alpha,26-dihydroxycholest-4-en-3-one
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestan-26-oyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: Taurine
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 5beta-cholestane-3alpha,7alpha,12alpha,26-tetrol
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 7-alpha-Hydroxycholesterol
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oic acid
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3alpha,7alpha-Dihydroxy-5beta-cholest-24-enoyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 27-Hydroxycholesterol
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3beta,7alpha-Dihydroxy-5-cholestenoate
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 5beta-Cholestane-3alpha,7alpha,27-triol
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: (25S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: cholyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: Chenodeoxycholoyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-al
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy -5beta-cholestan-26-oyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3alpha,7alpha-dihydroxy-5beta-cholestan-26-al
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholest-24-enoyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: (25R)-3alpha,7alpha,12alpha-Trihydroxy-5beta-cholestan-26-oyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3alpha,7alpha,24-trihydroxy -5beta-cholestan-26-oyl-CoA
• https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3beta-Hydroxy-5-cholestenoic acid

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

Interactions with Labels

Interactions found that involve Labels: 23

• http://classic.wikipathways.org/instance/WP5176_r128232 “Congenital bile acid synthesis defect 6” with graphId b5ee6
• http://classic.wikipathways.org/instance/WP5176_r128232 “Bile acid-CoA ligase deficiency” with graphId c0ad7
• http://classic.wikipathways.org/instance/WP5176_r128232 “D-bifunctional protein deficiency” with graphId aa859
• http://classic.wikipathways.org/instance/WP5176_r128232 “5β-Reductase deficiency” with graphId bbeac
• http://classic.wikipathways.org/instance/WP5176_r128232 “Bile acid amidation defect” with graphId b9802
• http://classic.wikipathways.org/instance/WP5176_r128232 “Bile acid-CoA ligase deficiency” with graphId d0e4e
• http://classic.wikipathways.org/instance/WP5176_r128232 “OATP1B3 disease” with graphId a0972
• http://classic.wikipathways.org/instance/WP5176_r128232 “Sterol 27-hydroxylase deficiency” with graphId dd5ab
• http://classic.wikipathways.org/instance/WP5176_r128232 “Spastic Paraplegia 5A” with graphId e61d9
• http://classic.wikipathways.org/instance/WP5176_r128232 “Sterol carrier protein 2 deficiency “ with graphId d3833
• http://classic.wikipathways.org/instance/WP5176_r128232 “Sterol 27-hydroxylase deficiency” with graphId a7126
• http://classic.wikipathways.org/instance/WP5176_r128232 “ABCC2 deficiency” with graphId cc569
• http://classic.wikipathways.org/instance/WP5176_r128232 “Congenital bile acid synthesis defect type 5” with graphId ab185
• http://classic.wikipathways.org/instance/WP5176_r128232 “Cholesterol 7α-hydroxylase deficiency” with graphId a293f
• http://classic.wikipathways.org/instance/WP5176_r128232 “ABCB4 deficiency” with graphId aee45
• http://classic.wikipathways.org/instance/WP5176_r128232 “5β-Reductase deficiency” with graphId c9359
• http://classic.wikipathways.org/instance/WP5176_r128232 “OATP1B1 disease” with graphId ce805
• http://classic.wikipathways.org/instance/WP5176_r128232 “AMACR deficiency” with graphId c5b2c
• http://classic.wikipathways.org/instance/WP5176_r128232 “Bile acid amidation defect” with graphId c5d24
• http://classic.wikipathways.org/instance/WP5176_r128232 “3β-Dehydrogenase deficiency” with graphId b0872
• http://classic.wikipathways.org/instance/WP5176_r128232 “3β-Dehydrogenase deficiency” with graphId bbe71
• http://classic.wikipathways.org/instance/WP5176_r128232 “ATP8B1 deficiency” with graphId d7f7d
• http://classic.wikipathways.org/instance/WP5176_r128232 “ABCB11 deficiency” with graphId ea3c9

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

Interactions with unconnected points

Interactions with unconnected points: 10

• http://classic.wikipathways.org/instance/WP5176_r128232

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

Possible MIM translocation

Interactions between identical nodes: 18

• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idbbfdd88e “Bile acid” (https://identifiers.org/chebi/CHEBI:36277) and Bile acid” (https://identifiers.org/chebi/CHEBI:36277)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/fa787 “Bilirubin glucuronide” (https://identifiers.org/chebi/CHEBI:16427) and Bilirubin glucuronide” (https://identifiers.org/chebi/CHEBI:16427)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id57a6c794 “phosphatidylcholines” (https://identifiers.org/chebi/CHEBI:49183) and phosphatidylcholines” (https://identifiers.org/chebi/CHEBI:49183)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f “taurocholate” (https://identifiers.org/chebi/CHEBI:36257) and taurocholate” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f “taurocholate” (https://identifiers.org/chebi/CHEBI:36257) and Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f “Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257) and taurocholate” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f “Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257) and Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/c0013 “glycocholate” (https://identifiers.org/chebi/CHEBI:29746) and glycocholate” (https://identifiers.org/chebi/CHEBI:29746)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e “taurocholate” (https://identifiers.org/chebi/CHEBI:36257) and taurocholate” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e “taurocholate” (https://identifiers.org/chebi/CHEBI:36257) and Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e “Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257) and taurocholate” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e “Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257) and Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada “taurocholate” (https://identifiers.org/chebi/CHEBI:36257) and taurocholate” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada “taurocholate” (https://identifiers.org/chebi/CHEBI:36257) and Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada “Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257) and taurocholate” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada “Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257) and Taurocholic acid” (https://identifiers.org/chebi/CHEBI:36257)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id5146a5f2 “Phosphatidylserine” (https://identifiers.org/chebi/CHEBI:18303) and Phosphatidylserine” (https://identifiers.org/chebi/CHEBI:18303)
• http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf6fc40c0 “glycocholate” (https://identifiers.org/chebi/CHEBI:29746) and glycocholate” (https://identifiers.org/chebi/CHEBI:29746)

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