imd-pathway-curation

WikiPathways WP5176

• WikiPathways: WP5176
• Scholia: WP5176
• WPRDF file: wp/Human/WP5176.ttl
• GPMLRDF file: wp/gpml/Human/WP5176.ttl
• SBML file: sbml/WP5176.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 4 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 4 tests OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 3 tests OK!
• GeneralTests: all 13 tests OK!
• HMDBMetabolitesTests: all 1 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests
  • allMetabolitesInteract: .x we found 1 problem(s):
    • Found metabolites without interaction: 19
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .. all OK!
  • metabolicConversionIdentifiersCommon: .x we found 1 problem(s):
    • Unexpected data source for the metabolic conversion: 5
  • 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: 27
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 8
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 7 tests OK!
• PathwayTests: all 6 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests
  • nonNumericPubMedIDs: .. all OK!
  • zeroPubMedIDs: .. all OK!
  • atLeastOneReference: .x we found 1 problem(s):
    • Found 1 pathways with zero (PubMed) references
  • citesRetractedArticle: .. all OK!
• UniProtTests: all 5 tests OK!
• WikidataTests
  • keggWithoutMapping: .. all OK!
  • pubchemCIDWithoutMapping: .. all OK!
  • hmdbWithoutMapping: .x we found 1 problem(s):
    • HMDB identifiers without Wikidata mappings: 4
  • casWithoutMapping: .. all OK!
  • wikDataTypo: .. all OK!
  • duplicateWikidataMappings: .. all OK!
  • wikidataIdentifiersWrong: .. all OK!
  • chemspiderCIDWithoutMapping: .. all OK!
  • lipidMapsWithoutMapping: .. all OK!
  • kNApSAcKWithoutMapping: .. all OK!
  • replaceWikipedia: .. all OK!
  • chebiWithoutMapping_Reactome: .. all OK!
  • chebiWithoutMapping: .. all OK!
  • hmdbWithoutMapping: .. all OK!
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 22
• Number of tests: 110
• Number of assertions: 220
• Number of fails: 6

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 19

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: 3alpha,7alpha-Dihydroxy-5beta-cholest-24-enoyl-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: 3beta,7alpha-Dihydroxy-5-cholestenoate
https://identifiers.org/wikipathways/WP5176 has an metabolite not linked to an interaction: 3beta-Hydroxy-5-cholestenoic acid
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: (25S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-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: Chenodeoxycholoyl-CoA
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: 7alpha,26-dihydroxycholest-4-en-3-one
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: 7-alpha-Hydroxycholesterol
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-Dihydroxy-5beta-cholestanoyl-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: 27-Hydroxycholesterol
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: (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oyl-CoA

IEMPathwayTests.metabolicConversionIdentifiersCommon

Unexpected data source for the metabolic conversion: 5

https://identifiers.org/wikipathways/WP5176 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/idaba191b Reactome R-HSA-193401
https://identifiers.org/wikipathways/WP5176 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/id2452e40d Reactome R-HSA-192160
https://identifiers.org/wikipathways/WP5176 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/ida7fdfba6 Reactome R-HSA-193424
https://identifiers.org/wikipathways/WP5176 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/idd570d3dd Reactome R-HSA-192036
https://identifiers.org/wikipathways/WP5176 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/idb2b8e9c2 Reactome R-HSA-192033

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 27

http://www.wikipathways.org/instance/WP5176_r123799 "OATP1B1 disease" with graphId ce805
http://www.wikipathways.org/instance/WP5176_r123799 "Sterol carrier protein 2 deficiency " with graphId d3833
http://www.wikipathways.org/instance/WP5176_r123799 "D-bifunctional protein deficiency" with graphId aa859
http://www.wikipathways.org/instance/WP5176_r123799 "Congenital bile acid synthesis defect 6" with graphId b5ee6
http://www.wikipathways.org/instance/WP5176_r123799 "Sterol 27-hydroxylase deficiency" with graphId f7290
http://www.wikipathways.org/instance/WP5176_r123799 "ATP8B1 deficiency" with graphId d7f7d
http://www.wikipathways.org/instance/WP5176_r123799 "Cholesterol 7α-hydroxylase deficiency" with graphId a293f
http://www.wikipathways.org/instance/WP5176_r123799 "AMACR deficiency" with graphId c5b2c
http://www.wikipathways.org/instance/WP5176_r123799 "Bile acid-CoA ligase deficiency" with graphId c0ad7
http://www.wikipathways.org/instance/WP5176_r123799 "ABCC2 deficiency" with graphId cc569
http://www.wikipathways.org/instance/WP5176_r123799 "5β-Reductase deficiency" with graphId bbeac
http://www.wikipathways.org/instance/WP5176_r123799 "5β-Reductase deficiency" with graphId c9359
http://www.wikipathways.org/instance/WP5176_r123799 "5β-Reductase deficiency" with graphId ce962
http://www.wikipathways.org/instance/WP5176_r123799 "3β-Dehydrogenase deficiency" with graphId bbe71
http://www.wikipathways.org/instance/WP5176_r123799 "Bile acid amidation defect" with graphId b9802
http://www.wikipathways.org/instance/WP5176_r123799 "ABCB4 deficiency" with graphId aee45
http://www.wikipathways.org/instance/WP5176_r123799 "3β-Dehydrogenase deficiency" with graphId b0872
http://www.wikipathways.org/instance/WP5176_r123799 "OATP1B3 disease" with graphId a0972
http://www.wikipathways.org/instance/WP5176_r123799 "Sterol 27-hydroxylase deficiency" with graphId ea22b
http://www.wikipathways.org/instance/WP5176_r123799 "Sterol 27-hydroxylase deficiency" with graphId a7126
http://www.wikipathways.org/instance/WP5176_r123799 "D-bifunctional protein deficiency" with graphId bf07e
http://www.wikipathways.org/instance/WP5176_r123799 "Sterol 27-hydroxylase deficiency" with graphId dd5ab
http://www.wikipathways.org/instance/WP5176_r123799 "Spastic Paraplegia 5A" with graphId e61d9
http://www.wikipathways.org/instance/WP5176_r123799 "Bile acid amidation defect" with graphId c5d24
http://www.wikipathways.org/instance/WP5176_r123799 "D-bifunctional protein deficiency" with graphId e6218
http://www.wikipathways.org/instance/WP5176_r123799 "Sterol 27-hydroxylase deficiency" with graphId feb66
http://www.wikipathways.org/instance/WP5176_r123799 "ABCB11 deficiency" with graphId ea3c9

InteractionTests.possibleTranslocations

Interactions between identical nodes: 8

http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/idc7133ada "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and 
taurocholate" (https://identifiers.org/chebi/CHEBI:36257)
http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/idf6fc40c0 "glycocholate" (https://identifiers.org/chebi/CHEBI:29746) and 
glycocholate" (https://identifiers.org/chebi/CHEBI:29746)
http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/id5146a5f2 "Phosphatidylserine" (https://identifiers.org/chebi/CHEBI:18303) and 
Phosphatidylserine" (https://identifiers.org/chebi/CHEBI:18303)
http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/id8dde6d9e "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and 
taurocholate" (https://identifiers.org/chebi/CHEBI:36257)
http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/fa787 "Bilirubin glucuronide" (https://identifiers.org/chebi/CHEBI:16427) and 
Bilirubin glucuronide" (https://identifiers.org/chebi/CHEBI:16427)
http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/idbbfdd88e "Bile acid" (https://identifiers.org/chebi/CHEBI:36277) and 
Bile acid" (https://identifiers.org/chebi/CHEBI:36277)
http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/id57a6c794 "phosphatidylcholines" (https://identifiers.org/chebi/CHEBI:49183) and 
phosphatidylcholines" (https://identifiers.org/chebi/CHEBI:49183)
http://www.wikipathways.org/instance/WP5176_r123799 http://rdf.wikipathways.org/Pathway/WP5176_r123799/WP/Interaction/c0013 "glycocholate" (https://identifiers.org/chebi/CHEBI:29746) and 
glycocholate" (https://identifiers.org/chebi/CHEBI:29746)

More details at https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations

ReferencesTests.atLeastOneReference

Found 1 pathways with zero (PubMed) references

http://www.wikipathways.org/instance/WP5176_r123799 'Disorders of bile acid synthesis and biliary transport' in Homo sapiens has zero references; 

More details at https://wikipathways.github.io/WikiPathwaysCurator/ReferencesTests/atLeastOneReference

WikidataTests.hmdbWithoutMapping

HMDB identifiers without Wikidata mappings: 4

https://identifiers.org/hmdb/HMDB0012454 (3beta,7alpha-Dihydroxy-5-cholestenoate) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5176_r123799 ; 
https://identifiers.org/hmdb/HMDB0060138 (5beta-Cholestane-3alpha,7alpha,27-triol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5176_r123799 ; 
https://identifiers.org/hmdb/HMDB0060304 ((25R)-3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5176_r123799 ; 
https://identifiers.org/hmdb/HMDB0060306 ((25S)-3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5176_r123799 ;