sr24-curation

WikiPathways WP5173

• WikiPathways: WP5173
• Scholia: WP5173
• WPRDF file: wp/Human/WP5173.ttl
• GPMLRDF file: wp/gpml/Human/WP5173.ttl
• SBML file: sbml/WP5173.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 4 tests OK!
• ChemSpiderTests: all 2 tests OK!
• CovidDiseaseMapsTests
  • interactionsWithoutReferences: .x we found 1 problem(s):
    • Interactions without literature references: 12
  • missingHGNC: .. all OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 5 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 13 tests OK!
• HMDBMetabolitesTests: all 2 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests
  • allMetabolitesInteract: .x we found 1 problem(s):
    • Found metabolites without interaction: 3
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .. all OK!
  • metabolicConversionIdentifiersCommon: .x we found 1 problem(s):
    • Unexpected data source for the metabolic conversion: 1
  • 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: 13
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 2
  • 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 7 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: 120
• Number of assertions: 242
• Number of fails: 5

Fails

CovidDiseaseMapsTests.interactionsWithoutReferences

Interactions without literature references: 12

http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/d5868
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/ac8fc
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/e0131
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a84b2_1
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/e5a6a
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a4ae6
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a84b2_2
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/fe651
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f16aa
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f0f1e
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f075d
http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/c030e

More details at https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 3

https://identifiers.org/wikipathways/WP5173 has an metabolite not linked to an interaction: UDP-galactose
https://identifiers.org/wikipathways/WP5173 has an metabolite not linked to an interaction: Glycogen
https://identifiers.org/wikipathways/WP5173 has an metabolite not linked to an interaction: Glucose-6-phosphate

IEMPathwayTests.metabolicConversionIdentifiersCommon

Unexpected data source for the metabolic conversion: 1

https://identifiers.org/wikipathways/WP5173 http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/e0131 Wikidata Q22281942

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 13

http://classic.wikipathways.org/instance/WP5173_r134383 "Polyglucosan body myopathy 2" with graphId b5440
http://classic.wikipathways.org/instance/WP5173_r134383 "Congenital disorder of glycosylation, 
type It" with graphId de139
http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage disease 0, muscle" with graphId fbaa3
http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage 
disease VI" with graphId ae5e6
http://classic.wikipathways.org/instance/WP5173_r134383 "Galactokinase deficiency" with graphId d2625
http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage disease XV" with graphId abc2c
http://classic.wikipathways.org/instance/WP5173_r134383 "Polyglucosan body neuropathy" with graphId eba21
http://classic.wikipathways.org/instance/WP5173_r134383 "Uridine diphosphate 
galactose-4-epimerase 
deficiency" with graphId c9ff6
http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage disease 0, liver" with graphId f124e
http://classic.wikipathways.org/instance/WP5173_r134383 "Galactosaemia" with graphId a8706
http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage 
disease IV" with graphId aaa50
http://classic.wikipathways.org/instance/WP5173_r134383 "Fanconi-Bickel syndrome" with graphId fd3d0
http://classic.wikipathways.org/instance/WP5173_r134383 "Intestinal glucose-galactose 
malabsorption" with graphId d61c1

InteractionTests.possibleTranslocations

Interactions between identical nodes: 2

http://classic.wikipathways.org/instance/WP5173_r134383 http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a4ae6 "Galactose" (https://identifiers.org/chebi/CHEBI:28260) and 
Galactose" (https://identifiers.org/chebi/CHEBI:28260)
http://classic.wikipathways.org/instance/WP5173_r134383 http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f075d "Galactose" (https://identifiers.org/chebi/CHEBI:28260) and 
Galactose" (https://identifiers.org/chebi/CHEBI:28260)

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