imd-pathway-curation

WikiPathways WP5190

• WikiPathways: WP5190
• Scholia: WP5190
• WPRDF file: wp/Human/WP5190.ttl
• GPMLRDF file: wp/gpml/Human/WP5190.ttl
• SBML file: sbml/WP5190.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: 4
  • 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: 6
  • 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 14 tests OK!
• OudatedDataSourcesTests: all 7 tests OK!
• PathwayTests: all 6 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 4 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 15 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 110
• Number of assertions: 220
• Number of fails: 3

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 4

https://identifiers.org/wikipathways/WP5190 has an metabolite not linked to an interaction: Glycine
https://identifiers.org/wikipathways/WP5190 has an metabolite not linked to an interaction: S-Adenosylhomocysteine
https://identifiers.org/wikipathways/WP5190 has an metabolite not linked to an interaction: Arginine
https://identifiers.org/wikipathways/WP5190 has an metabolite not linked to an interaction: S-adenosylmethionine

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 6

http://www.wikipathways.org/instance/WP5190_r122630 "Fanconi 
renotubular 
syndrome 1" with graphId b63a7
http://www.wikipathways.org/instance/WP5190_r122630 "Guanidinoacetate 
methyltransferase 
deficiency" with graphId cdd76
http://www.wikipathways.org/instance/WP5190_r122630 "Arginine/glycine
amidinotransferase
deficiency" with graphId b885b
http://www.wikipathways.org/instance/WP5190_r122630 "Ornithine 
aminotransferase 
deficiency" with graphId b9a19
http://www.wikipathways.org/instance/WP5190_r122630 "Creatine
transporter
deficiency" with graphId ed29a
http://www.wikipathways.org/instance/WP5190_r122630 "Gyrate atrophy 
of choroid 
and retina" with graphId ebf2e

InteractionTests.possibleTranslocations

Interactions between identical nodes: 2

http://www.wikipathways.org/instance/WP5190_r122630 http://rdf.wikipathways.org/Pathway/WP5190_r122630/WP/Interaction/id56c64cc3 "Creatinine" (https://identifiers.org/chebi/CHEBI:16737) and 
Creatinine" (https://identifiers.org/chebi/CHEBI:16737)
http://www.wikipathways.org/instance/WP5190_r122630 http://rdf.wikipathways.org/Pathway/WP5190_r122630/WP/Interaction/id1dd22822 "Creatine" (https://identifiers.org/chebi/CHEBI:16919) and 
Creatine" (https://identifiers.org/chebi/CHEBI:16919)

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