imd-pathway-curation

WikiPathways WP5166

• WikiPathways: WP5166
• Scholia: WP5166
• WPRDF file: wp/Human/WP5166.ttl
• GPMLRDF file: wp/gpml/Human/WP5166.ttl
• SBML file: sbml/WP5166.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: 1
  • 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: 8
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 9
  • 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: 1

https://identifiers.org/wikipathways/WP5166 has an metabolite not linked to an interaction: Calcium

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 8

http://www.wikipathways.org/instance/WP5166_r122169 "Kidney" with graphId ea841
http://www.wikipathways.org/instance/WP5166_r122169 "Blood" with graphId fa818
http://www.wikipathways.org/instance/WP5166_r122169 "Secondary hyperoxaluria" with graphId b7761
http://www.wikipathways.org/instance/WP5166_r122169 "Primary hyperoxaluria II" with graphId f625c
http://www.wikipathways.org/instance/WP5166_r122169 "Tissue deposition and CaOx kidney stones" with graphId f0675
http://www.wikipathways.org/instance/WP5166_r122169 "Primary hyperoxaluria II" with graphId eb383
http://www.wikipathways.org/instance/WP5166_r122169 "Primary hyperoxaluria III" with graphId b8675
http://www.wikipathways.org/instance/WP5166_r122169 "Primary hyperoxaluria I" with graphId b66bd

InteractionTests.possibleTranslocations

Interactions between identical nodes: 9

http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/b6598 "3-hydroxypyruvate" (https://identifiers.org/chebi/CHEBI:17180) and 
3-hydroxypyruvate" (https://identifiers.org/chebi/CHEBI:17180)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/ae961 "Hydroxyproline" (https://identifiers.org/chebi/CHEBI:18095) and 
Hydroxyproline" (https://identifiers.org/chebi/CHEBI:18095)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/e9259 "Glyoxylate" (https://identifiers.org/chebi/CHEBI:36655) and 
Glyoxylate" (https://identifiers.org/chebi/CHEBI:36655)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/fbc58 "Oxalate" (https://identifiers.org/chebi/CHEBI:30623) and 
Oxalate" (https://identifiers.org/chebi/CHEBI:30623)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/f8eb1 "Glycolate" (https://identifiers.org/chebi/CHEBI:29805) and 
Glycolate" (https://identifiers.org/chebi/CHEBI:29805)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/fbc9b "Glycolate" (https://identifiers.org/chebi/CHEBI:29805) and 
Glycolate" (https://identifiers.org/chebi/CHEBI:29805)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/e2679 "HOG" (https://identifiers.org/chebi/CHEBI:17742) and 
HOG" (https://identifiers.org/chebi/CHEBI:17742)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/fd795 "Oxalate" (https://identifiers.org/chebi/CHEBI:30623) and 
Oxalate" (https://identifiers.org/chebi/CHEBI:30623)
http://www.wikipathways.org/instance/WP5166_r122169 http://rdf.wikipathways.org/Pathway/WP5166_r122169/WP/Interaction/e8e75 "Glyoxylate" (https://identifiers.org/chebi/CHEBI:36655) and 
Glyoxylate" (https://identifiers.org/chebi/CHEBI:36655)

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