imd-pathway-curation

WikiPathways WP4595

• WikiPathways: WP4595
• Scholia: WP4595
• WPRDF file: wp/Human/WP4595.ttl
• GPMLRDF file: wp/gpml/Human/WP4595.ttl
• SBML file: sbml/WP4595.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: .. all OK!
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .. all OK!
  • metabolicConversionIdentifiersCommon: .. all OK!
  • diseasesHaveIdentifiers: .. all OK!
  • omimIdentifiers: .x we found 1 problem(s):
    • OMIM links should start with “https://omim.org/entry/”: 10
• 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: 3
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • 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.omimIdentifiers

OMIM links should start with “https://omim.org/entry/”: 10

https://identifiers.org/wikipathways/WP4595 "N-acetylglutamate  synthase deficiency" has unexpected OMIM href: https://omim.org/237310
https://identifiers.org/wikipathways/WP4595 "Ornithine  transcarbamylase  deficiency" has unexpected OMIM href: https://omim.org/311250
https://identifiers.org/wikipathways/WP4595 "Citrullinemia  type I " has unexpected OMIM href: https://omim.org/215700
https://identifiers.org/wikipathways/WP4595 "Carbamoyl- phosphate  synthetase I  deficiency" has unexpected OMIM href: https://omim.org/237300
https://identifiers.org/wikipathways/WP4595 "Glutamine  synthetase  deficiency" has unexpected OMIM href: https://omim.org/610015
https://identifiers.org/wikipathways/WP4595 "Citrullinemia Type II, Adult-onset" has unexpected OMIM href: https://omim.org/603471
https://identifiers.org/wikipathways/WP4595 "Citrullinemia Type II, Neonatal-onset" has unexpected OMIM href: https://omim.org/605814
https://identifiers.org/wikipathways/WP4595 "Arginino- succinic  aciduria " has unexpected OMIM href: https://omim.org/207900
https://identifiers.org/wikipathways/WP4595 "Arginase  deficiency" has unexpected OMIM href: https://omim.org/207800
https://identifiers.org/wikipathways/WP4595 "Pyrroline- 5-carboxylate  synthase  deficiency" has unexpected OMIM href: https://omim.org/219150

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 3

http://www.wikipathways.org/instance/WP4595_r123765 "Portal Blood" with graphId f26bb
http://www.wikipathways.org/instance/WP4595_r123765 "Urine" with graphId c7af0
http://www.wikipathways.org/instance/WP4595_r123765 "Suprahepatic Blood" with graphId b60fd

InteractionTests.possibleTranslocations

Interactions between identical nodes: 1

http://www.wikipathways.org/instance/WP4595_r123765 http://rdf.wikipathways.org/Pathway/WP4595_r123765/WP/Interaction/idf805350e "Malate" (https://identifiers.org/chebi/CHEBI:15589) and 
Malate" (https://identifiers.org/chebi/CHEBI:15589)

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