imd-pathway-curation

WikiPathways WP4224

• WikiPathways: WP4224
• Scholia: WP4224
• WPRDF file: wp/Human/WP4224.ttl
• GPMLRDF file: wp/gpml/Human/WP4224.ttl
• SBML file: sbml/WP4224.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: 6
  • 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/”: 1
• InteractionTests: all 8 tests 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
  • keggWithoutMapping: .. all OK!
  • pubchemCIDWithoutMapping: .. all OK!
  • hmdbWithoutMapping: .. all OK!
  • 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: .x we found 1 problem(s):
    • InChIKey identifiers without Wikidata mappings: 2
  • retiredIdentifiers: .. all 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: 6

https://identifiers.org/wikipathways/WP4224 has an metabolite not linked to an interaction: P(i)
https://identifiers.org/wikipathways/WP4224 has an metabolite not linked to an interaction: ADP
https://identifiers.org/wikipathways/WP4224 has an metabolite not linked to an interaction: H2O
https://identifiers.org/wikipathways/WP4224 has an metabolite not linked to an interaction: Asp
https://identifiers.org/wikipathways/WP4224 has an metabolite not linked to an interaction: Gln
https://identifiers.org/wikipathways/WP4224 has an metabolite not linked to an interaction: HCO3 -

IEMPathwayTests.omimIdentifiers

OMIM links should start with “https://omim.org/entry/”: 1

https://identifiers.org/wikipathways/WP4224 "Xanthinuria, Type II" has unexpected OMIM href: http://omim.org/entry/603592

WikidataTests.hmdbWithoutMapping

InChIKey identifiers without Wikidata mappings: 2

ORGWVAZZJZJVPV-UHFFFAOYSA-N	6-oxopyrimidine (M1)
RBAHIIPVJVMACF-UHFFFAOYSA-N	auglurant