imd-pathway-curation

WikiPathways WP4545

• WikiPathways: WP4545
• Scholia: WP4545
• WPRDF file: wp/Human/WP4545.ttl
• GPMLRDF file: wp/gpml/Human/WP4545.ttl
• SBML file: sbml/WP4545.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: 3
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .x we found 1 problem(s):
    • Unexpected data source for catalysts: 14
  • 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: 1
  • possibleTranslocations: .. all OK!
  • 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
  • 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: 1
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 22
• Number of tests: 110
• Number of assertions: 220
• Number of fails: 4

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 3

https://identifiers.org/wikipathways/WP4545 has an metabolite not linked to an interaction: Chenodeoxycholic acid
https://identifiers.org/wikipathways/WP4545 has an metabolite not linked to an interaction: 7-Dehydrocholesterol
https://identifiers.org/wikipathways/WP4545 has an metabolite not linked to an interaction: 3β-Hydroxy-7-oxochol-5-en- 24-oic acid

IEMPathwayTests.catalystsWithCommonDataSource

Unexpected data source for catalysts: 14

https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC
https://identifiers.org/wikipathways/WP4545 HGNC

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 1

http://www.wikipathways.org/instance/WP4545_r123863 "CD4+ Th17 cells" with graphId c67d5

WikidataTests.hmdbWithoutMapping

InChIKey identifiers without Wikidata mappings: 1

DUYGXKURNABVMD-KOGONGFSSA-N	7α,25-Dihydroxy-3-oxocholest -5-en-26-oic acid