imd-pathway-curation

WikiPathways WP4292

• WikiPathways: WP4292 (classic)
• Species: Homo sapiens
• Scholia: WP4292

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 15 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: .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 9 tests OK!
• PathwayTests: all 7 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 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: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 1
  • inchikeyWithoutMapping: .. all OK!
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 22
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 3

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 4

https://identifiers.org/wikipathways/WP4292 has an metabolite not linked to an interaction: Phosphate ion
https://identifiers.org/wikipathways/WP4292 has an metabolite not linked to an interaction: H2O
https://identifiers.org/wikipathways/WP4292 has an metabolite not linked to an interaction: ATP
https://identifiers.org/wikipathways/WP4292 has an metabolite not linked to an interaction: Diphosphate ion

IEMPathwayTests.omimIdentifiers

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

https://identifiers.org/wikipathways/WP4292 "MAT deficiency" has unexpected OMIM href: http://omim.org/entry/250850

ChEBI identifier without a match in Wikidata

ChEBI identifiers without Wikidata mappings: 1

https://identifiers.org/chebi/CHEBI:28115 (Methyl- cobalamin) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4292_r128219 ; 

More details at https://www.wikipathways.org/WikiPathwaysCurator/WikidataTests/chebiWithoutMapping