imd-pathway-curation

WikiPathways WP4288

• WikiPathways: WP4288
• Scholia: WP4288
• WPRDF file: wp/Human/WP4288.ttl
• GPMLRDF file: wp/gpml/Human/WP4288.ttl
• SBML file: sbml/WP4288.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: 2
  • 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
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 2
  • 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: 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: 2

https://identifiers.org/wikipathways/WP4288 has an metabolite not linked to an interaction: [Myelin basic protein]-N-methylarginine
https://identifiers.org/wikipathways/WP4288 has an metabolite not linked to an interaction: [Myelin basic protein]-arginine

IEMPathwayTests.omimIdentifiers

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

https://identifiers.org/wikipathways/WP4288 "MTHFR deficiency" has unexpected OMIM href: https://www.omim.org/236250

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 2

http://www.wikipathways.org/instance/WP4288_r124269 "MTHFR deficiency" with graphId e42a5
http://www.wikipathways.org/instance/WP4288_r124269 "Homocystein levels are
elevated in MTHFR deficiency." with graphId c37fc