lipidmaps-wp-curation

WikiPathways WP1531

• WikiPathways: WP1531 (classic)
• Species: Homo sapiens
• Scholia: WP1531
• WPRDF file: wp/Human/WP1531.ttl
• GPMLRDF file: wp/gpml/Human/WP1531.ttl
• SBML file: sbml/WP1531.sbml (SVG) (conversion notes)

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 5 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 1 tests OK!
• HMDBSecMetabolitesTests: all 3 tests 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: 2
  • UnconnectedPoints: .. all OK!
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests
  • retiredIdentifiers: .. all OK!
  • onlyLIPIDMAPS: .x we found 1 problem(s):
    • Expected a LIPID MAPS identifier, but found other identifiers: 9
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 9 tests OK!
• PathwayTests: all 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 14 tests OK!

Summary

• Number of test classes: 21
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 3

Fails

Interactions with Labels

Interactions found that involve Labels: 2

• http://classic.wikipathways.org/instance/WP1531_rr137603 “Spontaneous isomerization” with graphId cbc34
• http://classic.wikipathways.org/instance/WP1531_rr137603 “UV B radiation from sunlight” with graphId f2831

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP1531_r137603 http://rdf.wikipathways.org/Pathway/WP1531_rr137603/WP/Interaction/idb2536244 “Calcidiol” (https://identifiers.org/hmdb/HMDB0003550) and Calcidiol” (https://identifiers.org/hmdb/HMDB0003550)

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 9

http://classic.wikipathways.org/instance/WP1531_rr137603 Previtamin D3 has CHEBI:8403 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 7-Dehydro- cholesterol has HMDB0000032 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 Cholesterol has HMDB0000067 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 Inactive 24,25-OH- vitamin D has HMDB0000430 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 Ca has HMDB0000464 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 Cholecalciferol has HMDB0000876 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 Pi has HMDB0001429 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 Calcitriol has HMDB0001903 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP1531_rr137603 Calcidiol has HMDB0003550 from HMDB but expected a LIPID MAPS identifier

More details at https://www.wikipathways.org/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS