lipidmaps-wp-curation

WikiPathways WP3601

• WikiPathways: WP3601 (classic)
• Species: Homo sapiens
• Scholia: WP3601
• WPRDF file: wp/Human/WP3601.ttl
• GPMLRDF file: wp/gpml/Human/WP3601.ttl
• SBML file: sbml/WP3601.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 3
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all 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: .. all OK!
  • 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: 10
• 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

Data nodes without an identifier

The following DataNodes have no identifier: 3

• http://classic.wikipathways.org/instance/WP3601_r137976 http://rdf.wikipathways.org/Pathway/WP3601_rr137976/DataNode/abdd7 (Apo B-48)
• http://classic.wikipathways.org/instance/WP3601_r137976 http://rdf.wikipathways.org/Pathway/WP3601_rr137976/DataNode/c8eb7 (Chylomicron)
• http://classic.wikipathways.org/instance/WP3601_r137976 http://rdf.wikipathways.org/Pathway/WP3601_rr137976/DataNode/e3358 (IDL)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP3601_r137976 http://rdf.wikipathways.org/Pathway/WP3601_rr137976/WP/Interaction/idd424c752 “cholesteryl ester” (https://identifiers.org/chebi/CHEBI:17002) and cholesteryl ester” (https://identifiers.org/chebi/CHEBI:17002)

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

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 10

http://classic.wikipathways.org/instance/WP3601_rr137976 cholesteryl ester has CHEBI:17002 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 TG has CHEBI:17855 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 ROS has CHEBI:26523 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 FA has CHEBI:35366 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 HDL has CHEBI:39025 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 LDL has CHEBI:39026 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 VLDL has CHEBI:39027 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 oxLDL has CHEBI:60151 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 cholesterol has HMDB0000067 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP3601_rr137976 glycerol has HMDB0000131 from HMDB but expected a LIPID MAPS identifier

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