lipidmaps-wp-curation

WikiPathways WP4347

• WikiPathways: WP4347 (classic)
• Species: Mus musculus
• WPRDF file: wp/Human/WP4347.ttl
• GPMLRDF file: wp/gpml/Human/WP4347.ttl
• SBML file: sbml/WP4347.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: 1
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 1
  • 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: .x we found 1 problem(s):
    • Interactions with unconnected points: 8
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 4
  • 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: 1
• 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: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 1

• http://classic.wikipathways.org/instance/WP4347_r137731 http://rdf.wikipathways.org/Pathway/WP4347_rr137731/DataNode/d952e (Spontaneous)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 1

• http://classic.wikipathways.org/instance/WP4347_r137731 http://rdf.wikipathways.org/Pathway/WP4347_rr137731/DataNode/d952e (Spontaneous)

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

Interactions with unconnected points

Interactions with unconnected points: 8

• http://classic.wikipathways.org/instance/WP4347_rr137731

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

Possible MIM translocation

Interactions between identical nodes: 4

• http://classic.wikipathways.org/instance/WP4347_r137731 http://rdf.wikipathways.org/Pathway/WP4347_rr137731/WP/Interaction/ida9533e87 “15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022) and 15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022)
• http://classic.wikipathways.org/instance/WP4347_r137731 http://rdf.wikipathways.org/Pathway/WP4347_rr137731/WP/Interaction/ida9533e87 “15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022) and 13,14-dihydro- 15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022)
• http://classic.wikipathways.org/instance/WP4347_r137731 http://rdf.wikipathways.org/Pathway/WP4347_rr137731/WP/Interaction/ida9533e87 “13,14-dihydro- 15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022) and 15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022)
• http://classic.wikipathways.org/instance/WP4347_r137731 http://rdf.wikipathways.org/Pathway/WP4347_rr137731/WP/Interaction/ida9533e87 “13,14-dihydro- 15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022) and 13,14-dihydro- 15-keto-PGD2” (https://identifiers.org/lipidmaps/LMFA03010022)

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

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 1

http://classic.wikipathways.org/instance/WP4347_rr137731 Glycerophospholipids has CHEBI:37739 from ChEBI but expected a LIPID MAPS identifier

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