lipidmaps-wp-curation

WikiPathways WP5186

• WikiPathways: WP5186 (classic)
• Species: Homo sapiens
• Scholia: WP5186
• WPRDF file: wp/Human/WP5186.ttl
• GPMLRDF file: wp/gpml/Human/WP5186.ttl
• SBML file: sbml/WP5186.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: .x we found 1 problem(s):
    • Interactions with unconnected points: 2
  • possibleTranslocations: .. all OK!
  • 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: 20
• 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
  • casWithoutMapping: .. all OK!
  • chebiWithoutMapping: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 2
  • chebiWithoutMapping_Reactome: .. all OK!
  • chemspiderCIDWithoutMapping: .. all OK!
  • duplicateWikidataMappings: .. all OK!
  • hmdbWithoutMapping: .. all OK!
  • kNApSAcKWithoutMapping: .. all OK!
  • keggWithoutMapping: .. all OK!
  • lipidMapsWithoutMapping: .. all OK!
  • pubchemCIDWithoutMapping: .. all OK!
  • replaceWikipedia: .. all OK!
  • retiredIdentifiers: .. all OK!
  • wikDataTypo: .. all OK!
  • wikidataIdentifiersWrong: .. all OK!

Summary

• Number of test classes: 21
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 3

• http://classic.wikipathways.org/instance/WP5186_r137694 http://rdf.wikipathways.org/Pathway/WP5186_rr137694/DataNode/cc54d (LOO•)
• http://classic.wikipathways.org/instance/WP5186_r137694 http://rdf.wikipathways.org/Pathway/WP5186_rr137694/DataNode/a498c (Men)
• http://classic.wikipathways.org/instance/WP5186_r137694 http://rdf.wikipathways.org/Pathway/WP5186_rr137694/DataNode/ef4d2 (Mqn)

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

Interactions with unconnected points

Interactions with unconnected points: 2

• http://classic.wikipathways.org/instance/WP5186_rr137694

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

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 20

http://classic.wikipathways.org/instance/WP5186_rr137694 glutamate has CHEBI:14321 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Vitamin K epoxide (VKO) has CHEBI:15759 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 vitamin K2 has CHEBI:16374 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 NADP+ has CHEBI:18009 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Dietary  Vitamin K1 has CHEBI:18067 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Vitamin K1 has CHEBI:18067 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 dithiols has CHEBI:23853 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Vitamin K has CHEBI:28384 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Vitamin K (VK) has CHEBI:28384 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Vitamin K hydroquinone (VKH2) has CHEBI:28433 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Vitamin K3 has CHEBI:28869 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 vitamin K2 (MK7) has CHEBI:44245 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 disulfides has CHEBI:48343 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 geranylgeranyl diphosphate has CHEBI:58756 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 gamma-carboxyglutamate has CHEBI:61938 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Menadiol has CHEBI:6746 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 vitamin K2 (MK4) has CHEBI:78277 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 NADPH has HMDB0000221 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 Warfarin has HMDB0001935 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5186_rr137694 LOOH has Q76617139 from Wikidata but expected a LIPID MAPS identifier

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

ChEBI identifier without a match in Wikidata

ChEBI identifiers without Wikidata mappings: 2

• https://identifiers.org/chebi/CHEBI:48343 (disulfides) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5186_rr137694
• https://identifiers.org/chebi/CHEBI:61938 (gamma-carboxyglutamate) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5186_rr137694

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