lipidmaps-wp-curation

WikiPathways WP5188

• WikiPathways: WP5188
• Scholia: WP5188
• WPRDF file: wp/Human/WP5188.ttl
• GPMLRDF file: wp/gpml/Human/WP5188.ttl
• SBML file: sbml/WP5188.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 4 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 13 tests OK!
• HMDBMetabolitesTests: all 1 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests: all 8 tests 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: 16
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 7 tests OK!
• PathwayTests: all 7 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: .. all OK!
  • chebiWithoutMapping_Reactome: .. all OK!
  • chemspiderCIDWithoutMapping: .. all OK!
  • duplicateWikidataMappings: .. all OK!
  • hmdbWithoutMapping: .x we found 1 problem(s):
    • HMDB identifiers without Wikidata mappings: 1
  • 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: 109
• Number of assertions: 220
• Number of fails: 2

Fails

LIPIDMAPSTests.onlyLIPIDMAPS

Expected a LIPID MAPS identifier, but found other identifiers: 16

http://classic.wikipathways.org/instance/WP5188_r122585 11-cis-retinyl tetradecanoate has CHEBI:138676 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 11-cis-retinyl palmitate has CHEBI:16254 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 11-cis-retinol has CHEBI:16302 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 all-trans-retinol has CHEBI:17336 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 all-trans-retinal has CHEBI:17898 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 all-trans-retinoate has CHEBI:35291 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 Iodopsin has CHEBI:5949 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 all-trans-retinyl esters has CHEBI:63410 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 9-cis-retinol has CHEBI:78272 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 9-cis-retinal has CHEBI:78273 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 9-cis-retinoate has CHEBI:78630 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 4-oxo RA has CHEBI:80656 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 beta-Carotene has HMDB0000561 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 18-hydroxy RA has HMDB0012452 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 11-cis retinal has Q17002962 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5188_r122585 4-hydroxy RA has Q27132808 from Wikidata but expected a LIPID MAPS identifier

More details at https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS

WikidataTests.hmdbWithoutMapping

HMDB identifiers without Wikidata mappings: 1

https://identifiers.org/hmdb/HMDB0012452 (18-hydroxy RA) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5188_r122585 ;