lipidmaps-wp-curation

WikiPathways WP5192

• WikiPathways: WP5192 (classic)
• Species: Homo sapiens
• Scholia: WP5192
• WPRDF file: wp/Human/WP5192.ttl
• GPMLRDF file: wp/gpml/Human/WP5192.ttl
• SBML file: sbml/WP5192.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 4 tests OK!
• GeneralTests: all 13 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: 8
  • 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: 6
• 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: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 1
  • 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: 110
• Number of assertions: 222
• Number of fails: 3

Fails

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 8

http://classic.wikipathways.org/instance/WP5192_r134496 "Stimulation or inhibition depending on the animal model used " with graphId febd3
http://classic.wikipathways.org/instance/WP5192_r134496 "Stress response" with graphId dd844
http://classic.wikipathways.org/instance/WP5192_r134496 "Aging" with graphId e215e
http://classic.wikipathways.org/instance/WP5192_r134496 "Neuro degeneration" with graphId b1af8
http://classic.wikipathways.org/instance/WP5192_r134496 "Aging" with graphId e60cb
http://classic.wikipathways.org/instance/WP5192_r134496 "Stimulation or inhibition depending on the animal model used " with graphId a7d9c
http://classic.wikipathways.org/instance/WP5192_r134496 "Neurodegeneration" with graphId dfc5d
http://classic.wikipathways.org/instance/WP5192_r134496 "Stimulation or inhibition depending on the animal model used " with graphId ab173

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 6

http://classic.wikipathways.org/instance/WP5192_r134496 RNS has 62764 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_r134496 Ceramide 1-phosphates has CHEBI:16197 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_r134496 Sphingosine has CHEBI:45719 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_r134496 Ceramide has CHEBI:52639 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_r134496 Inhibitor of NF-kB kinase has CHEBI:77113 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_r134496 Sphingosine 1-phosphate has HMDB0000277 from HMDB 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: 1

https://identifiers.org/chebi/CHEBI:77113 (Inhibitor of NF-kB kinase) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5192_r134496 ; 

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