lipidmaps-wp-curation

WikiPathways WP4142

• WikiPathways: WP4142 (classic)
• Species: Homo sapiens
• Scholia: WP4142
• WPRDF file: wp/Human/WP4142.ttl
• GPMLRDF file: wp/gpml/Human/WP4142.ttl
• SBML file: sbml/WP4142.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: .. 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: 37
• 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: 7
  • 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

Possible MIM translocation

Interactions between identical nodes: 1

http://classic.wikipathways.org/instance/WP4142_r128518 http://rdf.wikipathways.org/Pathway/WP4142_r128518/WP/Interaction/idea071e50 "Galactosyl-ceramide" (https://identifiers.org/wikidata/Q2756638) and 
Galactosylceramide" (https://identifiers.org/chebi/CHEBI:36498)

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

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 37

http://classic.wikipathways.org/instance/WP4142_r128518 GM3 has CHEBI:15681 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Ceramide has CHEBI:17761 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Serine has CHEBI:17822 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GD1a has CHEBI:18163 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GM1a has CHEBI:18216 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Neutral GSLs has CHEBI:25513 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GA2 has CHEBI:27731 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GA1 has CHEBI:27938 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GT1b has CHEBI:28058 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GD1b has CHEBI:28175 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GT3 has CHEBI:28541 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GD2 has CHEBI:28648 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Galactosylceramide has CHEBI:36498 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GM2 has CHEBI:51013 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GT2 has CHEBI:61732 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GM1b has CHEBI:62370 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GT1c has CHEBI:87992 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GQ1c has CHEBI:87994 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 GD3 has CHEBI:89636 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Sphinganine has HMDB0000269 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Dihydroceramide has HMDB0006752 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Dihydroceramide desaturase has Q17117943 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 DEGS1 has Q21105760 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 DEGS2 has Q21115762 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 3-ketosphinganine has Q27073739 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Sphinganine 1-phosphate has Q27077062 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Hexadecanal has Q27077978 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Galactosyl-ceramide has Q2756638 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Lactosylceramide has Q3215908 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Palmitoyl CoA has Q3361645 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Glucosylceramide has Q35662896 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Ceramide-1-phosphate has Q35664620 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Sulfatide has Q408584 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Sphingosine-1-phosphate has Q418267 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Ethanolamine phosphate has Q418826 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Sphingomyelin has Q423143 from Wikidata but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP4142_r128518 Sphingosine has Q46298 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: 7

https://identifiers.org/chebi/CHEBI:18163 (GD1a) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4142_r128518 ; 
https://identifiers.org/chebi/CHEBI:28541 (GT3) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4142_r128518 ; 
https://identifiers.org/chebi/CHEBI:51013 (GM2) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4142_r128518 ; 
https://identifiers.org/chebi/CHEBI:61732 (GT2) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4142_r128518 ; 
https://identifiers.org/chebi/CHEBI:62370 (GM1b) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4142_r128518 ; 
https://identifiers.org/chebi/CHEBI:87992 (GT1c) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4142_r128518 ; 
https://identifiers.org/chebi/CHEBI:87994 (GQ1c) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4142_r128518 ; 

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