lipidmaps-wp-curation

WikiPathways WP5179

• WikiPathways: WP5179
• Scholia: WP5179
• WPRDF file: wp/Human/WP5179.ttl
• GPMLRDF file: wp/gpml/Human/WP5179.ttl
• SBML file: sbml/WP5179.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 4 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 2
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all 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: 13
• 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: 109
• Number of assertions: 220
• Number of fails: 3

Fails

DataNodesTests.dataNodesWithoutIdentifier

The following DataNodes have no identifier: 2

http://classic.wikipathways.org/instance/WP5179_r121899 http://rdf.wikipathways.org/Pathway/WP5179_r121899/DataNode/abd39 (CoA (26:1))
http://classic.wikipathways.org/instance/WP5179_r121899 http://rdf.wikipathways.org/Pathway/WP5179_r121899/DataNode/c8a0a (desaturases 
)

LIPIDMAPSTests.onlyLIPIDMAPS

Expected a LIPID MAPS identifier, but found other identifiers: 13

http://classic.wikipathways.org/instance/WP5179_r121899 CoA (20:0) has 15527 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxysphingosine has 193222-34-3 from CAS but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxy-3-ketosphinganine has 67176 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxysphinganine-2OH has AADNOUNRPCOGMI-BFWZDYSYSA-N from InChIKey but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxysphinganine-OH has BJWFMCNWESUWNO-PXKIYYGHSA-N from InChIKey but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 H2O has CHEBI:15377 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 Palmitoyl-CoA has CHEBI:15525 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 L-alanine has CHEBI:16977 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 ADP has CHEBI:456216 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxysphinganine has CHEBI:67106 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxy-dihydroceramide has CHEBI:67111 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxysphingadiene has KSKFOMCZXQEJBA-PXKIYYGHSA-N from InChIKey but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_r121899 1-deoxysphingosine-OH has KSKFOMCZXQEJBA-PXKIYYGHSA-N from InChIKey but expected a LIPID MAPS identifier

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

WikidataTests.chebiWithoutMapping

ChEBI identifiers without Wikidata mappings: 1

https://identifiers.org/chebi/CHEBI:67111 (1-deoxy-dihydroceramide) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5179_r121899 ;