lipidmaps-wp-curation

WikiPathways WP148

• WikiPathways: WP148 (classic)
• Species: Caenorhabditis elegans
• WPRDF file: wp/Human/WP148.ttl
• GPMLRDF file: wp/gpml/Human/WP148.ttl
• SBML file: sbml/WP148.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
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: …. all OK!
  • nonNumericHGNCAccessionNumbers: .. all OK!
  • genesWithoutEnsemblMapping: .x we found 1 problem(s):
    • The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 1 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests: all 9 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: 11
• 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: all 14 tests OK!

Summary

• Number of test classes: 21
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 2

Fails

Genes with identifier but no Ensembl identifier mapping

The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1

http://classic.wikipathways.org/instance/WP148_rr121852 T08G2.3 with datasource Entrez Gene

More details at https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 11

http://classic.wikipathways.org/instance/WP148_rr121852 trans-Dec-2-enoyl-CoA has CHEBI:10723 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 butanoyl-CoA has CHEBI:15517 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 trans-Oct-2-enoyl-CoA has CHEBI:27537 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 3-Oxohexanoyl-CoA has CHEBI:27648 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 3-oxo-octanoyl-CoA has CHEBI:28264 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 (S)-3-Hydroxydecanoyl-CoA has CHEBI:28325 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 Decanoyl-CoA has CHEBI:28493 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 (S)-3-Hydroxyoctanoyl-CoA has CHEBI:28632 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 trans-Hex-2-enoyl-CoA has CHEBI:28706 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 hexanoyl-CoA has CHEBI:62620 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP148_rr121852 Acetyl-CoA has HMDB0001206 from HMDB but expected a LIPID MAPS identifier

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