lipidmaps-wp-curation

WikiPathways WP5179

• WikiPathways: WP5179 (classic)
• Species: Homo sapiens
• 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 5 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 5 tests OK!
• GeneralTests: all 15 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!
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 1
  • 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: 13
• 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP5179_r139553 http://rdf.wikipathways.org/Pathway/WP5179_rr139553/DataNode/abd39 (CoA (26:1))
• http://classic.wikipathways.org/instance/WP5179_r139553 http://rdf.wikipathways.org/Pathway/WP5179_rr139553/DataNode/c8a0a (Desaturases)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

Interactions with unconnected points

Interactions with unconnected points: 1

• http://classic.wikipathways.org/instance/WP5179_rr139553

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

Only LIPID MAPS identifiers

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

http://classic.wikipathways.org/instance/WP5179_rr139553 CoA (20:0) has 15527 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxysphingosine has 193222-34-3 from CAS but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxy-3-ketosphinganine has 67176 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxysphinganine-2OH has AADNOUNRPCOGMI-BFWZDYSYSA-N from InChIKey but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxysphinganine-OH has BJWFMCNWESUWNO-PXKIYYGHSA-N from InChIKey but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 H₂O has CHEBI:15377 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 Palmitoyl-CoA has CHEBI:15525 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 L-alanine has CHEBI:16977 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 ADP has CHEBI:456216 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxysphinganine has CHEBI:67106 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxy-dihydroceramide has CHEBI:67111 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxysphingadiene has KSKFOMCZXQEJBA-PXKIYYGHSA-N from InChIKey but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5179_rr139553 1-Deoxysphingosine-OH has KSKFOMCZXQEJBA-PXKIYYGHSA-N from InChIKey but expected a LIPID MAPS identifier

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