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
  • 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: .x we found 1 problem(s):
    • Interactions found that involve Labels: 8
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 6
  • 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 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: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP5192_r135482 http://rdf.wikipathways.org/Pathway/WP5192_rr135482/DataNode/d0bf2 (Protein associated with Myc)
• http://classic.wikipathways.org/instance/WP5192_r135482 http://rdf.wikipathways.org/Pathway/WP5192_rr135482/DataNode/c1f4b (Ras homolog enriched in the brain)

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

Interactions with Labels

Interactions found that involve Labels: 8

• http://classic.wikipathways.org/instance/WP5192_rr135482 “Stress response” with graphId dd844
• http://classic.wikipathways.org/instance/WP5192_rr135482 “Aging” with graphId e215e
• http://classic.wikipathways.org/instance/WP5192_rr135482 “Neuro degeneration” with graphId b1af8
• http://classic.wikipathways.org/instance/WP5192_rr135482 “Stimulation or inhibition depending on the animal model used “ with graphId a7d9c
• http://classic.wikipathways.org/instance/WP5192_rr135482 “Aging” with graphId e60cb
• http://classic.wikipathways.org/instance/WP5192_rr135482 “Stimulation or inhibition depending on the animal model used “ with graphId febd3
• http://classic.wikipathways.org/instance/WP5192_rr135482 “Neurodegeneration” with graphId dfc5d
• http://classic.wikipathways.org/instance/WP5192_rr135482 “Stimulation or inhibition depending on the animal model used “ with graphId ab173

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

Interactions with unconnected points

Interactions with unconnected points: 6

• http://classic.wikipathways.org/instance/WP5192_rr135482

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

Only LIPID MAPS identifiers

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

http://classic.wikipathways.org/instance/WP5192_rr135482 RNS has 62764 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_rr135482 Ceramide 1-phosphates has CHEBI:16197 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_rr135482 Sphingosine has CHEBI:45719 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_rr135482 Ceramide has CHEBI:52639 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_rr135482 Sphingosine 1-phosphate has HMDB0000277 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP5192_rr135482 Inhibitor of NF-kB kinase has Q130305247 from Wikidata but expected a LIPID MAPS identifier

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