lipidmaps-wp-curation

WikiPathways WP5393

• WikiPathways: WP5393 (classic)
• Species: Homo sapiens
• Scholia: WP5393
• WPRDF file: wp/Human/WP5393.ttl
• GPMLRDF file: wp/gpml/Human/WP5393.ttl
• SBML file: sbml/WP5393.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: 4
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all 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
  • 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: 14
  • possibleTranslocations: .. all OK!
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 2 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 9 tests OK!
• PathwayTests
  • deletedPathways: .. all OK!
  • linksToDeletedPathways: .. all OK!
  • linksToDeletedPathways_All: .. all OK!
  • speciesMismatch: .. all OK!
  • testRoundedRectangle: .. all OK!
  • youMustCite: .. all OK!
  • oldLicenses: .. all OK!
  • mediawikiLinks: .. all OK!
  • allEmptyDescriptions: .. all OK!
  • allShortDescriptions: .x we found 1 problem(s):
    • Pathways of with a very short description: 1
  • multipleDescriptions: .. all 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: 4

• http://classic.wikipathways.org/instance/WP5393_r20230308 http://rdf.wikipathways.org/Pathway/WP5393_r20230308/DataNode/ff03b (16alpha-hydroxy androst-4-ene-3,17-dione)
• http://classic.wikipathways.org/instance/WP5393_r20230308 http://rdf.wikipathways.org/Pathway/WP5393_r20230308/DataNode/ac899 (Other)
• http://classic.wikipathways.org/instance/WP5393_r20230308 http://rdf.wikipathways.org/Pathway/WP5393_r20230308/DataNode/b39a7 (Other)
• http://classic.wikipathways.org/instance/WP5393_r20230308 http://rdf.wikipathways.org/Pathway/WP5393_r20230308/DataNode/d1e43 (Other)

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

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/WP5393_r20230308 STS with datasource UniProtKB

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

Interactions with unconnected points

Interactions with unconnected points: 14

• http://classic.wikipathways.org/instance/WP5393_r20230308

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

Pathway description is too short

Pathways of with a very short description: 1

• http://classic.wikipathways.org/instance/WP5393_r20230308

More details at https://www.wikipathways.org/WikiPathwaysCurator/PathwayTests/allShortDescriptions