imd-pathway-curation

WikiPathways WP5171

• WikiPathways: WP5171
• Scholia: WP5171
• WPRDF file: wp/Human/WP5171.ttl
• GPMLRDF file: wp/gpml/Human/WP5171.ttl
• SBML file: sbml/WP5171.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: 4
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 3 tests OK!
• GeneralTests: all 13 tests OK!
• HMDBMetabolitesTests: all 1 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests
  • allMetabolitesInteract: .x we found 1 problem(s):
    • Found metabolites without interaction: 1
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .. all OK!
  • metabolicConversionIdentifiersCommon: .. all OK!
  • diseasesHaveIdentifiers: .. all OK!
  • omimIdentifiers: .. all 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: 5
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 7 tests OK!
• PathwayTests: all 6 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 4 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 15 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 110
• Number of assertions: 220
• Number of fails: 4

Fails

DataNodesTests.dataNodesWithoutIdentifier

The following DataNodes have no identifier: 4

http://www.wikipathways.org/instance/WP5171_r122629 http://rdf.wikipathways.org/Pathway/WP5171_r122629/DataNode/f14c9 ((C2)-COOH-LTB)
http://www.wikipathways.org/instance/WP5171_r122629 http://rdf.wikipathways.org/Pathway/WP5171_r122629/DataNode/a5851 ((C2)-COOH-LTE)
http://www.wikipathways.org/instance/WP5171_r122629 http://rdf.wikipathways.org/Pathway/WP5171_r122629/DataNode/df1b4 (16-carboxy-LTB4)
http://www.wikipathways.org/instance/WP5171_r122629 http://rdf.wikipathways.org/Pathway/WP5171_r122629/DataNode/b8ae7 (16-carboxy-LTE4)

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 1

https://identifiers.org/wikipathways/WP5171 has an metabolite not linked to an interaction: Glutathione

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 5

http://www.wikipathways.org/instance/WP5171_r122629 "Cysteinylglycinase 
deficiency " with graphId b1780
http://www.wikipathways.org/instance/WP5171_r122629 "Ischemic
Stroke" with graphId d032c
http://www.wikipathways.org/instance/WP5171_r122629 "Glutathionuria" with graphId f6994
http://www.wikipathways.org/instance/WP5171_r122629 "LTC4 synthase
deficiency" with graphId edbd2
http://www.wikipathways.org/instance/WP5171_r122629 "Deafness" with graphId c8316

InteractionTests.possibleTranslocations

Interactions between identical nodes: 1

http://www.wikipathways.org/instance/WP5171_r122629 http://rdf.wikipathways.org/Pathway/WP5171_r122629/WP/Interaction/idabf0aac0 "LTC4" (https://identifiers.org/chebi/CHEBI:16978) and 
LTC4" (https://identifiers.org/chebi/CHEBI:16978)

More details at https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations