imd-pathway-curation

WikiPathways WP5175

• WikiPathways: WP5175
• Scholia: WP5175
• WPRDF file: wp/Human/WP5175.ttl
• GPMLRDF file: wp/gpml/Human/WP5175.ttl
• SBML file: sbml/WP5175.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 4 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 4 tests 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: 5
  • 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: 6
  • possibleTranslocations: .. all OK!
  • 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
  • nonNumericPubMedIDs: .. all OK!
  • zeroPubMedIDs: .. all OK!
  • atLeastOneReference: .x we found 1 problem(s):
    • Found 1 pathways with zero (PubMed) references
  • citesRetractedArticle: .. all 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: 3

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 5

https://identifiers.org/wikipathways/WP5175 has an metabolite not linked to an interaction: NADH
https://identifiers.org/wikipathways/WP5175 has an metabolite not linked to an interaction: NAD+
https://identifiers.org/wikipathways/WP5175 has an metabolite not linked to an interaction: H+
https://identifiers.org/wikipathways/WP5175 has an metabolite not linked to an interaction: CoASH
https://identifiers.org/wikipathways/WP5175 has an metabolite not linked to an interaction: Coenzym A

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 6

http://www.wikipathways.org/instance/WP5175_r122904 "SCOT deficiency" with graphId b3000
http://www.wikipathways.org/instance/WP5175_r122904 "Methylacetoacetyl- CoA 
thiolase deficiency" with graphId f88a8
http://www.wikipathways.org/instance/WP5175_r122904 "Pyruvate metabolism" with graphId a2df9
http://www.wikipathways.org/instance/WP5175_r122904 "3-Hydroxy-3- methylglutaryl-CoA 
synthase deficiency" with graphId f73a9
http://www.wikipathways.org/instance/WP5175_r122904 "Fatty acid metabolism" with graphId c9f63
http://www.wikipathways.org/instance/WP5175_r122904 "3-Hydroxy-3-methylglutaryl-CoA 
lyase deficiency" with graphId d0958

ReferencesTests.atLeastOneReference

Found 1 pathways with zero (PubMed) references

http://www.wikipathways.org/instance/WP5175_r122904 'Disorders in ketone body synthesis' in Homo sapiens has zero references; 

More details at https://wikipathways.github.io/WikiPathwaysCurator/ReferencesTests/atLeastOneReference