imd-pathway-curation

WikiPathways WP5029

• WikiPathways: WP5029 (classic)
• Species: Homo sapiens
• Scholia: WP5029

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 1 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests
  • allMetabolitesInteract: .x we found 1 problem(s):
    • Found metabolites without interaction: 23
  • 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: 4
  • 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 9 tests OK!
• PathwayTests: all 7 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests
  • keggWithoutMapping: .. all OK!
  • pubchemCIDWithoutMapping: .. all OK!
  • hmdbWithoutMapping: .. all OK!
  • casWithoutMapping: .. all OK!
  • wikDataTypo: .. all OK!
  • duplicateWikidataMappings: .. all OK!
  • wikidataIdentifiersWrong: .. all OK!
  • chemspiderCIDWithoutMapping: .. all OK!
  • lipidMapsWithoutMapping: .. all OK!
  • kNApSAcKWithoutMapping: .. all OK!
  • replaceWikipedia: .. all OK!
  • chebiWithoutMapping_Reactome: .. all OK!
  • chebiWithoutMapping: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 1
  • inchikeyWithoutMapping: .. all OK!
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 22
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 3

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 23

https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Alanine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Serine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Asparagine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: D-aspartate
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Glutamine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Histidine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Tyrosine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Arginine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: H+
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Leucine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Lysine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: L-aspartate
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Cysteine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Tryptophan
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Isoleucine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Threonine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Methionine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: L-glutamate
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Cl-
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Phenylalanine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Valine
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Proline
https://identifiers.org/wikipathways/WP5029 has an metabolite not linked to an interaction: Glycine

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 4

http://classic.wikipathways.org/instance/WP5029_r128556 "Basic AA" with graphId c820b
http://classic.wikipathways.org/instance/WP5029_r128556 "Basic AA" with graphId caff5
http://classic.wikipathways.org/instance/WP5029_r128556 "Neutral AA" with graphId c2e4b
http://classic.wikipathways.org/instance/WP5029_r128556 "Neutral AA" with graphId ade1d

ChEBI identifier without a match in Wikidata

ChEBI identifiers without Wikidata mappings: 1

https://identifiers.org/chebi/CHEBI:26986 (Threonine) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5029_r128556 ; 

More details at https://www.wikipathways.org/WikiPathwaysCurator/WikidataTests/chebiWithoutMapping