sr24-curation

WikiPathways WP5506

• WikiPathways: WP5506 (classic)
• Species: Homo sapiens
• Scholia: WP5506

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• CovidDiseaseMapsTests
  • interactionsWithoutReferences: .x we found 1 problem(s):
    • Interactions without literature references: 11
  • missingHGNC: .. all OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 5 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 2 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests: all 6 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: 3
  • 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
  • metaboliteAlsoOtherType: .. all OK!
  • casNumbersNotMarkedAsMetabolite: .. all OK!
  • chemspiderIDsNotMarkedAsMetabolite: .. all OK!
  • HMDBIDsNotMarkedAsMetabolite: .. all OK!
  • KEGGIDsNotMarkedAsMetabolite: .. all OK!
  • metabolitesWithAnEnsembleID: .. all OK!
  • metabolitesWithAnEntrezGeneID: .. all OK!
  • metabolitesWithDbButNoIdentifier: .. all OK!
  • metabolitesWithIdentifierButNoDb: .. all OK!
  • ChEBIIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotNumbers: .. all OK!
  • PubChemSubstanceIDsNotNumbers: .. all OK!
  • tooManyInChIKeys: .x we found 1 problem(s):
    • Non-zero count of metabolites with more than one InChIKey: 1
• OudatedDataSourcesTests: all 24 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: .. all OK!
  • inchikeyWithoutMapping: .x we found 1 problem(s):
    • InChIKey identifiers without Wikidata mappings: 1
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 23
• Number of tests: 140
• Number of assertions: 281
• Number of fails: 4

Fails

Interactions without references

Interactions without literature references: 11

• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/idc3f9ca71
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/idf02016cf
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/fca0e
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/ebf19
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/idbf91fee3
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/e4a6c
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/idcb736366
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/afd58
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/idfe78d24b
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/idb83ec8f6
• http://classic.wikipathways.org/instance/WP5506_r136162 -> http://rdf.wikipathways.org/Pathway/WP5506_r136162/WP/Interaction/idfd836518

More details at https://www.wikipathways.org/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences

Interactions with Labels

Interactions found that involve Labels: 3

• http://classic.wikipathways.org/instance/WP5506_r136162 “NAD synthetase 1 deficiency” with graphId d7a82
• http://classic.wikipathways.org/instance/WP5506_r136162 “NAD(P)HX epimerase deficiency” with graphId cf0ea
• http://classic.wikipathways.org/instance/WP5506_r136162 “NAD(P)HX dehydratase deficiency” with graphId f7ea7

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

Too many InChIKeys for the used identifier

Non-zero count of metabolites with more than one InChIKey: 1

• http://classic.wikipathways.org/instance/WP5506_r136162 has: ADP-D-ribose (CHEBI:16960) with InChIKeys: SRNWOUGRCWSEMX-UHFFFAOYSA-N, SRNWOUGRCWSEMX-TYASJMOZSA-N

More details at https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/tooManyInChIKeys

InChIKey without a match in Wikidata

InChIKey identifiers without Wikidata mappings: 1

XHATZBPBVXWMQQ-GGFUHNOESA-N	cyclo-NADHX