sr24-curation

WikiPathways WP5083

• WikiPathways: WP5083 (classic)
• Species: Homo sapiens
• Scholia: WP5083

  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: 77
  • 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
  • allMetabolitesInteract: .x we found 1 problem(s):
    • Found metabolites without interaction: 7
  • 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: 2
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 9
  • 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: all 15 tests OK!

Summary

• Number of test classes: 23
• Number of tests: 140
• Number of assertions: 281
• Number of fails: 5

Fails

CovidDiseaseMapsTests.interactionsWithoutReferences

Interactions without literature references: 77

http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/ff222
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a77f1
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/b7caa
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e9f69
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/d2cd7
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/f56e7
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e981f
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/f34fd
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/d0f2e
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e99b8
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/c10a5
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/de829
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/cf912
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/dabc0
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/d9f0f
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e3fbb
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/ebc35
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/d1dd4
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/f75b9
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/ec10e
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/f00db
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/c5268
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/be102
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a56f3
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/f5053
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/ac570
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e04b8
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/be93f
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a670d
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/ac4c0
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/ef7aa
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/bab85
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e5ccd
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/cd6cb
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/cb268
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/f9af1
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/ddf66
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/aafae
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/bfa32
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a6025
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/db078
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/fae75
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/d3e99
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/cfab2
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/b0aea
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/b8fac
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/d347d
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/fc990
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/ba7de
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a9c41
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e22c9
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/b20fc
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e6068
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/f66c7
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/c90bb
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/cc484
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a1c7f
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/dce42
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/de1e9
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/b97cd
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a3f4d
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/cb05f
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/ea893
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/f5bc9
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/cdcf5
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a534f
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a6972
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e343f
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/b07be
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/f230d
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/a3456
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/acfc7
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/f24fc
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/ComplexBinding/ec7fe
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/c98da
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/b7dc4
http://classic.wikipathways.org/instance/WP5083_r135193 -> http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/fa69c

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 7

https://identifiers.org/wikipathways/WP5083 has an metabolite not linked to an interaction: NH3(+)
https://identifiers.org/wikipathways/WP5083 has an metabolite not linked to an interaction: NADH
https://identifiers.org/wikipathways/WP5083 has an metabolite not linked to an interaction: H+
https://identifiers.org/wikipathways/WP5083 has an metabolite not linked to an interaction: 1,3-diglycerides
https://identifiers.org/wikipathways/WP5083 has an metabolite not linked to an interaction: H2O2
https://identifiers.org/wikipathways/WP5083 has an metabolite not linked to an interaction: nitric oxide
https://identifiers.org/wikipathways/WP5083 has an metabolite not linked to an interaction: 1,2-diglycerides

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 2

http://classic.wikipathways.org/instance/WP5083_r135193 "Mechanical Strength" with graphId ef62c
http://classic.wikipathways.org/instance/WP5083_r135193 "Spine shrinkage" with graphId bedee

Possible MIM translocation

Interactions between identical nodes: 9

http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a77f1 "glutamate" (https://identifiers.org/chebi/CHEBI:14321) and 
glutamate" (https://identifiers.org/chebi/CHEBI:14321)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e981f "Glycine" (https://identifiers.org/chebi/CHEBI:15428) and 
Glycine" (https://identifiers.org/chebi/CHEBI:15428)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/e6704 "glucose" (https://identifiers.org/chebi/CHEBI:17234) and 
glucose" (https://identifiers.org/chebi/CHEBI:17234)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/ec10e "Glycine" (https://identifiers.org/chebi/CHEBI:15428) and 
Glycine" (https://identifiers.org/chebi/CHEBI:15428)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/a1698 "D-serine" (https://identifiers.org/chebi/CHEBI:35247) and 
D-serine" (https://identifiers.org/chebi/CHEBI:35247)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/adeb0 "D-serine" (https://identifiers.org/chebi/CHEBI:35247) and 
D-serine" (https://identifiers.org/chebi/CHEBI:35247)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/efe0a "L-serine" (https://identifiers.org/chebi/CHEBI:17115) and 
L-serine" (https://identifiers.org/chebi/CHEBI:17115)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/b20fc "glutamate" (https://identifiers.org/chebi/CHEBI:14321) and 
glutamate" (https://identifiers.org/chebi/CHEBI:14321)
http://classic.wikipathways.org/instance/WP5083_r135193 http://rdf.wikipathways.org/Pathway/WP5083_r135193/WP/Interaction/b9a4a "glutamine" (https://identifiers.org/chebi/CHEBI:28300) and 
glutamine" (https://identifiers.org/chebi/CHEBI:28300)

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

MetabolitesTests.tooManyInChIKeys

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

http://classic.wikipathways.org/instance/WP5083_r135193 (example) has: glutamine CHEBI:28300 with InChIKeys: ZDXPYRJPNDTMRX-UHFFFAOYSA-N, RSOHUXCZIQMEMQ-JLHYYAGUSA-N