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 5 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
- UnconnectedPoints: .x we found 1 problem(s):
  - Interactions with unconnected points: 30
- 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: .. all OK!
- achiralAminoAcids: .x we found 1 problem(s):
  - Metabolites with ChEBI identifiers of achiral amino acids: 1
OudatedDataSourcesTests: all 24 tests OK!
PathwayTests: all 11 tests OK!
ProteinsTests: all 2 tests OK!
PubChemMetabolitesTests: all 3 tests OK!
ReferencesTests: all 6 tests OK!
UniProtTests: all 5 tests OK!
UnicodeTests: all 2 tests OK!
WikidataTests: all 15 tests OK!

Summary

Number of test classes: 24
Number of tests: 149
Number of assertions: 299
Number of fails: 6

Fails

Interactions without references

Interactions without literature references: 77

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

All metabolites are involved in interactions

Found metabolites without interaction: 7

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

More details at https://www.wikipathways.org/WikiPathwaysCurator/IEMPathwayTests/allMetabolitesInteract

Interactions with Labels

Interactions found that involve Labels: 2

http://classic.wikipathways.org/instance/WP5083_r139848 “Mechanical Strength” with graphId ef62c
http://classic.wikipathways.org/instance/WP5083_r139848 “Spine shrinkage” with graphId bedee

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

Interactions with unconnected points

Interactions with unconnected points: 30

http://classic.wikipathways.org/instance/WP5083_r139848

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

Possible MIM translocation

Interactions between identical nodes: 9

http://classic.wikipathways.org/instance/WP5083_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/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_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/WP/Interaction/e981f “Glycine” (https://identifiers.org/chebi/CHEBI:15428) and Glycine” (https://identifiers.org/chebi/CHEBI:15428)
http://classic.wikipathways.org/instance/WP5083_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/WP/Interaction/e6704 “glucose” (https://identifiers.org/chebi/CHEBI:17234) and glucose” (https://identifiers.org/chebi/CHEBI:17234)
http://classic.wikipathways.org/instance/WP5083_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/WP/Interaction/a77f1 “glutamate” (https://identifiers.org/chebi/CHEBI:14321) and glutamate” (https://identifiers.org/chebi/CHEBI:14321)
http://classic.wikipathways.org/instance/WP5083_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/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_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/WP/Interaction/b20fc “glutamate” (https://identifiers.org/chebi/CHEBI:14321) and glutamate” (https://identifiers.org/chebi/CHEBI:14321)
http://classic.wikipathways.org/instance/WP5083_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/WP/Interaction/b9a4a “glutamine” (https://identifiers.org/chebi/CHEBI:28300) and glutamine” (https://identifiers.org/chebi/CHEBI:28300)
http://classic.wikipathways.org/instance/WP5083_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/WP/Interaction/ec10e “Glycine” (https://identifiers.org/chebi/CHEBI:15428) and Glycine” (https://identifiers.org/chebi/CHEBI:15428)
http://classic.wikipathways.org/instance/WP5083_r139848 http://rdf.wikipathways.org/Pathway/WP5083_r139848/WP/Interaction/a1698 “D-serine” (https://identifiers.org/chebi/CHEBI:35247) and D-serine” (https://identifiers.org/chebi/CHEBI:35247)

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

Identifier used of a amino acid with undefined stereochemistry

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP5083_r139848 glutamine CHEBI:28300

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