sr24-curation

WikiPathways WP4290

WikiPathways: WP4290 (classic)
Species: Homo sapiens
Scholia: WP4290
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: 69
- missingHGNC: .. all OK!
DataNodesTests
- dataNodesWithoutIdentifier: .x we found 1 problem(s):
  - The following DataNodes have no identifier: 4
- unknownTypes_knownDatasource: .. all OK!
- unknownTypes: .. all OK!
- unknownTypes_Reactome: .. all OK!
- otherDataSource: .. all 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: 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: 1
- UnconnectedPoints: .x we found 1 problem(s):
  - Interactions with unconnected points: 1
- possibleTranslocations: .x we found 1 problem(s):
  - Interactions between identical nodes: 2
- 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: 2
- achiralAminoAcids: .x we found 1 problem(s):
  - Metabolites with ChEBI identifiers of achiral amino acids: 3
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: 7

Fails

Interactions without references

Interactions without literature references: 69

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

Data nodes without an identifier

The following DataNodes have no identifier: 4

http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/b2ba1 (Amino acid synthesis)
http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/c28b6 (Cell cycle Proliferation)
http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/ded28 (Nucleotide synthesis)
http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/DataNode/bd312 (Purine synthesis)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

Interactions with Labels

Interactions found that involve Labels: 1

http://classic.wikipathways.org/instance/WP4290_r136156 “pH balance Nitrogen source” with graphId f0da4

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

Interactions with unconnected points

Interactions with unconnected points: 1

http://classic.wikipathways.org/instance/WP4290_r136156

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

Possible MIM translocation

Interactions between identical nodes: 2

http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/WP/Interaction/id35c246c6 “glutamine” (https://identifiers.org/chebi/CHEBI:28300) and glutamine” (https://identifiers.org/chebi/CHEBI:28300)
http://classic.wikipathways.org/instance/WP4290_r136156 http://rdf.wikipathways.org/Pathway/WP4290_r136156/WP/Interaction/idd3a00f33 “Lactate” (https://identifiers.org/hmdb/HMDB0000190) and Lactate” (https://identifiers.org/hmdb/HMDB0000190)

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

Too many InChIKeys for the used identifier

Non-zero count of metabolites with more than one InChIKey: 2

http://classic.wikipathways.org/instance/WP4290_r136156 has: Asparagine (CHEBI:17196) with InChIKeys: DCXYFEDJOCDNAF-REOHCLBHSA-N, UYPYRKYUKCHHIB-UHFFFAOYSA-N
http://classic.wikipathways.org/instance/WP4290_r136156 has: IMP (CHEBI:17202) with InChIKeys: GRSZFWQUAKGDAV-UHFFFAOYSA-N, GRSZFWQUAKGDAV-KQYNXXCUSA-N

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

Identifier used of a amino acid with undefined stereochemistry

Metabolites with ChEBI identifiers of achiral amino acids: 3

http://classic.wikipathways.org/instance/WP4290_r136156 glutamine CHEBI:28300
http://classic.wikipathways.org/instance/WP4290_r136156 Proline CHEBI:26271
http://classic.wikipathways.org/instance/WP4290_r136156 serine CHEBI:17822

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