sr24-curation

WikiPathways WP4022

WikiPathways: WP4022 (classic)
Species: Homo sapiens
Scholia: WP4022
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: 110
- missingHGNC: .. all OK!
DataNodesTests
- dataNodesWithoutIdentifier: .x we found 1 problem(s):
  - The following DataNodes have no identifier: 5
- unknownTypes_knownDatasource: .. all OK!
- unknownTypes: .. all OK!
- unknownTypes_Reactome: .. all OK!
- otherDataSource: .. all 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: 1
- metabolicConversions: .. all OK!
- catalystsWithCommonDataSource: .. all OK!
- metabolicConversionIdentifiersCommon: .. all OK!
- diseasesHaveIdentifiers: .. all OK!
- omimIdentifiers: .. all OK!
InteractionTests: all 8 tests 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
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: 4

Fails

Interactions without references

Interactions without literature references: 110

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

Data nodes without an identifier

The following DataNodes have no identifier: 5

http://classic.wikipathways.org/instance/WP4022_r136149 http://rdf.wikipathways.org/Pathway/WP4022_r136149/DataNode/c2466 (Alanine, aspartate and glutamate metabolism)
http://classic.wikipathways.org/instance/WP4022_r136149 http://rdf.wikipathways.org/Pathway/WP4022_r136149/DataNode/ab91f (Arginine and proline metabolism)
http://classic.wikipathways.org/instance/WP4022_r136149 http://rdf.wikipathways.org/Pathway/WP4022_r136149/DataNode/b38a3 (Pentose phosphate pathway)
http://classic.wikipathways.org/instance/WP4022_r136149 http://rdf.wikipathways.org/Pathway/WP4022_r136149/DataNode/f1a59 (Valine, leucine and isoleucine metabolism)
http://classic.wikipathways.org/instance/WP4022_r136149 http://rdf.wikipathways.org/Pathway/WP4022_r136149/DataNode/deb08 (beta-Alanine metabolism)

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

All metabolites are involved in interactions

Found metabolites without interaction: 1

https://identifiers.org/wikipathways/WP4022 has an metabolite not linked to an interaction: 2-deoxy-D-ribose-1P

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

Too many InChIKeys for the used identifier

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

http://classic.wikipathways.org/instance/WP4022_r136149 has: dTMP (C00364) with InChIKeys: GYOZYWVXFNDGLU-XLPZGREQSA-N, QSJFDOVQWZVUQG-KAVNDROISA-N, GYOZYWVXFNDGLU-XLPZGREQSA-L
http://classic.wikipathways.org/instance/WP4022_r136149 has: Orotidine 5’-phosphate (C01103) with InChIKeys: KYOBSHFOBAOFBF-XVFCMESISA-N, FKCRAVPPBFWEJD-XVFCMESISA-N

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