sr24-curation

WikiPathways WP176

WikiPathways: WP176 (classic)
Species: Homo sapiens
Scholia: WP176
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: 170
- 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: .x we found 1 problem(s):
  - Unexpected interactions, not from metabolite to metabolite and not from RNA to RNA: 1
- 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: .. all OK!
- possibleTranslocations: .x we found 1 problem(s):
  - Interactions between identical nodes: 8
- 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
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

Interactions without references

Interactions without literature references: 170

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/WP176 has an metabolite not linked to an interaction: RNS
https://identifiers.org/wikipathways/WP176 has an metabolite not linked to an interaction: HNO2
https://identifiers.org/wikipathways/WP176 has an metabolite not linked to an interaction: ONOO/ONOOH
https://identifiers.org/wikipathways/WP176 has an metabolite not linked to an interaction: NO2
https://identifiers.org/wikipathways/WP176 has an metabolite not linked to an interaction: FMN
https://identifiers.org/wikipathways/WP176 has an metabolite not linked to an interaction: O3
https://identifiers.org/wikipathways/WP176 has an metabolite not linked to an interaction: Riboflavin

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

Unexpected metabolic conversion

Unexpected interactions, not from metabolite to metabolite and not from RNA to RNA: 1

https://identifiers.org/wikipathways/WP176 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/c17af

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

Possible MIM translocation

Interactions between identical nodes: 8

http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/dba81 “Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174)
http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/dba81 “Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174)
http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/dba81 “Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174)
http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/dba81 “Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174)
http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/be290 “Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174)
http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/be290 “Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174)
http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/be290 “Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(I)alamin” (https://identifiers.org/hmdb/HMDB0002174)
http://classic.wikipathways.org/instance/WP176_r134132 http://rdf.wikipathways.org/Pathway/WP176_r134132/WP/Interaction/be290 “Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174) and Cob(II)alamin” (https://identifiers.org/hmdb/HMDB0002174)

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/WP176_r134132 has: FGAR (CHEBI:18272) with InChIKeys: VDXLUNDMVKSKHO-ZRTZXPPTSA-N, VDXLUNDMVKSKHO-XVFCMESISA-N
http://classic.wikipathways.org/instance/WP176_r134132 has: O3 (CHEBI:25812) with InChIKeys: CBENFWSGALASAD-UHFFFAOYSA-N, XQOAKYYZMDCSIA-UHFFFAOYSA-N

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