imd-pathway-curation

WikiPathways WP4259

• WikiPathways: WP4259
• Scholia: WP4259
• WPRDF file: wp/Human/WP4259.ttl
• GPMLRDF file: wp/gpml/Human/WP4259.ttl
• SBML file: sbml/WP4259.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 4 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 1
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 3 tests OK!
• GeneralTests: all 13 tests OK!
• HMDBMetabolitesTests: all 1 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: .x we found 1 problem(s):
    • Likely diseases without identifiers: 1
  • omimIdentifiers: .x we found 1 problem(s):
    • OMIM links should start with “https://omim.org/entry/”: 12
• InteractionTests: all 8 tests OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 7 tests OK!
• PathwayTests: all 6 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 4 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests
  • keggWithoutMapping: .. all OK!
  • pubchemCIDWithoutMapping: .. all OK!
  • hmdbWithoutMapping: .. all OK!
  • casWithoutMapping: .. all OK!
  • wikDataTypo: .. all OK!
  • duplicateWikidataMappings: .. all OK!
  • wikidataIdentifiersWrong: .. all OK!
  • chemspiderCIDWithoutMapping: .. all OK!
  • lipidMapsWithoutMapping: .. all OK!
  • kNApSAcKWithoutMapping: .. all OK!
  • replaceWikipedia: .. all OK!
  • chebiWithoutMapping_Reactome: .. all OK!
  • chebiWithoutMapping: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 1
  • hmdbWithoutMapping: .x we found 1 problem(s):
    • InChIKey identifiers without Wikidata mappings: 1
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 22
• Number of tests: 110
• Number of assertions: 220
• Number of fails: 6

Fails

DataNodesTests.dataNodesWithoutIdentifier

The following DataNodes have no identifier: 1

http://www.wikipathways.org/instance/WP4259_r124234 http://rdf.wikipathways.org/Pathway/WP4259_r124234/DataNode/bb389 (p-amino-benzoyl-polyglutamate)

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 1

https://identifiers.org/wikipathways/WP4259 has an metabolite not linked to an interaction: CO2

IEMPathwayTests.diseasesHaveIdentifiers

Likely diseases without identifiers: 1

https://identifiers.org/wikipathways/WP4259 "FTHFI" does not have an identifier

IEMPathwayTests.omimIdentifiers

OMIM links should start with “https://omim.org/entry/”: 12

https://identifiers.org/wikipathways/WP4259 "QDPRD" has unexpected OMIM href: https://www.omim.org/261630
https://identifiers.org/wikipathways/WP4259 "Folate Receptor Alpha Deficiency" has unexpected OMIM href: https://www.omim.org/613068
https://identifiers.org/wikipathways/WP4259 "Heriditary Folate  Malabsorption" has unexpected OMIM href: https://www.omim.org/229050
https://identifiers.org/wikipathways/WP4259 "DHFR deficiency" has unexpected OMIM href: https://www.omim.org/613839
https://identifiers.org/wikipathways/WP4259 "NEDCASB" has unexpected OMIM href: https://www.omim.org/619121
https://identifiers.org/wikipathways/WP4259 "Reduced folate  carrier deficiency" has unexpected OMIM href: https://www.omim.org/601775
https://identifiers.org/wikipathways/WP4259 "MTHFR deficiency" has unexpected OMIM href: https://www.omim.org/236250
https://identifiers.org/wikipathways/WP4259 "ATIC  Deficiency" has unexpected OMIM href: https://www.omim.org/608688
https://identifiers.org/wikipathways/WP4259 "MTHFD1 deficiency" has unexpected OMIM href: https://www.omim.org/172460
https://identifiers.org/wikipathways/WP4259 "MTHFS deficiency" has unexpected OMIM href: https://www.omim.org/618367
https://identifiers.org/wikipathways/WP4259 "FIGLU-Uria" has unexpected OMIM href: https://www.omim.org/229100
https://identifiers.org/wikipathways/WP4259 "FTHFDH" has unexpected OMIM href: https://www.omim.org/613584

WikidataTests.chebiWithoutMapping

ChEBI identifiers without Wikidata mappings: 1

https://identifiers.org/chebi/CHEBI:35286 (iminium ion) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4259_r124234 ; 

WikidataTests.hmdbWithoutMapping

InChIKey identifiers without Wikidata mappings: 1

AIZSNLNTIFEHJG-KIYNQFGBSA-N	qDHF