imd-pathway-curation

WikiPathways WP5064

• WikiPathways: WP5064
• Scholia: WP5064
• WPRDF file: wp/Human/WP5064.ttl
• GPMLRDF file: wp/gpml/Human/WP5064.ttl
• SBML file: sbml/WP5064.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: 8
  • 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: .. all OK!
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .x we found 1 problem(s):
    • Unexpected data source for catalysts: 6
  • 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: 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: .. all OK!
  • hmdbWithoutMapping: .x we found 1 problem(s):
    • InChIKey identifiers without Wikidata mappings: 16
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 22
• Number of tests: 110
• Number of assertions: 220
• Number of fails: 3

Fails

DataNodesTests.dataNodesWithoutIdentifier

The following DataNodes have no identifier: 8

http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/b52a9 (+1O2)
http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/d4bc2 (+3O2)
http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/c699f (5alpha-specific
DDA synthase)
http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/e375f (LO*)
http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/dd89e (LOH)
http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/c66f0 (LOO*)
http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/f62ad (LOO*)
http://www.wikipathways.org/instance/WP5064_r120384 http://rdf.wikipathways.org/Pathway/WP5064_r120384/DataNode/bc5e8 (LOOH)

IEMPathwayTests.catalystsWithCommonDataSource

Unexpected data source for catalysts: 6

https://identifiers.org/wikipathways/WP5064 HGNC
https://identifiers.org/wikipathways/WP5064 HGNC
https://identifiers.org/wikipathways/WP5064 HGNC
https://identifiers.org/wikipathways/WP5064 HGNC
https://identifiers.org/wikipathways/WP5064 HGNC
https://identifiers.org/wikipathways/WP5064 HGNC

WikidataTests.hmdbWithoutMapping

InChIKey identifiers without Wikidata mappings: 16

AXBXXYALPXTOOI-UBKHJBOVSA-N	3b-Hydroxy-7-oxochol-5-en-24-oyl-glycine
BMRAURDLHOPSBE-FRMRTHFDSA-N	3b,7b-Dihydroxychol-5-en-24-oyl-glycine
BZALPCSTIFZGTP-YBYDULIXSA-N	3b,7b,24R-Trihydroxycholest-5-en-(25R)26-oyl-CoA
GYJSAWZGYQXRBS-WMYDBBFWSA-N	3b,7b-Dihydroxycholest-5-en-(25R)26-oic acid
HEPNPBUPTRNGJT-ILFWFKRZSA-N	3b-Hydroxy-7-oxochol-5-en-24-oyl-CoA
KJIGLXGIVLBXCF-UOQFGJKXSA-N	7b-Peroxycholesterol
LMWUOMGULHFSQR-HDEGCWFHSA-N	3b,5a,6b-Trihydroxycholestan-(25R)26-oic acid
PFYSRSDOSXYIFG-JKYVJSSTSA-N	Cholestane-3b,5a,6b,(25R)26-tetrol
PJJHUKDTGITXML-MFOUGJSISA-N	3b,5a,6b,24R-Tetrahydroxycholestan-(25R)26-oyl-CoA
PRYIJAGAEJZDBO-XXGHXXDPSA-N	5,6-Epoxycholesterol
PVXZQUUYXFMXMF-ABSIFXOISA-N	3b,5a,6b-Trihydroxycholan-24-oyl-glycine
PXHCARRJGFGPAC-SZQOYVLDSA-N	3b,7b-Dihydroxychol-5-en-24-oic acid
SJZZRXMQSAXCFD-FRAMIZMOSA-N	3b,5a-DiH-cholestan-6-one
UOHZUNSDJHLARD-JLLVOJIKSA-N	3b,24R-Dihydroxy-7-oxocholest-5-en-(25R)26-oyl-CoA
WRWBXZATSFAUGF-UJKOPXFNSA-N	3b,5a,6b-Trihydroxycholan-24-oyl-CoA
XRRIYAPQOCXHCP-NRNJIOKESA-N	3b,7b-Dihydroxychol-5-en-24-oyl-CoA