imd-pathway-curation

WikiPathways WP5169

• WikiPathways: WP5169
• Scholia: WP5169
• WPRDF file: wp/Human/WP5169.ttl
• GPMLRDF file: wp/gpml/Human/WP5169.ttl
• SBML file: sbml/WP5169.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 4 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 4 tests 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: 5
  • metabolicConversions: .. all OK!
  • 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: .x we found 1 problem(s):
    • Interactions found that involve Labels: 16
  • possibleTranslocations: .. all OK!
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all 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: .x we found 1 problem(s):
    • HMDB identifiers without Wikidata mappings: 5
  • 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: .. all OK!
  • retiredIdentifiers: .. all OK!

Summary

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

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 5

https://identifiers.org/wikipathways/WP5169 has an metabolite not linked to an interaction: Porphobilinogen
https://identifiers.org/wikipathways/WP5169 has an metabolite not linked to an interaction: Uroporphyrinogen III
https://identifiers.org/wikipathways/WP5169 has an metabolite not linked to an interaction: Protoporphyrinogen IX
https://identifiers.org/wikipathways/WP5169 has an metabolite not linked to an interaction: protoporphyrin IX
https://identifiers.org/wikipathways/WP5169 has an metabolite not linked to an interaction: hydroxymethylbilane

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 16

http://www.wikipathways.org/instance/WP5169_r122351 "Hepatoerythropoietic porphyria" with graphId c2a46
http://www.wikipathways.org/instance/WP5169_r122351 "Porphyria cutanea tarda

" with graphId c5f80
http://www.wikipathways.org/instance/WP5169_r122351 "X-linked protophyria" with graphId d6c81
http://www.wikipathways.org/instance/WP5169_r122351 "Erythropoietic protoporphyria
" with graphId b9cb4
http://www.wikipathways.org/instance/WP5169_r122351 "Lead poisoning" with graphId e03fb
http://www.wikipathways.org/instance/WP5169_r122351 "Lead poisoning" with graphId c929d
http://www.wikipathways.org/instance/WP5169_r122351 "X-linked sideroblastic anemia" with graphId b0352
http://www.wikipathways.org/instance/WP5169_r122351 "Harderoporphyria" with graphId b1fc4
http://www.wikipathways.org/instance/WP5169_r122351 "Lead poisoning" with graphId d9fe0
http://www.wikipathways.org/instance/WP5169_r122351 "Congenital erythropoietic porphyria" with graphId eeff0
http://www.wikipathways.org/instance/WP5169_r122351 "Acute intermittent porphyria" with graphId f3658
http://www.wikipathways.org/instance/WP5169_r122351 "Hypertyrosinemia type I
" with graphId a2a0b
http://www.wikipathways.org/instance/WP5169_r122351 "Hereditary coproporphyria
" with graphId d6d5e
http://www.wikipathways.org/instance/WP5169_r122351 "Variegate porphyria" with graphId c23b9
http://www.wikipathways.org/instance/WP5169_r122351 "5-aminolevulinate dehydratase 
porphyria
" with graphId ee6da
http://www.wikipathways.org/instance/WP5169_r122351 "Negative feedback" with graphId cd87e

WikidataTests.hmdbWithoutMapping

HMDB identifiers without Wikidata mappings: 5

https://identifiers.org/hmdb/HMDB0000743 (Hexacarboxylporphyrin I) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5169_r122351 ; 
https://identifiers.org/hmdb/HMDB0000789 (Pentacarboxylporphyrin I) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5169_r122351 ; 
https://identifiers.org/hmdb/HMDB0001952 (Hexacarboxylporphyrin III) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5169_r122351 ; 
https://identifiers.org/hmdb/HMDB0001956 (Heptacarboxylporphyrin III) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5169_r122351 ; 
https://identifiers.org/hmdb/HMDB0001957 (Pentacarboxyl porphyrinogen III) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP5169_r122351 ;