imd-pathway-curation

WikiPathways WP4521

• WikiPathways: WP4521
• Scholia: WP4521
• WPRDF file: wp/Human/WP4521.ttl
• GPMLRDF file: wp/gpml/Human/WP4521.ttl
• SBML file: sbml/WP4521.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: 6
  • 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: .. all OK!
  • metabolicConversionIdentifiersCommon: .. all OK!
  • diseasesHaveIdentifiers: .. all OK!
  • omimIdentifiers: .x we found 1 problem(s):
    • OMIM links should start with “https://omim.org/entry/”: 1
• 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: 22
  • 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

DataNodesTests.dataNodesWithoutIdentifier

The following DataNodes have no identifier: 6

http://www.wikipathways.org/instance/WP4521_r124518 http://rdf.wikipathways.org/Pathway/WP4521_r124518/DataNode/c23cb (Gal2Man3-GlcNac4-Prot)
http://www.wikipathways.org/instance/WP4521_r124518 http://rdf.wikipathways.org/Pathway/WP4521_r124518/DataNode/ab946 (Glc3Man9-GlcNac2-PP-Dol)
http://www.wikipathways.org/instance/WP4521_r124518 http://rdf.wikipathways.org/Pathway/WP4521_r124518/DataNode/bccaf (Man4GIcNAc2-PP-Dol)
http://www.wikipathways.org/instance/WP4521_r124518 http://rdf.wikipathways.org/Pathway/WP4521_r124518/DataNode/b8f00 (Man6-GlcNac2-PP-Dol)
http://www.wikipathways.org/instance/WP4521_r124518 http://rdf.wikipathways.org/Pathway/WP4521_r124518/DataNode/ed4a0 (Sia2Gal2Man3-GlcNac4-Prot)
http://www.wikipathways.org/instance/WP4521_r124518 http://rdf.wikipathways.org/Pathway/WP4521_r124518/DataNode/d5aa3 (SiaGalMan3-GlcNac3-Prot)

IEMPathwayTests.omimIdentifiers

OMIM links should start with “https://omim.org/entry/”: 1

https://identifiers.org/wikipathways/WP4521 "Mannosyltransferase- 2-deficiency-CDG-Ii" has unexpected OMIM href: https://omim.org/entry607906

WikidataTests.chebiWithoutMapping

ChEBI identifiers without Wikidata mappings: 22

https://identifiers.org/chebi/CHEBI:132510 (Man2GIcNAc2PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132511 (Man3GIcNAc2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132515 (Man5GIcNAc2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132516 (Man5-GlcNac2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132517 (Man7-GlcNac2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132519 (Man8-GlcNac2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132520 (Man9-GlcNac2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132521 (GlcMan9-GlcNac2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132522 (Glc2Man9-GlcNac2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:132537 (Glc3Man9-GlcNac2-Prot) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:57269 (GlcNAc2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:57683 (Dolichol phosphate) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:57683 (Dolichyl phosphate) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:57683 (dolichyl  phosphate) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:58211 (Dol-P-Man) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:58211 (dolichyl  beta-D-mannosyl  phosphate) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:58427 (GlcNAc-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:58472 (ManGlcNAc2-PP-Dol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:59082 (Glc2Man9-GlcNac2-Prot) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:60615 (Man3-GlcNac3-Prot) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:60615 (Man3-GlcNac4-Prot) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ; 
https://identifiers.org/chebi/CHEBI:67132 (Polyprenol) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4521_r124518 ;