imd-pathway-curation

WikiPathways WP4504

• WikiPathways: WP4504
• Scholia: WP4504
• WPRDF file: wp/Human/WP4504.ttl
• GPMLRDF file: wp/gpml/Human/WP4504.ttl
• SBML file: sbml/WP4504.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: 2
  • 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: 3
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .x we found 1 problem(s):
    • Unexpected data source for catalysts: 2
  • 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: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 1
  • hmdbWithoutMapping: .. all OK!
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 22
• Number of tests: 110
• Number of assertions: 220
• Number of fails: 4

Fails

DataNodesTests.dataNodesWithoutIdentifier

The following DataNodes have no identifier: 2

http://www.wikipathways.org/instance/WP4504_r119316 http://rdf.wikipathways.org/Pathway/WP4504_r119316/DataNode/ed273 (ST)
http://www.wikipathways.org/instance/WP4504_r119316 http://rdf.wikipathways.org/Pathway/WP4504_r119316/DataNode/f21ac (Transsulfuration pathway)

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 3

https://identifiers.org/wikipathways/WP4504 has an metabolite not linked to an interaction: alpha-KB
https://identifiers.org/wikipathways/WP4504 has an metabolite not linked to an interaction: NH4+
https://identifiers.org/wikipathways/WP4504 has an metabolite not linked to an interaction: Glu

IEMPathwayTests.catalystsWithCommonDataSource

Unexpected data source for catalysts: 2

https://identifiers.org/wikipathways/WP4504 BRENDA
https://identifiers.org/wikipathways/WP4504 BRENDA

WikidataTests.chebiWithoutMapping

ChEBI identifiers without Wikidata mappings: 1

https://identifiers.org/chebi/CHEBI:30605 (RSSH) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4504_r119316 ;