imd-pathway-curation

WikiPathways WP4507

• WikiPathways: WP4507
• Scholia: WP4507
• WPRDF file: wp/Human/WP4507.ttl
• GPMLRDF file: wp/gpml/Human/WP4507.ttl
• SBML file: sbml/WP4507.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: 4
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 3 tests OK!
• GeneralTests
  • curationAndHypothetical: .. all OK!
  • curationAndNeedsWork: .. all OK!
  • curationAndReactome: .. all OK!
  • dataNodeWithoutGraphId: .. all OK!
  • duplicateTitles: .. all OK!
  • emptyLabelOfNodeWithIdentifier: .. all OK!
  • groupsHaveDetail: .. all OK!
  • noTags: .. all OK!
  • nullDataSources: .. all OK!
  • titlesShortEnough: .. all OK!
  • undefinedDataSources: .. all OK!
  • undefinedIdentifier: .. all OK!
  • weirdCharacterTitles: .x we found 1 problem(s):
    • Titles with unexpected characters (only allow alphanumerics and spaces):1
• 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: .. all OK!
  • omimIdentifiers: .x we found 1 problem(s):
    • OMIM links should start with “https://omim.org/entry/”: 4
• 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: all 15 tests 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: 4

http://www.wikipathways.org/instance/WP4507_r119314 http://rdf.wikipathways.org/Pathway/WP4507_r119314/DataNode/b0197 (MOCS1AB)
http://www.wikipathways.org/instance/WP4507_r119314 http://rdf.wikipathways.org/Pathway/WP4507_r119314/DataNode/a578f (R-H)
http://www.wikipathways.org/instance/WP4507_r119314 http://rdf.wikipathways.org/Pathway/WP4507_r119314/DataNode/b0eac (R-NH)
http://www.wikipathways.org/instance/WP4507_r119314 http://rdf.wikipathways.org/Pathway/WP4507_r119314/DataNode/cf606 (R=N-OH)

GeneralTests.weirdCharacterTitles

Titles with unexpected characters (only allow alphanumerics and spaces):1

http://www.wikipathways.org/instance/WP4507_r119314 'Molybdenum cofactor (Moco) biosynthesis' has 2 weird characters

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 1

https://identifiers.org/wikipathways/WP4507 has an metabolite not linked to an interaction: R-OH

IEMPathwayTests.omimIdentifiers

OMIM links should start with “https://omim.org/entry/”: 4

https://identifiers.org/wikipathways/WP4507 "MoCD type A" has unexpected OMIM href: https://omim.org/603707
https://identifiers.org/wikipathways/WP4507 "MoCD type C" has unexpected OMIM href: https://omim.org/603930
https://identifiers.org/wikipathways/WP4507 "MoCD type B" has unexpected OMIM href: https://omim.org/603708
https://identifiers.org/wikipathways/WP4507 "Sulphite oxidase  deficiency" has unexpected OMIM href: https://omim.org/272300