imd-pathway-curation

WikiPathways WP4686

• WikiPathways: WP4686
• Scholia: WP4686
• WPRDF file: wp/Human/WP4686.ttl
• GPMLRDF file: wp/gpml/Human/WP4686.ttl
• SBML file: sbml/WP4686.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: 3
  • 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: 43
  • 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: 1
  • 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: .. 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: 3
  • 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: 3

http://www.wikipathways.org/instance/WP4686_r122622 http://rdf.wikipathways.org/Pathway/WP4686_r122622/DataNode/b04fe (C5-Hydroxyacylcarnitine)
http://www.wikipathways.org/instance/WP4686_r122622 http://rdf.wikipathways.org/Pathway/WP4686_r122622/DataNode/d06d7 (C5-Hydroxyacylcarnitine)
http://www.wikipathways.org/instance/WP4686_r122622 http://rdf.wikipathways.org/Pathway/WP4686_r122622/DataNode/f2471 (C5-Hydroxyacylcarnitine)

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 43

https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Propionylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Hydroxyisocaproate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Isovaleric acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: R,S-Methylcitrate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Aminoisobutyric acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Methylbutyrylglycine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Methylglutarylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Isovalerylglycine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Propionylglycine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Tiglylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Tiglycarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Hydroxypropionate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Methyl-3-hydroxy-butyrylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Methyl-3-hydroxybutyryl-carnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Malonylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Methylglutaconate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Hydroxybutyrate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Methylbutyrylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Isovaleryglucuronide
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Isobutyrylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Hydroxy-3-methylvalerate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Methylmalonylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Methylglutarate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Methylmalonic acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 4-Hydroxyisovaleric acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Hydroxyisovalerate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Hydroxyhexanoyl-carnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Malonic acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Hydroxypropionic acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: S-2-carboxypropylcysteamine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Methylcrotonylglycine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: alloisoleucine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Ethylhydracrylic acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Hydroxy-3-methylglutarate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Methyl-3-hydroxybutyrate
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Ethylmalonic acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Beta-alanine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Isovalerylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Methylacetoacetic acid
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: Isobutyrylglycine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 3-Hydroxyisobutyrylcarnitine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: S-2-carboxypropylcysteine
https://identifiers.org/wikipathways/WP4686 has an metabolite not linked to an interaction: 2-Hydroxyisovalerate

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 1

http://www.wikipathways.org/instance/WP4686_r122622 "Hydratase" with graphId f832a

WikidataTests.chebiWithoutMapping

ChEBI identifiers without Wikidata mappings: 3

https://identifiers.org/chebi/CHEBI:133513 (3-Methylglutaconate) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4686_r122622 ; 
https://identifiers.org/chebi/CHEBI:133577 (2-Hydroxyisocaproate) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4686_r122622 ; 
https://identifiers.org/chebi/CHEBI:184285 (S-2-carboxypropylcysteamine) does not have a Wikidata mapping in http://www.wikipathways.org/instance/WP4686_r122622 ;