imd-pathway-curation

WikiPathways WP5178

• WikiPathways: WP5178
• Scholia: WP5178
• WPRDF file: wp/Human/WP5178.ttl
• GPMLRDF file: wp/gpml/Human/WP5178.ttl
• SBML file: sbml/WP5178.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: 3
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .. all OK!
  • metabolicConversionIdentifiersCommon: .x we found 1 problem(s):
    • Unexpected data source for the metabolic conversion: 1
  • 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: 23
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 10
  • 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: all 15 tests OK!

Summary

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

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 3

https://identifiers.org/wikipathways/WP5178 has an metabolite not linked to an interaction: Dihydroxyacetone-P
https://identifiers.org/wikipathways/WP5178 has an metabolite not linked to an interaction: Frc-1-P
https://identifiers.org/wikipathways/WP5178 has an metabolite not linked to an interaction: Sucrose

IEMPathwayTests.metabolicConversionIdentifiersCommon

Unexpected data source for the metabolic conversion: 1

https://identifiers.org/wikipathways/WP5178 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/id4ba3a08f Reactome R-HSA-5652195.5

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 23

http://www.wikipathways.org/instance/WP5178_r124895 "Glucose phosphate isomerase
deficiency" with graphId b9270
http://www.wikipathways.org/instance/WP5178_r124895 "" with graphId d7103
http://www.wikipathways.org/instance/WP5178_r124895 "conversion" with graphId f7775
http://www.wikipathways.org/instance/WP5178_r124895 "Catalysis" with graphId a7fac
http://www.wikipathways.org/instance/WP5178_r124895 "" with graphId a6339
http://www.wikipathways.org/instance/WP5178_r124895 "Fructose-1,6-biphosphatase
deficiency" with graphId f3427
http://www.wikipathways.org/instance/WP5178_r124895 "HMSNR" with graphId b8b74
http://www.wikipathways.org/instance/WP5178_r124895 "Aldolase B
deficiency" with graphId b7faa
http://www.wikipathways.org/instance/WP5178_r124895 "Phosphoglucomutase 1
deficiency" with graphId bd5eb
http://www.wikipathways.org/instance/WP5178_r124895 "Fanconi-Bickel syndrome" with graphId b262a
http://www.wikipathways.org/instance/WP5178_r124895 "Hexokinase deficiency" with graphId b592e
http://www.wikipathways.org/instance/WP5178_r124895 "Triosephosphate isomerase
deficiency" with graphId c3189
http://www.wikipathways.org/instance/WP5178_r124895 "Glucose-6-phosphatase
deficiency" with graphId b1b23
http://www.wikipathways.org/instance/WP5178_r124895 "NEDVIBA" with graphId e6b46
http://www.wikipathways.org/instance/WP5178_r124895 "connection to
disease" with graphId a96b3
http://www.wikipathways.org/instance/WP5178_r124895 "" with graphId a09d4
http://www.wikipathways.org/instance/WP5178_r124895 "Intestinal glucose-galactose
malabsorption" with graphId aaf8e
http://www.wikipathways.org/instance/WP5178_r124895 "Sorbitol dehydrogenase deficiency
with peripheral neuropathy" with graphId ef2de
http://www.wikipathways.org/instance/WP5178_r124895 "alternative conversion or conversion
in alternative entry" with graphId db4d3
http://www.wikipathways.org/instance/WP5178_r124895 "" with graphId f708f
http://www.wikipathways.org/instance/WP5178_r124895 "Retinitis pigmentosa 79" with graphId ffa6b
http://www.wikipathways.org/instance/WP5178_r124895 "Glycerate kinase
deficiency" with graphId b83c3
http://www.wikipathways.org/instance/WP5178_r124895 "Ketohexokinase
deficiency" with graphId e55be

InteractionTests.possibleTranslocations

Interactions between identical nodes: 10

http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/id92a3d684 "Fructose" (https://identifiers.org/chebi/CHEBI:28645) and 
Fructose" (https://identifiers.org/chebi/CHEBI:28645)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/id131d5722 "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and 
Glucose" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/id131d5722 "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and 
Glc" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/id131d5722 "Glc" (https://identifiers.org/chebi/CHEBI:17234) and 
Glucose" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/id131d5722 "Glc" (https://identifiers.org/chebi/CHEBI:17234) and 
Glc" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/idb199c6df "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and 
Glucose" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/idb199c6df "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and 
Glc" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/idb199c6df "Glc" (https://identifiers.org/chebi/CHEBI:17234) and 
Glucose" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/idb199c6df "Glc" (https://identifiers.org/chebi/CHEBI:17234) and 
Glc" (https://identifiers.org/chebi/CHEBI:17234)
http://www.wikipathways.org/instance/WP5178_r124895 http://rdf.wikipathways.org/Pathway/WP5178_r124895/WP/Interaction/id20c278e1 "Sorbitol" (https://identifiers.org/chebi/CHEBI:30911) and 
Sorbitol" (https://identifiers.org/chebi/CHEBI:30911)

More details at https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations