wikipathways-collection

WikiPathways WP5224

• WikiPathways: WP5224 (classic)
• Species: Homo sapiens
• Scholia: WP5224

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 8
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 31
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 5 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests 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: 11
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 15
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 7
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 15 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 8 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• UnicodeTests
  • water: .x we found 1 problem(s):
    • Metabolite can use H₂O instead of H2O: 1
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 21
• Number of tests: 122
• Number of assertions: 245
• Number of fails: 6

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 8

• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/caa23 ()
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d572f (Alzheimer disease)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d50b2 (Filament-forming complex)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/be250 (Protein)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d6f49 (Protein phosphatase 1)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/c5527 (SCF-like ECS E3 ligase complex)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/bd85f (SCF-like ECS E3 ligase complex)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/f5fc7 (UBA3-NAE1 E1 complex)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

Datanodes of unknown type

The following DataNodes have Unknown @Type: 31

• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/caa23 ()
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/e5489 (Actin cytoskeleton reorganization)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d572f (Alzheimer disease)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/e62c3 (Aminopeptidase activity)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/f44f1 (Clathrin-dependent endocytosis)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/dcfc2 (Cysteine protease)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d3fd3 (D-2-HYDROXYGLUTARIC ACIDURIA 1; D2HGA1)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/e0313 (Histone deacetylase activity)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/cfa86 (MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 22; MC1DN22)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/c45a6 (Melanosome transport)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/eac7c (Mitotic spindle assembly)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/a50cf (Protein ubiquitination)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/f1e5d (Protein-serine-threonine kinases)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/f55a2 (Protein-tyrosine-phosphatase)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/b4df6 (SPASTIC PARAPLEGIA 30, AUTOSOMAL DOMINANT; SPG30)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/bb9d2 (Sterol metabolic process)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d373c (Transferrin receptor)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d3e4e (Transferrin receptor)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/dcc9a (Tubulin)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/b0fff (actin)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/b65bc (bleeding )
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/ed80b (bone remodeling)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/e492f (erythroblast)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d2e66 (extracellular matrix)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/f8f59 (intercellular bridge)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/efc7b (melanosome)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/e969c (microtubule)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/f4048 (oxidative stress)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/e21ea (positive Regulation of smooth muscle cell proliferation)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/d07b7 (sensory perception of sound )
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/DataNode/edfbb (vesicle transport along microtubule)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/unknownTypes

Interactions with Labels

Interactions found that involve Labels: 11

• http://classic.wikipathways.org/instance/WP5224_r137401 “Exact function unknown” with graphId e715f
• http://classic.wikipathways.org/instance/WP5224_r137401 “Exact function unknown” with graphId f125e
• http://classic.wikipathways.org/instance/WP5224_r137401 “Exact function unknown” with graphId e29c3
• http://classic.wikipathways.org/instance/WP5224_r137401 “Cold temperatures and cooling agents” with graphId a4063
• http://classic.wikipathways.org/instance/WP5224_r137401 “Exact function unknown” with graphId ac1ba
• http://classic.wikipathways.org/instance/WP5224_r137401 “Exact function unknown” with graphId f4672
• http://classic.wikipathways.org/instance/WP5224_r137401 “Changing environmental conditions “ with graphId a2068
• http://classic.wikipathways.org/instance/WP5224_r137401 “Sensation of cold” with graphId c57cf
• http://classic.wikipathways.org/instance/WP5224_r137401 “Exact function unknown” with graphId bc803
• http://classic.wikipathways.org/instance/WP5224_r137401 “Exact function unknown” with graphId a9780
• http://classic.wikipathways.org/instance/WP5224_r137401 “Depolarization” with graphId bbd0d

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/interactionsWithLabels

Interactions with unconnected points

Interactions with unconnected points: 15

• http://classic.wikipathways.org/instance/WP5224_r137401

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/UnconnectedPoints

Possible MIM translocation

Interactions between identical nodes: 7

• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/WP/Interaction/id5570c82b “H2O” (https://identifiers.org/chebi/CHEBI:15377) and H2O” (https://identifiers.org/chebi/CHEBI:15377)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/WP/Interaction/da3f7 “Galactosylceramide” (https://identifiers.org/chebi/CHEBI:18390) and Galactosylceramide” (https://identifiers.org/chebi/CHEBI:18390)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/WP/Interaction/ida1787ddf “cholesterol” (https://identifiers.org/chebi/CHEBI:16113) and cholesterol” (https://identifiers.org/chebi/CHEBI:16113)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/WP/Interaction/id382409e5 “Phosphatidylserine” (https://identifiers.org/chebi/CHEBI:57262) and Phosphatidylserine” (https://identifiers.org/chebi/CHEBI:57262)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/WP/Interaction/idf374a72a “Ca2+” (https://identifiers.org/chebi/CHEBI:29108) and Ca2+” (https://identifiers.org/chebi/CHEBI:29108)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/WP/Interaction/d0ba4 “Phosphatidylcholine” (https://identifiers.org/chebi/CHEBI:57643) and Phosphatidylcholine” (https://identifiers.org/chebi/CHEBI:57643)
• http://classic.wikipathways.org/instance/WP5224_r137401 http://rdf.wikipathways.org/Pathway/WP5224_r137401/WP/Interaction/id7f44203f “Na+” (https://identifiers.org/chebi/CHEBI:29101) and Na+” (https://identifiers.org/chebi/CHEBI:29101)

More details at https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations

Water chemical formula can use Unicode

Metabolite can use H₂O instead of H2O: 1

* [http://classic.wikipathways.org/instance/WP5224_r137401](http://classic.wikipathways.org/instance/WP5224_r137401)

More details at https://www.wikipathways.org/WikiPathwaysCurator/UnicodeTests/water