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: 18
  • 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 4 tests OK!
• GeneralTests: all 13 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
  • 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 14 tests OK!
• OudatedDataSourcesTests: all 8 tests OK!
• PathwayTests: all 7 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 20
• Number of tests: 99
• Number of assertions: 200
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 18

http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d572f (Alzheimer disease)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/b84e5 (CENP-A nucleosome complex)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/b018d (COP9 signalosome)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/e5ce8 (COP9 signalosome variant 1)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d3fd3 (D-2-HYDROXYGLUTARIC ACIDURIA 1; D2HGA1)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d50b2 (Filament-forming complex)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/c8e1d (HBO1-5.1 histone
acetyltransferase complex)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/cfa86 (MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 22; MC1DN22)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/b67fe (MOZ1 histone
acetyltransferase complex)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/fec7a (Mitochondrial respiratory chain complex I)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/caa23 (NEUROPATHOLOGY)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/be250 (Protein)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d6f49 (Protein phosphatase 1)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/c5527 (SCF-like ECS E3
ligase complex)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/bd85f (SCF-like ECS E3 ligase complex)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/b4df6 (SPASTIC PARAPLEGIA 30, AUTOSOMAL DOMINANT; SPG30)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/f5fc7 (UBA3-NAE1 E1 complex)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d2cab (collagen VI)

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

DataNodesTests.unknownTypes

The following DataNodes have Unknown @Type: 31

http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d572f (Alzheimer disease)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d3fd3 (D-2-HYDROXYGLUTARIC ACIDURIA 1; D2HGA1)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/cfa86 (MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 22; MC1DN22)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/caa23 (NEUROPATHOLOGY)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/f55a2 (Protein-tyrosine-phosphatase)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/b4df6 (SPASTIC PARAPLEGIA 30, AUTOSOMAL DOMINANT; SPG30)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d373c (Transferrin receptor)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d3e4e (Transferrin receptor)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/b0fff (actin)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/e5489 (actin cytoskeleton reorganization)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/e62c3 (aminopeptidase activity)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/b65bc (bleeding )
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/ed80b (bone remodeling)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/f44f1 (clathrin-dependent endocytosis)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/dcfc2 (cysteine protease)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/e492f (erythroblast)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d2e66 (extracellular matrix)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/e0313 (histone deacetylase activity)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/f8f59 (intercellular bridge)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/efc7b (melanosome)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/c45a6 (melanosome transport)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/e969c (microtubule)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/eac7c (mitotic spindle assembly)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/f4048 (oxidative stress)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/e21ea (positive regulation of smooth muscle cell proliferation)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/a50cf (protein ubiquitination)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/f1e5d (protein-serine-threonine kinases)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/d07b7 (sensory perception of sound )
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/bb9d2 (sterol metabolic process)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/dcc9a (tubulin)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/DataNode/edfbb (vesicle transport
along microtubule)

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 11

http://classic.wikipathways.org/instance/WP5224_r127064 "Sensation of cold" with graphId c57cf
http://classic.wikipathways.org/instance/WP5224_r127064 "Depolarization" with graphId bbd0d
http://classic.wikipathways.org/instance/WP5224_r127064 "Changing environmental conditions " with graphId a2068
http://classic.wikipathways.org/instance/WP5224_r127064 "Cold temperatures and cooling agents" with graphId a4063
http://classic.wikipathways.org/instance/WP5224_r127064 "Exact function unknown" with graphId e715f
http://classic.wikipathways.org/instance/WP5224_r127064 "Exact function unknown" with graphId f4672
http://classic.wikipathways.org/instance/WP5224_r127064 "Exact function unknown" with graphId a9780
http://classic.wikipathways.org/instance/WP5224_r127064 "Exact function unknown" with graphId bc803
http://classic.wikipathways.org/instance/WP5224_r127064 "Exact function unknown" with graphId ac1ba
http://classic.wikipathways.org/instance/WP5224_r127064 "Exact function unknown" with graphId f125e
http://classic.wikipathways.org/instance/WP5224_r127064 "Exact function unknown" with graphId e29c3

Possible MIM translocation

Interactions between identical nodes: 7

http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/WP/Interaction/id5570c82b "H2O" (https://identifiers.org/chebi/CHEBI:15377) and 
H2O" (https://identifiers.org/chebi/CHEBI:15377)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/WP/Interaction/ida1787ddf "cholesterol" (https://identifiers.org/chebi/CHEBI:16113) and 
cholesterol" (https://identifiers.org/chebi/CHEBI:16113)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/WP/Interaction/id382409e5 "phosphatidylserine" (https://identifiers.org/chebi/CHEBI:57262) and 
phosphatidylserine" (https://identifiers.org/chebi/CHEBI:57262)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/WP/Interaction/d0ba4 "phosphatidylcholine" (https://identifiers.org/chebi/CHEBI:57643) and 
phosphatidylcholine" (https://identifiers.org/chebi/CHEBI:57643)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/WP/Interaction/da3f7 "galactosylceramide" (https://identifiers.org/chebi/CHEBI:18390) and 
galactosylceramide" (https://identifiers.org/chebi/CHEBI:18390)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/WP/Interaction/id7f44203f "Na+" (https://identifiers.org/chebi/CHEBI:29101) and 
Na+" (https://identifiers.org/chebi/CHEBI:29101)
http://classic.wikipathways.org/instance/WP5224_r127064 http://rdf.wikipathways.org/Pathway/WP5224_r127064/WP/Interaction/idf374a72a "Ca2+" (https://identifiers.org/chebi/CHEBI:29108) and 
Ca2+" (https://identifiers.org/chebi/CHEBI:29108)

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