wikipathways-collection

WikiPathways WP5124

• WikiPathways: WP5124 (classic)
• Species: Homo sapiens
• Scholia: WP5124

  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: 10
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • 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: 21
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 11
  • 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 10

http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/e5e62 (APP processing)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/dc14d (Calcium signaling 
pathway)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/ef149 (Cx I)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/ac24c (Cx II)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/a9615 (Cx III)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/fafc5 (Cx IV)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/c89ba (Cx V)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/cbb7c (DNA damage)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/a2796 (GPCR)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/DataNode/dd4d5 (Protein oxidation)

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

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 21

http://classic.wikipathways.org/instance/WP5124_r128389 "APP intracellular 
domain" with graphId cb4ce
http://classic.wikipathways.org/instance/WP5124_r128389 "Reduction in LTP" with graphId fbc7a
http://classic.wikipathways.org/instance/WP5124_r128389 "Senile plaque" with graphId ba133
http://classic.wikipathways.org/instance/WP5124_r128389 "Defective insulin 
signaling" with graphId a80b0
http://classic.wikipathways.org/instance/WP5124_r128389 "Synaptic dysfunction" with graphId a1729
http://classic.wikipathways.org/instance/WP5124_r128389 "ER chaperones
ERAD" with graphId be64b
http://classic.wikipathways.org/instance/WP5124_r128389 "Cell death" with graphId b597b
http://classic.wikipathways.org/instance/WP5124_r128389 "Neurofibrillary
tangles" with graphId e1af1
http://classic.wikipathways.org/instance/WP5124_r128389 "Paired helical 
filaments" with graphId e73e1
http://classic.wikipathways.org/instance/WP5124_r128389 "(Tau-p)n" with graphId dfc85
http://classic.wikipathways.org/instance/WP5124_r128389 "Neurofibrillary 
tangles" with graphId db2b3
http://classic.wikipathways.org/instance/WP5124_r128389 "Sequestration of 
IDE" with graphId e248c
http://classic.wikipathways.org/instance/WP5124_r128389 "Hyperinsulinemia" with graphId ed1e9
http://classic.wikipathways.org/instance/WP5124_r128389 "Impaired memory" with graphId c7fff
http://classic.wikipathways.org/instance/WP5124_r128389 "Neuronal Injury" with graphId c2d38
http://classic.wikipathways.org/instance/WP5124_r128389 "Concentrated into
endosome/lysosome" with graphId c6aeb
http://classic.wikipathways.org/instance/WP5124_r128389 "ER stress" with graphId e8a08
http://classic.wikipathways.org/instance/WP5124_r128389 "Degradation" with graphId b5fa4
http://classic.wikipathways.org/instance/WP5124_r128389 "AB aggregation" with graphId da5db
http://classic.wikipathways.org/instance/WP5124_r128389 "Insulin resistance" with graphId ba592
http://classic.wikipathways.org/instance/WP5124_r128389 "Decreased energy 
production?" with graphId fac3f

Possible MIM translocation

Interactions between identical nodes: 11

http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id5225f92c "Ca2+" (https://identifiers.org/hmdb/HMDB0000464) and 
Ca2+" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id6ab9bac4 "CDK5R1 / p35" (https://identifiers.org/ensembl/ENSG00000176749) and 
CDK5R1 / p35" (https://identifiers.org/ensembl/ENSG00000176749)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id6ab9bac4 "CDK5R1 / p35" (https://identifiers.org/ensembl/ENSG00000176749) and 
CDK5R1 / p25" (https://identifiers.org/ensembl/ENSG00000176749)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id6ab9bac4 "CDK5R1 / p25" (https://identifiers.org/ensembl/ENSG00000176749) and 
CDK5R1 / p35" (https://identifiers.org/ensembl/ENSG00000176749)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id6ab9bac4 "CDK5R1 / p25" (https://identifiers.org/ensembl/ENSG00000176749) and 
CDK5R1 / p25" (https://identifiers.org/ensembl/ENSG00000176749)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id41e74657 "ATF6" (https://identifiers.org/ensembl/ENSG00000118217) and 
ATF6" (https://identifiers.org/ensembl/ENSG00000118217)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id41e74657 "ATF6" (https://identifiers.org/ensembl/ENSG00000118217) and 
p50 ATF6" (https://identifiers.org/ensembl/ENSG00000118217)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id41e74657 "p50 ATF6" (https://identifiers.org/ensembl/ENSG00000118217) and 
ATF6" (https://identifiers.org/ensembl/ENSG00000118217)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/id41e74657 "p50 ATF6" (https://identifiers.org/ensembl/ENSG00000118217) and 
p50 ATF6" (https://identifiers.org/ensembl/ENSG00000118217)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/idd4f5d70a "Ca2+" (https://identifiers.org/hmdb/HMDB0000464) and 
Ca2+" (https://identifiers.org/hmdb/HMDB0000464)
http://classic.wikipathways.org/instance/WP5124_r128389 http://rdf.wikipathways.org/Pathway/WP5124_r128389/WP/Interaction/bc7d3 "Ca2+" (https://identifiers.org/hmdb/HMDB0000464) and 
Ca2+" (https://identifiers.org/hmdb/HMDB0000464)

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