wikipathways-collection

WikiPathways WP4932

• WikiPathways: WP4932
• Scholia: WP4932

  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: 6
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 3 tests OK!
• GeneralTests
  • curationAndHypothetical: .. all OK!
  • curationAndNeedsWork: .. all OK!
  • curationAndReactome: .. all OK!
  • dataNodeWithoutGraphId: .. all OK!
  • duplicateTitles: .. all OK!
  • emptyLabelOfNodeWithIdentifier: .. all OK!
  • groupsHaveDetail: .. all OK!
  • noTags: .. all OK!
  • nullDataSources: .. all OK!
  • titlesShortEnough: .. all OK!
  • undefinedDataSources: .. all OK!
  • undefinedIdentifier: .. all OK!
  • weirdCharacterTitles: .x we found 1 problem(s):
    • Titles with unexpected characters (only allow alphanumerics and spaces):1
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .x we found 1 problem(s):
    • Unexpected metabolite to non-metabolite conversions:2
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 10
  • 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 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 4 tests OK!

Summary

• Number of test classes: 20
• Number of tests: 93
• Number of assertions: 186
• Number of fails: 5

Fails

DataNodesTests.dataNodesWithoutIdentifier

The following DataNodes have no identifier: 6

http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/DataNode/ea3b1 (ATP synthase F0 and F1 complex)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/DataNode/f62aa (Endosomal budding)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/DataNode/ad7dc (Oxoglutarate dehydrogenase complex)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/DataNode/c52fb (SNARE complex)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/DataNode/c1aec (Virus budding)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/DataNode/e5169 (synaptonemal complex)

GeneralTests.weirdCharacterTitles

Titles with unexpected characters (only allow alphanumerics and spaces):1

http://www.wikipathways.org/instance/WP4932_rr118797 '7q11.23 copy number variation syndrome' has 1 weird characters

InteractionTests.noMetaboliteToNonMetaboliteConversions

Unexpected metabolite to non-metabolite conversions:2

Homo sapiens http://www.wikipathways.org/instance/WP4932_rr118797 -> https://identifiers.org/chebi/CHEBI:9168 https://identifiers.org/ensembl/ENSG00000077800 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/ebd5c
Homo sapiens http://www.wikipathways.org/instance/WP4932_rr118797 -> https://identifiers.org/chebi/CHEBI:61049 https://identifiers.org/ensembl/ENSG00000077800 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/iddb82bf9e

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

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 10

http://www.wikipathways.org/instance/WP4932_rr118797 "Brain development" with graphId cfa31
http://www.wikipathways.org/instance/WP4932_rr118797 "important for embryonic 
development, especialy
of cranio-facial features" with graphId c9b57
http://www.wikipathways.org/instance/WP4932_rr118797 "dendrite phenotype
development" with graphId d1a53
http://www.wikipathways.org/instance/WP4932_rr118797 "links microtubules to 
dendritic lamellar body
cytosol organization" with graphId ed7ac
http://www.wikipathways.org/instance/WP4932_rr118797 "chaperone function" with graphId f3ebc
http://www.wikipathways.org/instance/WP4932_rr118797 "unknown 
function" with graphId eb0dd
http://www.wikipathways.org/instance/WP4932_rr118797 "Involved in histone methylation" with graphId d5b2c
http://www.wikipathways.org/instance/WP4932_rr118797 "synaptic plasticity
heart development" with graphId c3a3e
http://www.wikipathways.org/instance/WP4932_rr118797 "DNA replication" with graphId eb646
http://www.wikipathways.org/instance/WP4932_rr118797 "methyl-transferase
activity

no specific functions
known" with graphId ce06f

InteractionTests.possibleTranslocations

Interactions between identical nodes: 7

http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/bc7e9 "Serotonin" (https://identifiers.org/chebi/CHEBI:28790) and 
Serotonin" (https://identifiers.org/chebi/CHEBI:28790)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/dc603 "GABA" (https://identifiers.org/chebi/CHEBI:16865) and 
GABA" (https://identifiers.org/chebi/CHEBI:16865)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/e5ca9 "Acetylcholine" (https://identifiers.org/chebi/CHEBI:15355) and 
Acetylcholine" (https://identifiers.org/chebi/CHEBI:15355)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/ccae8 "Glutamate" (https://identifiers.org/chebi/CHEBI:14321) and 
Glutamate" (https://identifiers.org/chebi/CHEBI:14321)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/e0ae1 "Cl-" (https://identifiers.org/chebi/CHEBI:17996) and 
Cl-" (https://identifiers.org/chebi/CHEBI:17996)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/b415f "Dopamine" (https://identifiers.org/chebi/CHEBI:18243) and 
Dopamine" (https://identifiers.org/chebi/CHEBI:18243)
http://www.wikipathways.org/instance/WP4932_rr118797 http://rdf.wikipathways.org/Pathway/WP4932_rr118797/WP/Interaction/be34d "Norepinephrine" (https://identifiers.org/chebi/CHEBI:18357) and 
Norepinephrine" (https://identifiers.org/chebi/CHEBI:18357)

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