wikipathways-collection

WikiPathways WP5298

• WikiPathways: WP5298 (classic)
• Species: Mus musculus

  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: 4
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: .. all OK!
  • numericHGNCIDs: .. all OK!
  • nonNumericHGNCAccessionNumbers: .. all OK!
  • genesWithoutEnsemblMapping: .x we found 1 problem(s):
    • The following genes with an identifier have been found but that do not have a mapping to Ensembl: 2
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .. all OK!
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 9
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 4
  • 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 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• Sec2PriProjectTests
  • outdatedHGNCSymbol: .. all OK!
  • outdatedHGNCAccessionNumber: .. all OK!
  • outdatedNCBIIdentifiers: .. all OK!
  • outdatedChEBIIdentifiers: .. all OK!
  • outdatedHMDBIdentifiers: .. all OK!
  • outdatedUniProtKBIdentifiers2: .x we found 1 problem(s):
    • Old UniProtKB identifiers detected: 1
• UniProtTests: all 5 tests OK!
• UnicodeTests
  • water: .. all OK!
  • calcium: .. all OK!
  • hydron: .. all OK!
  • sodium: .. all OK!
  • potassium: .. all OK!
  • oxygen: .. all OK!
  • carbondioxide: .. all OK!
  • iron2: .. all OK!
  • iron3: .. all OK!
  • copper: .. all OK!
  • copper2: .. all OK!
  • manganese: .. all OK!
  • magnesium: .. all OK!
  • ammonia: .. all OK!
  • chloride: .x we found 1 problem(s):
    • Metabolite can use Cl⁻ instead of Cl-: 1
  • bicarbonate: .. all OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 147
• Number of assertions: 293
• Number of fails: 6

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 4

• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/DataNode/cda8e (Dopamine signalling)
• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/DataNode/ef5b0 (Dopamine signalling)
• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/DataNode/bbc73 (Glutamine synthesis)
• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/DataNode/afadf (Pyrimidine metabolism)

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

Genes with identifier but no Ensembl identifier mapping

The following genes with an identifier have been found but that do not have a mapping to Ensembl: 2

http://classic.wikipathways.org/instance/WP5298_r140230 Protein kinase C beta type with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5298_r140230 Epb41l1 with datasource UniProtKB

More details at https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping

Interactions with unconnected points

Interactions with unconnected points: 9

• http://classic.wikipathways.org/instance/WP5298_r140230

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

Possible MIM translocation

Interactions between identical nodes: 4

• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/WP/Interaction/c0fd6 “Glutamate” (https://identifiers.org/chebi/CHEBI:16015) and Glutamate” (https://identifiers.org/chebi/CHEBI:16015)
• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/WP/Interaction/f86fe “L(+)-lactate” (https://identifiers.org/chebi/CHEBI:16651) and L(+)-lactate” (https://identifiers.org/chebi/CHEBI:16651)
• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/WP/Interaction/e599c “L(+)-lactate” (https://identifiers.org/chebi/CHEBI:16651) and L(+)-lactate” (https://identifiers.org/chebi/CHEBI:16651)
• http://classic.wikipathways.org/instance/WP5298_r140230 http://rdf.wikipathways.org/Pathway/WP5298_r140230/WP/Interaction/b58b7 “L(+)-lactate” (https://identifiers.org/chebi/CHEBI:16651) and L(+)-lactate” (https://identifiers.org/chebi/CHEBI:16651)

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

UniProtKB identifier has been retracted

Old UniProtKB identifiers detected: 1

• http://classic.wikipathways.org/instance/WP5298_r140230 Calm1 has UniProtKB ID P62204 but has been replaced by P0DP28

More details at https://www.wikipathways.org/WikiPathwaysCurator/Sec2PriProjectTests/outdatedUniProtKBIdentifiers2

The chloride ion formula can use Unicode

Metabolite can use Cl⁻ instead of Cl-: 1

• http://classic.wikipathways.org/instance/WP5298_r140230

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