wikipathways-collection

WikiPathways WP5046

• WikiPathways: WP5046 (classic)
• Species: Homo sapiens
• Scholia: WP5046

  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: 5
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 5
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: …. 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: 1
• 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: 6
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 2
  • 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 24 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: 118
• Number of assertions: 237
• Number of fails: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 5

• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/b1016 (ADP/ATP)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/db94a (NAD/NADH)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/c11ca (SA-B-Gal)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/ecc9d (p16)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/c4573 (p21)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 5

• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/b1016 (ADP/ATP)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/db94a (NAD/NADH)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/c11ca (SA-B-Gal)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/ecc9d (p16)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/DataNode/c4573 (p21)

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

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: 1

http://classic.wikipathways.org/instance/WP5046_r135695 p38 MAPK with datasource UniProtKB

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

Interactions with Labels

Interactions found that involve Labels: 6

• http://classic.wikipathways.org/instance/WP5046_r135695 “Cell senescence” with graphId d4683
• http://classic.wikipathways.org/instance/WP5046_r135695 “High proinflammatory SASP” with graphId b3b2f
• http://classic.wikipathways.org/instance/WP5046_r135695 “Mitochondrial dysfunction- associated senescence” with graphId ea4cd
• http://classic.wikipathways.org/instance/WP5046_r135695 “Promotion of cancer progression” with graphId ed395
• http://classic.wikipathways.org/instance/WP5046_r135695 “Pentose phospate pathway” with graphId c8486
• http://classic.wikipathways.org/instance/WP5046_r135695 “Growth arrest” with graphId c63ba

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/WP/Interaction/id8a29eb96 “Malate” (https://identifiers.org/chebi/CHEBI:30797) and Malate” (https://identifiers.org/chebi/CHEBI:30797)
• http://classic.wikipathways.org/instance/WP5046_r135695 http://rdf.wikipathways.org/Pathway/WP5046_r135695/WP/Interaction/idc80a552b “Aspartate” (https://identifiers.org/chebi/CHEBI:35391) and Aspartate” (https://identifiers.org/chebi/CHEBI:35391)

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