wikipathways-collection

WikiPathways WP2882

• WikiPathways: WP2882 (classic)
• Species: Homo sapiens
• Scholia: WP2882

  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: 4
  • 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: 9
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 14
  • 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/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/c582b (Co-activators )
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/dc04b (Co-activators )
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/dcc47 (Nuclear receptors)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/e897e (PPAR alpha ligand)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/d2f6d (Unknown)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 4

• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/c582b (Co-activators )
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/dc04b (Co-activators )
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/e897e (PPAR alpha ligand)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/DataNode/d2f6d (Unknown)

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/WP2882_r126680 MT1IP with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 9

• http://classic.wikipathways.org/instance/WP2882_r126680 “VDR ligand” with graphId fec41
• http://classic.wikipathways.org/instance/WP2882_r126680 “ER ligand” with graphId b8e64
• http://classic.wikipathways.org/instance/WP2882_r126680 “CAR/PXR Ligand” with graphId e0f7e
• http://classic.wikipathways.org/instance/WP2882_r126680 “FXR ligand” with graphId e017f
• http://classic.wikipathways.org/instance/WP2882_r126680 “NRF2 ligand” with graphId b82e2
• http://classic.wikipathways.org/instance/WP2882_r126680 “LXR ligand” with graphId ed878
• http://classic.wikipathways.org/instance/WP2882_r126680 “GR ligand” with graphId ad7a3
• http://classic.wikipathways.org/instance/WP2882_r126680 “AhR Ligand” with graphId bb415
• http://classic.wikipathways.org/instance/WP2882_r126680 “FXR Target genes” with graphId c1651

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

Possible MIM translocation

Interactions between identical nodes: 14

• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/idc3e30c77 “RXRA” (https://identifiers.org/ensembl/ENSG00000186350) and RXRA” (https://identifiers.org/ensembl/ENSG00000186350)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/id845d8be8 “NR1I3” (https://identifiers.org/ensembl/ENSG00000143257) and NR1I3” (https://identifiers.org/ensembl/ENSG00000143257)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/ida9df0723 “NR1I2” (https://identifiers.org/ensembl/ENSG00000144852) and NR1I2” (https://identifiers.org/ensembl/ENSG00000144852)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/ide426961c “NFE2L2” (https://identifiers.org/ensembl/ENSG00000116044) and NFE2L2” (https://identifiers.org/ensembl/ENSG00000116044)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/fa0d4 “PPARA” (https://identifiers.org/ensembl/ENSG00000186951) and PPARA” (https://identifiers.org/ensembl/ENSG00000186951)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/ecd1c “NFE2L2” (https://identifiers.org/ensembl/ENSG00000116044) and NFE2L2” (https://identifiers.org/ensembl/ENSG00000116044)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/idf13776e “RXRA” (https://identifiers.org/ensembl/ENSG00000186350) and RXRA” (https://identifiers.org/ensembl/ENSG00000186350)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/id996b1555 “NR1H3” (https://identifiers.org/ensembl/ENSG00000025434) and NR1H3” (https://identifiers.org/ensembl/ENSG00000025434)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/ef334 “SRC” (https://identifiers.org/ensembl/ENSG00000197122) and SRC” (https://identifiers.org/ensembl/ENSG00000197122)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/fccd4 “PPARA” (https://identifiers.org/ensembl/ENSG00000186951) and PPARA” (https://identifiers.org/ensembl/ENSG00000186951)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/ide30920ff “NR1I3” (https://identifiers.org/ensembl/ENSG00000143257) and NR1I3” (https://identifiers.org/ensembl/ENSG00000143257)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/idc5581697 “RXRA” (https://identifiers.org/ensembl/ENSG00000186350) and RXRA” (https://identifiers.org/ensembl/ENSG00000186350)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/idd3f66ad8 “RXRA” (https://identifiers.org/ensembl/ENSG00000186350) and RXRA” (https://identifiers.org/ensembl/ENSG00000186350)
• http://classic.wikipathways.org/instance/WP2882_r126680 http://rdf.wikipathways.org/Pathway/WP2882_r126680/WP/Interaction/id9b3d5fd6 “NR1H3” (https://identifiers.org/ensembl/ENSG00000025434) and NR1H3” (https://identifiers.org/ensembl/ENSG00000025434)

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