wikipathways-collection

WikiPathways WP4630

• WikiPathways: WP4630 (classic)
• Species: Homo sapiens
• Scholia: WP4630

  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!
  • 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: 9
• 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: 12
  • possibleTranslocations: .. all OK!
  • 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 4

• http://classic.wikipathways.org/instance/WP4630_r129207 http://rdf.wikipathways.org/Pathway/WP4630_r129207/DataNode/ba920 (?)
• http://classic.wikipathways.org/instance/WP4630_r129207 http://rdf.wikipathways.org/Pathway/WP4630_r129207/DataNode/e503e (?)
• http://classic.wikipathways.org/instance/WP4630_r129207 http://rdf.wikipathways.org/Pathway/WP4630_r129207/DataNode/f9389 (M)
• http://classic.wikipathways.org/instance/WP4630_r129207 http://rdf.wikipathways.org/Pathway/WP4630_r129207/DataNode/aca23 (RIG-1-like receptor signaling pathway)

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: 9

http://classic.wikipathways.org/instance/WP4630_r129207 P with datasource NCBI Protein
http://classic.wikipathways.org/instance/WP4630_r129207 V with datasource NCBI Protein
http://classic.wikipathways.org/instance/WP4630_r129207 N with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP4630_r129207 F with datasource NCBI Protein
http://classic.wikipathways.org/instance/WP4630_r129207 C with datasource NCBI Protein
http://classic.wikipathways.org/instance/WP4630_r129207 N with datasource NCBI Protein
http://classic.wikipathways.org/instance/WP4630_r129207 L with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP4630_r129207 P with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP4630_r129207 H with datasource NCBI Protein

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

Interactions with Labels

Interactions found that involve Labels: 12

• http://classic.wikipathways.org/instance/WP4630_r129207 “Measles virus infection” with graphId c9c68
• http://classic.wikipathways.org/instance/WP4630_r129207 “Inhibited host translation” with graphId e2cec
• http://classic.wikipathways.org/instance/WP4630_r129207 “MV RNA” with graphId ab2d1
• http://classic.wikipathways.org/instance/WP4630_r129207 “Measles virus entry and replication” with graphId de8b9
• http://classic.wikipathways.org/instance/WP4630_r129207 “Inhibition of cell death” with graphId f40c2
• http://classic.wikipathways.org/instance/WP4630_r129207 “Inhibition of T-cell proliferation” with graphId cf646
• http://classic.wikipathways.org/instance/WP4630_r129207 “Virus genome replication” with graphId d4715
• http://classic.wikipathways.org/instance/WP4630_r129207 “Cell cycle retardation” with graphId c1834
• http://classic.wikipathways.org/instance/WP4630_r129207 “Dendritic cell apoptosis” with graphId be5c8
• http://classic.wikipathways.org/instance/WP4630_r129207 “Virus budding” with graphId d23a7
• http://classic.wikipathways.org/instance/WP4630_r129207 “Immunosuppression” with graphId c76af
• http://classic.wikipathways.org/instance/WP4630_r129207 “Supression of inflammatory reactions” with graphId a49a1

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