SARS-CoV-2-WikiPathways

WikiPathways WP5146

• WikiPathways: WP5146 (classic)
• Species: Homo sapiens
• Scholia: WP5146
• WPRDF file: wp/Human/WP5146.ttl
• GPMLRDF file: wp/gpml/Human/WP5146.ttl
• SBML file: sbml/WP5146.sbml (SVG) (conversion notes)

Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• CovidDiseaseMapsTests
  • interactionsWithoutReferences: .x we found 1 problem(s):
    • Interactions without literature references: 2
  • missingHGNC: .. all OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .. all OK!
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 2
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 13 tests OK!
• HMDBMetabolitesTests: all 1 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: 1
  • 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 15 tests OK!
• OudatedDataSourcesTests: all 7 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 13 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 111
• Number of assertions: 224
• Number of fails: 4

Fails

Interactions without references

Interactions without literature references: 2

• http://classic.wikipathways.org/instance/WP5146_r128308 -> http://rdf.wikipathways.org/Pathway/WP5146_r128308/WP/Interaction/id6a8a8f45
• http://classic.wikipathways.org/instance/WP5146_r128308 -> http://rdf.wikipathways.org/Pathway/WP5146_r128308/WP/Interaction/aa288

More details at https://www.wikipathways.org/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences

Datanodes of unknown type

The following DataNodes have Unknown @Type: 2

• http://classic.wikipathways.org/instance/WP5146_r128308 http://rdf.wikipathways.org/Pathway/WP5146_r128308/DataNode/c8286 (IFN-I)
• http://classic.wikipathways.org/instance/WP5146_r128308 http://rdf.wikipathways.org/Pathway/WP5146_r128308/DataNode/d5519 (IFN-II )

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP5146_r128308 “Cell death” with graphId c86f7

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

Possible MIM translocation

Interactions between identical nodes: 2

• http://classic.wikipathways.org/instance/WP5146_r128308 http://rdf.wikipathways.org/Pathway/WP5146_r128308/WP/Interaction/id6a8a8f45 “IRF3” (https://identifiers.org/ensembl/ENSG00000126456) and IRF3” (https://identifiers.org/ensembl/ENSG00000126456)
• http://classic.wikipathways.org/instance/WP5146_r128308 http://rdf.wikipathways.org/Pathway/WP5146_r128308/WP/Interaction/aa288 “NFKB1” (https://identifiers.org/ensembl/ENSG00000109320) and NFKB1” (https://identifiers.org/ensembl/ENSG00000109320)

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

This site is open source. Improve this page.