SARS-CoV-2-WikiPathways

WikiPathways WP5258

• WikiPathways: WP5258 (classic)
• Species: Homo sapiens
• Scholia: WP5258
• WPRDF file: wp/Human/WP5258.ttl
• GPMLRDF file: wp/gpml/Human/WP5258.ttl
• SBML file: sbml/WP5258.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: 4
  • missingHGNC: .. all OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 2
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • 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: .x we found 1 problem(s):
    • Unexpected non-metabolite to metabolite conversions: 3
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 2
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 9
  • 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: 5

Fails

Interactions without references

Interactions without literature references: 4

• http://classic.wikipathways.org/instance/WP5258_r134248 -> http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id748b9d75
• http://classic.wikipathways.org/instance/WP5258_r134248 -> http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/idb14e7f6e
• http://classic.wikipathways.org/instance/WP5258_r134248 -> http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id260039df
• http://classic.wikipathways.org/instance/WP5258_r134248 -> http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id48739a9

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

Data nodes without an identifier

The following DataNodes have no identifier: 2

• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/DataNode/c09be (IFN signaling)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/DataNode/b397a (RAS signaling)

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

No non-metabolite to metabolite conversions

Unexpected non-metabolite to metabolite conversions: 3

• Homo sapiens http://classic.wikipathways.org/instance/WP5258_r134248 → https://identifiers.org/ensembl/ENSG00000130234 https://identifiers.org/hmdb/HMDB0001035 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id48739a9
• Homo sapiens http://classic.wikipathways.org/instance/WP5258_r134248 → https://identifiers.org/hgnc.symbol/NOX1 https://identifiers.org/chebi/CHEBI:26523 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id9a9ed424
• Homo sapiens http://classic.wikipathways.org/instance/WP5258_r134248 → https://identifiers.org/ensembl/ENSG00000130234 https://identifiers.org/hmdb/HMDB0001035 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/idb14e7f6e

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

Interactions with Labels

Interactions found that involve Labels: 2

• http://classic.wikipathways.org/instance/WP5258_r134248 “Increased permeability” with graphId b4158
• http://classic.wikipathways.org/instance/WP5258_r134248 “Disturbed vascular tone “ with graphId afb08

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

Possible MIM translocation

Interactions between identical nodes: 9

• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/idbed4e731 “ACE2” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/idbed4e731 “ACE2” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/idbed4e731 “ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/idbed4e731 “ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id1c7c5bd8 “ACE2” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id1c7c5bd8 “ACE2” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id1c7c5bd8 “ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/id1c7c5bd8 “ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234) and ACE2 (truncated)” (https://identifiers.org/ensembl/ENSG00000130234)
• http://classic.wikipathways.org/instance/WP5258_r134248 http://rdf.wikipathways.org/Pathway/WP5258_r134248/WP/Interaction/ide5f8fc10 “ICAM1” (https://identifiers.org/ensembl/ENSG00000090339) and ICAM1” (https://identifiers.org/ensembl/ENSG00000090339)

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

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