SARS-CoV-2-WikiPathways

WikiPathways WP5262

• WikiPathways: WP5262 (classic)
• Species: Homo sapiens
• Scholia: WP5262
• WPRDF file: wp/Human/WP5262.ttl
• GPMLRDF file: wp/gpml/Human/WP5262.ttl
• SBML file: sbml/WP5262.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: .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: all 8 tests 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
  • nonNumericPubMedIDs: .. all OK!
  • unexpectedPubMedIdentifier: .. all OK!
  • zeroPubMedIDs: .. all OK!
  • atLeastOneReference: .x we found 1 problem(s):
    • Found 1 pathways with zero (PubMed) references
  • citesRetractedArticle: .. all OK!
  • outdatedPubMedIdentifiers: .. all 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: 3

Fails

Interactions without references

Interactions without literature references: 2

• http://classic.wikipathways.org/instance/WP5262_r124649 -> http://rdf.wikipathways.org/Pathway/WP5262_r124649/WP/Interaction/ida02e4b1
• http://classic.wikipathways.org/instance/WP5262_r124649 -> http://rdf.wikipathways.org/Pathway/WP5262_r124649/WP/Interaction/id5f54755f

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/WP5262_r124649 http://rdf.wikipathways.org/Pathway/WP5262_r124649/DataNode/b458f (Arginase activation)
• http://classic.wikipathways.org/instance/WP5262_r124649 http://rdf.wikipathways.org/Pathway/WP5262_r124649/DataNode/a0bf6 (P38 MAPK)

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP5262_r124649 ‘Physiopathology of endothelial dysfunction in coronavirus disease’ in Homo sapiens has zero references;

More details at https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference

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