SARS-CoV-2-WikiPathways

WikiPathways WP5260

• WikiPathways: WP5260 (classic)
• Species: Homo sapiens
• Scholia: WP5260
• WPRDF file: wp/Human/WP5260.ttl
• GPMLRDF file: wp/gpml/Human/WP5260.ttl
• SBML file: sbml/WP5260.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: 9
  • missingHGNC: .. all OK!
• DataNodesTests: all 5 tests 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
  • casWithoutMapping: .. all OK!
  • chebiWithoutMapping: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 1
  • chebiWithoutMapping_Reactome: .. all OK!
  • chemspiderCIDWithoutMapping: .. all OK!
  • duplicateWikidataMappings: .. all OK!
  • hmdbWithoutMapping: .. all OK!
  • kNApSAcKWithoutMapping: .. all OK!
  • keggWithoutMapping: .. all OK!
  • lipidMapsWithoutMapping: .. all OK!
  • pubchemCIDWithoutMapping: .. all OK!
  • replaceWikipedia: .. all OK!
  • wikDataTypo: .. all OK!
  • wikidataIdentifiersWrong: .. all 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: 9

• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/ide87af51a
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/id22a67503
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/id17f32001
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/id613c9560
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/id4fd78cda
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/idaf482125
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/id3bcf6265
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/id72029093
• http://classic.wikipathways.org/instance/WP5260_r124647 -> http://rdf.wikipathways.org/Pathway/WP5260_r124647/WP/Interaction/id34434cee

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP5260_r124647 ‘Physiopathology of endothelial dysfunction in COVID-19’ in Homo sapiens has zero references;

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

ChEBI identifier without a match in Wikidata

ChEBI identifiers without Wikidata mappings: 1

• https://identifiers.org/chebi/CHEBI:48432 (ang II) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5260_r124647

More details at https://www.wikipathways.org/WikiPathwaysCurator/WikidataTests/chebiWithoutMapping

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