SARS-CoV-2-WikiPathways

WikiPathways WP5113

• WikiPathways: WP5113 (classic)
• Species: Homo sapiens
• Scholia: WP5113
• WPRDF file: wp/Human/WP5113.ttl
• GPMLRDF file: wp/gpml/Human/WP5113.ttl
• SBML file: sbml/WP5113.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: 29
  • 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
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 10
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests
  • metaboliteAlsoOtherType: .. all OK!
  • casNumbersNotMarkedAsMetabolite: .. all OK!
  • chemspiderIDsNotMarkedAsMetabolite: .. all OK!
  • HMDBIDsNotMarkedAsMetabolite: .. all OK!
  • KEGGIDsNotMarkedAsMetabolite: .. all OK!
  • metabolitesWithAnEnsembleID: .. all OK!
  • metabolitesWithAnEntrezGeneID: .. all OK!
  • metabolitesWithDbButNoIdentifier: .. all OK!
  • metabolitesWithIdentifierButNoDb: .. all OK!
  • ChEBIIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotNumbers: .. all OK!
  • PubChemSubstanceIDsNotNumbers: .. all OK!
  • tooManyInChIKeys: .x we found 1 problem(s):
    • Non-zero count of metabolites with more than one InChIKey: 1
• 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: 29

• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id799a92c8
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id84003b63
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/idcdee20b6
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id6db3f655
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id80337e77
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id4bed82f3
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id7d319e35
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/ComplexBinding/d6f98
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id2ce067d0
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id407b4cba
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id985cf82a
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/ComplexBinding/d1aaf
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id60b7f6ef
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/idfc2d23ef
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id461dc676
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id81a62627
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/idaf8188bc
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/idf4c13a25
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/ComplexBinding/e1b56
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/ComplexBinding/c6501
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/ComplexBinding/c118a
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id5f742b09
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id11298a73
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/idb56611eb
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/ida604b50
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id715b17be
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id212b2183
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id2ba69e50
• http://classic.wikipathways.org/instance/WP5113_r125765 -> http://rdf.wikipathways.org/Pathway/WP5113_r125765/ComplexBinding/c2cfa

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

Interactions with Labels

Interactions found that involve Labels: 10

• http://classic.wikipathways.org/instance/WP5113_r125765 “Pro-inflammatory stimuli” with graphId e22c7
• http://classic.wikipathways.org/instance/WP5113_r125765 “Viral Infection / Oxidative stress “ with graphId cab5c
• http://classic.wikipathways.org/instance/WP5113_r125765 “5. viral genome replication” with graphId e0205
• http://classic.wikipathways.org/instance/WP5113_r125765 “Inflammatory cytokines” with graphId ba91d
• http://classic.wikipathways.org/instance/WP5113_r125765 “ARE” with graphId b3ef3
• http://classic.wikipathways.org/instance/WP5113_r125765 “6. Subgenomic transription” with graphId d1f6e
• http://classic.wikipathways.org/instance/WP5113_r125765 “7. Translation of viral proteins” with graphId e1559
• http://classic.wikipathways.org/instance/WP5113_r125765 “9. Exocytosis” with graphId c5186
• http://classic.wikipathways.org/instance/WP5113_r125765 “Release” with graphId cc062
• http://classic.wikipathways.org/instance/WP5113_r125765 “Inflammation” with graphId e618f

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

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP5113_r125765 http://rdf.wikipathways.org/Pathway/WP5113_r125765/WP/Interaction/id461dc676 “KEAP1” (https://identifiers.org/ensembl/ENSG00000079999) and KEAP1” (https://identifiers.org/ensembl/ENSG00000079999)

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

Too many InChIKeys for the used identifier

Non-zero count of metabolites with more than one InChIKey: 1

• http://classic.wikipathways.org/instance/WP5113_r125765 has: Heme (HMDB0003178) with InChIKeys: KABFMIBPWCXCRK-RGGAHWMASA-J, RNQMHXMGXVQRMV-UHFFFAOYSA-L, KABFMIBPWCXCRK-RGGAHWMASA-L

More details at https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/tooManyInChIKeys

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