wikipathways-collection

WikiPathways WP3896

• WikiPathways: WP3896 (classic)
• Species: Homo sapiens
• Scholia: WP3896

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests
  • dataNodesWithoutIdentifier: .x we found 1 problem(s):
    • The following DataNodes have no identifier: 5
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: …. all OK!
  • nonNumericHGNCAccessionNumbers: .. all OK!
  • genesWithoutEnsemblMapping: .x we found 1 problem(s):
    • The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1
• GeneralTests: all 15 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: 12
  • possibleTranslocations: .. all OK!
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests: all 1 tests OK!
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 24 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 4 tests OK!

Summary

• Number of test classes: 20
• Number of tests: 118
• Number of assertions: 237
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 5

• http://classic.wikipathways.org/instance/WP3896_r134282 http://rdf.wikipathways.org/Pathway/WP3896_r134282/DataNode/c04 (CD59A)
• http://classic.wikipathways.org/instance/WP3896_r134282 http://rdf.wikipathways.org/Pathway/WP3896_r134282/DataNode/b10 (CRRY)
• http://classic.wikipathways.org/instance/WP3896_r134282 http://rdf.wikipathways.org/Pathway/WP3896_r134282/DataNode/d90 (Daf2)
• http://classic.wikipathways.org/instance/WP3896_r134282 http://rdf.wikipathways.org/Pathway/WP3896_r134282/DataNode/ba8f8 (PrM/Cap)
• http://classic.wikipathways.org/instance/WP3896_r134282 http://rdf.wikipathways.org/Pathway/WP3896_r134282/DataNode/ef655 (PrM/Cap)

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

Genes with identifier but no Ensembl identifier mapping

The following genes with an identifier have been found but that do not have a mapping to Ensembl: 1

http://classic.wikipathways.org/instance/WP3896_r134282 A2M with datasource Entrez Gene

More details at https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping

Interactions with Labels

Interactions found that involve Labels: 12

• http://classic.wikipathways.org/instance/WP3896_r134282 “Thrombin” with graphId afe
• http://classic.wikipathways.org/instance/WP3896_r134282 “Cell adhesion, migration, proliferation, etc” with graphId ede
• http://classic.wikipathways.org/instance/WP3896_r134282 “Platelet, monocyte, lymphocyte, endothelial cells, smooth muscle cells activation, etc” with graphId a5c
• http://classic.wikipathways.org/instance/WP3896_r134282 “C3 Convertase” with graphId cc5
• http://classic.wikipathways.org/instance/WP3896_r134282 “Cell lysis” with graphId f22
• http://classic.wikipathways.org/instance/WP3896_r134282 “fibrin degradation products” with graphId b49
• http://classic.wikipathways.org/instance/WP3896_r134282 “Zymosan, insulin, etc.” with graphId afa
• http://classic.wikipathways.org/instance/WP3896_r134282 “Clot” with graphId ae2
• http://classic.wikipathways.org/instance/WP3896_r134282 “Antibody/antigen complex” with graphId e67
• http://classic.wikipathways.org/instance/WP3896_r134282 “Collagen, basement membrane, activated platelets, etc.” with graphId fbf
• http://classic.wikipathways.org/instance/WP3896_r134282 “Cell adhesion, migration, proliferation, etc” with graphId a2a6b
• http://classic.wikipathways.org/instance/WP3896_r134282 “Vascular injury” with graphId d50

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP3896_r134282 ‘Dengue-2 interactions with complement and coagulation cascades’ in Homo sapiens has zero references;

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