wikipathways-collection

WikiPathways WP2272

• WikiPathways: WP2272 (classic)
• Species: Homo sapiens
• Scholia: WP2272

  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: 1
  • 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: 16
• 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: 15
  • 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: all 6 tests 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 1

• http://classic.wikipathways.org/instance/WP2272_r135055 http://rdf.wikipathways.org/Pathway/WP2272_r135055/DataNode/f9761 (Type III protein secretion system)

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: 16

http://classic.wikipathways.org/instance/WP2272_r135055 NleH with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 actin-related protein 2/3 complex subunit 1B-like with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2272_r135055 OCLN with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2272_r135055 Eae with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 EspG with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 StxA with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 EspG2 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 EspF with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 Bfp with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 EspH with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 EspFU with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 NleA with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 TUBB4Q with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2272_r135055 Tir with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 StxB with datasource UniProtKB
http://classic.wikipathways.org/instance/WP2272_r135055 Map with datasource UniProtKB

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

Interactions with Labels

Interactions found that involve Labels: 15

• http://classic.wikipathways.org/instance/WP2272_r135055 “Intestinal tract Kidney ……. Inhibition of protein synthesis” with graphId a2e36
• http://classic.wikipathways.org/instance/WP2272_r135055 “Alterations in the IF network architecture” with graphId ccb50
• http://classic.wikipathways.org/instance/WP2272_r135055 “Disruption of adherens junctions” with graphId f99af
• http://classic.wikipathways.org/instance/WP2272_r135055 “Retraction of filopodium” with graphId a7d42
• http://classic.wikipathways.org/instance/WP2272_r135055 “Stress fiber formation” with graphId bdb5d
• http://classic.wikipathways.org/instance/WP2272_r135055 “Cytoskeleton rearrangement” with graphId b51df
• http://classic.wikipathways.org/instance/WP2272_r135055 “Inflammation” with graphId dca84
• http://classic.wikipathways.org/instance/WP2272_r135055 “LPS” with graphId b77e1
• http://classic.wikipathways.org/instance/WP2272_r135055 “Flagellin” with graphId c0504
• http://classic.wikipathways.org/instance/WP2272_r135055 “outer membrane protein” with graphId a1180
• http://classic.wikipathways.org/instance/WP2272_r135055 “Pedestal formation” with graphId adf87
• http://classic.wikipathways.org/instance/WP2272_r135055 “Disruption of barrier function and increase in monolayer permeability” with graphId e6442
• http://classic.wikipathways.org/instance/WP2272_r135055 “Filipodium formation” with graphId f7913
• http://classic.wikipathways.org/instance/WP2272_r135055 “Disruption of tight junctions” with graphId d2eb2
• http://classic.wikipathways.org/instance/WP2272_r135055 “Redistribution” with graphId df6e5

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