wikipathways-collection

WikiPathways WP2038

• WikiPathways: WP2038 (classic)
• Species: Homo sapiens
• Scholia: WP2038

  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: 3
  • 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: 9
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 3
  • 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: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 3

• http://classic.wikipathways.org/instance/WP2038_r134122 http://rdf.wikipathways.org/Pathway/WP2038_r134122/DataNode/cf90c (ICIS)
• http://classic.wikipathways.org/instance/WP2038_r134122 http://rdf.wikipathways.org/Pathway/WP2038_r134122/DataNode/defee (RhoGEF)
• http://classic.wikipathways.org/instance/WP2038_r134122 http://rdf.wikipathways.org/Pathway/WP2038_r134122/DataNode/f1fc0 (XMAP215)

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/WP2038_r134122 PI3K with datasource WikiPathways

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

Interactions with Labels

Interactions found that involve Labels: 9

• http://classic.wikipathways.org/instance/WP2038_r134122 “MT catastrophe” with graphId e5807
• http://classic.wikipathways.org/instance/WP2038_r134122 “Neurotrophins” with graphId eb7fa
• http://classic.wikipathways.org/instance/WP2038_r134122 “+/- end destabilizing” with graphId d4e02
• http://classic.wikipathways.org/instance/WP2038_r134122 “Delivery to MT plus ends” with graphId e2458
• http://classic.wikipathways.org/instance/WP2038_r134122 “MT stability” with graphId aabf5
• http://classic.wikipathways.org/instance/WP2038_r134122 “Focal adhesion” with graphId ce1a0
• http://classic.wikipathways.org/instance/WP2038_r134122 ““Dynamic microtubules”” with graphId c02e7
• http://classic.wikipathways.org/instance/WP2038_r134122 “+ end growth promoting” with graphId dc00e
• http://classic.wikipathways.org/instance/WP2038_r134122 “MT polymerization” with graphId f8497

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

Possible MIM translocation

Interactions between identical nodes: 3

• http://classic.wikipathways.org/instance/WP2038_r134122 http://rdf.wikipathways.org/Pathway/WP2038_r134122/WP/Interaction/id5eaf198e “MAP1B” (https://identifiers.org/ensembl/ENSG00000131711) and MAP1B” (https://identifiers.org/ensembl/ENSG00000131711)
• http://classic.wikipathways.org/instance/WP2038_r134122 http://rdf.wikipathways.org/Pathway/WP2038_r134122/WP/Interaction/id31e91b21 “CLIP” (https://identifiers.org/ensembl/ENSG00000130779) and CLIP” (https://identifiers.org/ensembl/ENSG00000130779)
• http://classic.wikipathways.org/instance/WP2038_r134122 http://rdf.wikipathways.org/Pathway/WP2038_r134122/WP/Interaction/id3012968a “DIAPH1” (https://identifiers.org/ensembl/ENSG00000131504) and DIAPH1” (https://identifiers.org/ensembl/ENSG00000131504)

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