wikipathways-collection

WikiPathways WP2376

• WikiPathways: WP2376 (classic)
• Species: Rattus norvegicus

  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: 4
  • 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: 26
• GeneralTests: all 15 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 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: 3

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 4

• http://classic.wikipathways.org/instance/WP2376_r125515 http://rdf.wikipathways.org/Pathway/WP2376_r125515/DataNode/b766f (***)
• http://classic.wikipathways.org/instance/WP2376_r125515 http://rdf.wikipathways.org/Pathway/WP2376_r125515/DataNode/ef747 (DRUGS METABOLISM UV RADIATION RESPIRATORY BURST INFLAMATORY CYTOKINES HEAVY METALS)
• http://classic.wikipathways.org/instance/WP2376_r125515 http://rdf.wikipathways.org/Pathway/WP2376_r125515/DataNode/ae6dd (NFE2L2 DEGRADATION BY UBIQUITIN PROTEASOME)
• http://classic.wikipathways.org/instance/WP2376_r125515 http://rdf.wikipathways.org/Pathway/WP2376_r125515/DataNode/d599e (Ub2)

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: 26

http://classic.wikipathways.org/instance/WP2376_r125515 Txnrd1 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Gclc with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Maff with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Hsp90ab1 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Pik3cb with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Gsta2 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Cul3 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Aox1 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2376_r125515 Atm with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Pik3r4 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2376_r125515 Rbx1 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Map3k5 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Kras with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Map2k2 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Mdm2 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Bard1 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Mras with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Smarca4 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Gsta3 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2376_r125515 Map2k5 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2376_r125515 Atf4 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Keap1 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Me1 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Ep300 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2376_r125515 Gsta4 with datasource RGD
http://classic.wikipathways.org/instance/WP2376_r125515 Gsta1 with datasource RGD

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP2376_r125515 ‘Nuclear factor, erythroid-derived 2, like 2 signaling pathway’ in Rattus norvegicus has zero references;

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