wikipathways-collection

WikiPathways WP2562

• WikiPathways: WP2562 (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: 15
  • 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!
  • numericHGNCIDs: .. 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: 10
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .. all OK!
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 8
  • 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 15 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 11 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!
• Sec2PriProjectTests
  • outdatedHGNCSymbol: .. all OK!
  • outdatedHGNCAccessionNumber: .. all OK!
  • outdatedNCBIIdentifiers: .. all OK!
  • outdatedChEBIIdentifiers: .. all OK!
  • outdatedHMDBIdentifiers: .x we found 1 problem(s):
    • Old HMDB identifiers detected: 3
  • outdatedUniProtKBIdentifiers2: .. all OK!
• UniProtTests: all 5 tests OK!
• UnicodeTests: all 16 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 147
• Number of assertions: 293
• Number of fails: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 15

• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/c49f6 (Deoxyribonucleotide)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/aeaf0 (GSSG)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/bd1e3 (GSSG)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/a49be (Ggt1)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/b426c (Ggt1)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/de977 (Ggt1)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/db063 (LtA4)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/e1e68 (LtC4)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/f1362 (LtC4)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/c20b9 (LtD4)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/ff78d (LtE4)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/e9eed (OH*)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/f7538 (Ribonucleotide)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/a9291 (X)
• http://classic.wikipathways.org/instance/WP2562_r140351 http://rdf.wikipathways.org/Pathway/WP2562_r140351/DataNode/aafe1 (X-glucoronide)

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: 10

http://classic.wikipathways.org/instance/WP2562_r140351 Mapkapk2 with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Slc40a1 with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Mdm2 with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Pkm2 with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Tf with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Gsta4 with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Txnrd1 with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Gclc with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Pgk2 with datasource RGD
http://classic.wikipathways.org/instance/WP2562_r140351 Gpx4 with datasource RGD

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

Interactions with unconnected points

Interactions with unconnected points: 8

• http://classic.wikipathways.org/instance/WP2562_r140351

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP2562_r140351 ‘Relationship between glutathione and NADPH’ in Rattus norvegicus has zero references;

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

HMDB identifier has been retracted

Old HMDB identifiers detected: 3

• http://classic.wikipathways.org/instance/WP2562_r140351 Pyruvate has HMDB ID HMDB0002332 but has been replaced by HMDB0001405
• http://classic.wikipathways.org/instance/WP2562_r140351 Fe²⁺ has HMDB ID HMDB0012943 but has been replaced by HMDB0015531
• http://classic.wikipathways.org/instance/WP2562_r140351 Fe³⁺ has HMDB ID HMDB0012943 but has been replaced by HMDB0015531

More details at https://www.wikipathways.org/WikiPathwaysCurator/Sec2PriProjectTests/outdatedHMDBIdentifiers