wikipathways-collection

WikiPathways WP1451

• WikiPathways: WP1451 (classic)
• Species: Caenorhabditis elegans

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests 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: 21
• 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: 1
  • 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: 3

Fails

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: 21

http://classic.wikipathways.org/instance/WP1451_r126324 acdh-10 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 acdh-7 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 pccb-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-9 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 hacd-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 bcat-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ivd-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-5 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-3 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-8 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 acdh-3 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 Y39E4A.3 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ard-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-2 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-6 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 kat-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 pcca-1 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 acdh-8 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 tag-173 with datasource WormBase
http://classic.wikipathways.org/instance/WP1451_r126324 ech-7 with datasource WormBase

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

Interactions with Labels

Interactions found that involve Labels: 1

• http://classic.wikipathways.org/instance/WP1451_r126324 “Valine, leucine and isoleucine biosynthesis” with graphId aa998

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/WP1451_r126324 ‘Valine, leucine and isoleucine degradation’ in Caenorhabditis elegans has zero references;

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