wikipathways-collection

WikiPathways WP1631

• WikiPathways: WP1631 (classic)
• Species: Mycobacterium tuberculosis

  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: 13
• 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: 1

• http://classic.wikipathways.org/instance/WP1631_r128405 http://rdf.wikipathways.org/Pathway/WP1631_r128405/DataNode/f2656 (Tropane, piperidine and pyridine alkaloid biosynthesis)

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: 13

http://classic.wikipathways.org/instance/WP1631_r128405 bioF1 with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 mycP1 with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 bioA with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 bioF2 with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 bioB with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 bioD with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 Rv3668c with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 Rv2672 with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 mycP2 with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 Rv2223c with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 pepQ with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 Rv2224c with datasource TubercuList
http://classic.wikipathways.org/instance/WP1631_r128405 birA with datasource TubercuList

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/WP1631_r128405 ‘Biotin metabolism’ in Mycobacterium tuberculosis has zero references;

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