wikipathways-collection

WikiPathways WP5044

• WikiPathways: WP5044 (classic)
• Species: Homo sapiens
• Scholia: WP5044

  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: 6
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 2
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 5 tests OK!
• 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: 17
  • 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
  • ChEBIIDsNotMarkedAsMetabolite: .. all OK!
  • HMDBIDsNotMarkedAsMetabolite: .. all OK!
  • KEGGIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotNumbers: .. all OK!
  • PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemSubstanceIDsNotNumbers: .. all OK!
  • achiralAminoAcids: .x we found 1 problem(s):
    • Metabolites with ChEBI identifiers of achiral amino acids: 1
  • casNumbersNotMarkedAsMetabolite: .. all OK!
  • chemspiderIDsNotMarkedAsMetabolite: .. all OK!
  • metaboliteAlsoOtherType: .. all OK!
  • metabolitesWithAnEnsembleID: .. all OK!
  • metabolitesWithAnEntrezGeneID: .. all OK!
  • metabolitesWithDbButNoIdentifier: .. all OK!
  • metabolitesWithIdentifierButNoDb: .. all 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: 119
• Number of assertions: 239
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 6

• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/e1e70 (IDO1 promoter )
• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/e5a73 (JNK Signaling Pathway)
• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/dc239 (Liposaccharides)
• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/b04cb (NAD de novo Synthesis )
• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/a4c6f (Serotonin/Melatonin Pathway)
• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/d14fc (other miRNAs)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

Datanodes of unknown type

The following DataNodes have Unknown @Type: 2

• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/dc239 (Liposaccharides)
• http://classic.wikipathways.org/instance/WP5044_r134362 http://rdf.wikipathways.org/Pathway/WP5044_r134362/DataNode/d14fc (other miRNAs)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/unknownTypes

Interactions with Labels

Interactions found that involve Labels: 17

• http://classic.wikipathways.org/instance/WP5044_r134362 “Apoptosis” with graphId fd4f2
• http://classic.wikipathways.org/instance/WP5044_r134362 “Cell proliferation” with graphId add23
• http://classic.wikipathways.org/instance/WP5044_r134362 “Depletion of cytosolic tryptophan” with graphId b3b40
• http://classic.wikipathways.org/instance/WP5044_r134362 “Cell differentiation” with graphId e798c
• http://classic.wikipathways.org/instance/WP5044_r134362 “Autophagy” with graphId d39c2
• http://classic.wikipathways.org/instance/WP5044_r134362 “Reduction of ROS” with graphId c2253
• http://classic.wikipathways.org/instance/WP5044_r134362 “Oxidative stress” with graphId e6086
• http://classic.wikipathways.org/instance/WP5044_r134362 “Inflammation” with graphId ade9d
• http://classic.wikipathways.org/instance/WP5044_r134362 “Senescence” with graphId e811b
• http://classic.wikipathways.org/instance/WP5044_r134362 “Cell cycle arrest” with graphId f29f1
• http://classic.wikipathways.org/instance/WP5044_r134362 “Glutathionine metabolism” with graphId e8eb6
• http://classic.wikipathways.org/instance/WP5044_r134362 “Reduction of ROS” with graphId ee162
• http://classic.wikipathways.org/instance/WP5044_r134362 “Protection against ROS” with graphId cbea5
• http://classic.wikipathways.org/instance/WP5044_r134362 “change in NAD+/NADH” with graphId e1797
• http://classic.wikipathways.org/instance/WP5044_r134362 “Inflammation” with graphId f9d75
• http://classic.wikipathways.org/instance/WP5044_r134362 “Arachidonic acid metabolism” with graphId c6c38
• http://classic.wikipathways.org/instance/WP5044_r134362 “Fatty Acid Oxidation” with graphId bfec9

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

MetabolitesTests.achiralAminoAcids

Metabolites with ChEBI identifiers of achiral amino acids: 1

http://classic.wikipathways.org/instance/WP5044_r134362 Tryptophan CHEBI:27897