wikipathways-collection

WikiPathways WP1596

• WikiPathways: WP1596 (classic)
• Species: Mus musculus

  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: 8
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests: all 4 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: 2
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 3
  • 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: 117
• Number of assertions: 235
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 8

• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/efe7c (BMP1/2/4/9)
• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/d7a54 (BMPR-1)
• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/c9a17 (IL1R)
• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/d1d51 (JAK1/2)
• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/d488e (SMAD-1/5/8)
• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/c3b0c (STAT3)
• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/b12e8 (Trfr1)
• http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/DataNode/f1796 (cMyc)

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

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 2

http://classic.wikipathways.org/instance/WP1596_r126400 "Inflammation" with graphId e4dbb
http://classic.wikipathways.org/instance/WP1596_r126400 "Oxidative Stress" with graphId f04ec

Possible MIM translocation

Interactions between identical nodes: 3

http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/WP/Interaction/id748d82f "Iron" (https://identifiers.org/hmdb/HMDB0000692) and 
Iron" (https://identifiers.org/hmdb/HMDB0000692)
http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/WP/Interaction/idcf4701b4 "hepcidin" (https://identifiers.org/ensembl/ENSMUSG00000050440) and 
hepcidin" (https://identifiers.org/ensembl/ENSMUSG00000050440)
http://classic.wikipathways.org/instance/WP1596_r126400 http://rdf.wikipathways.org/Pathway/WP1596_r126400/WP/Interaction/id988524b3 "Iron" (https://identifiers.org/hmdb/HMDB0000692) and 
Iron" (https://identifiers.org/hmdb/HMDB0000692)

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP1596_r126400 ‘Iron homeostasis’ in Mus musculus has zero references;

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