wikipathways-collection

WikiPathways WP4673

• WikiPathways: WP4673 (classic)
• Species: Homo sapiens
• Scholia: WP4673

  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: 2
  • 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 13 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .x we found 1 problem(s):
    • Unexpected non-metabolite to metabolite conversions: 1
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .x we found 1 problem(s):
    • Interactions found that involve Labels: 6
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 5
  • 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 8 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: 99
• Number of assertions: 200
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 2

http://classic.wikipathways.org/instance/WP4673_r119920 http://rdf.wikipathways.org/Pathway/WP4673_r119920/DataNode/a8d38 (LOC203413)
http://classic.wikipathways.org/instance/WP4673_r119920 http://rdf.wikipathways.org/Pathway/WP4673_r119920/DataNode/cc765 (piRNA precursor)

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

InteractionTests.noNonMetaboliteToMetaboliteConversions

Unexpected non-metabolite to metabolite conversions: 1

Homo sapiens http://classic.wikipathways.org/instance/WP4673_r119920 -> https://identifiers.org/ensembl/ENSG00000278637 https://identifiers.org/hmdb/HMDB0001423 http://rdf.wikipathways.org/Pathway/WP4673_r119920/WP/Interaction/idf9d507f4

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 6

http://classic.wikipathways.org/instance/WP4673_r119920 "Sperm specific gene expression" with graphId e2d82
http://classic.wikipathways.org/instance/WP4673_r119920 "piRNA" with graphId e5545
http://classic.wikipathways.org/instance/WP4673_r119920 "DNA" with graphId d2a63
http://classic.wikipathways.org/instance/WP4673_r119920 "interacts with different proteins
that conctrol the translation of 
mRNAs of spermatogenesis associated proteins" with graphId acd5f
http://classic.wikipathways.org/instance/WP4673_r119920 "retrotransposons" with graphId cce8f
http://classic.wikipathways.org/instance/WP4673_r119920 "DNA
synapsed chromosome axis" with graphId eb246

Possible MIM translocation

Interactions between identical nodes: 5

http://classic.wikipathways.org/instance/WP4673_r119920 http://rdf.wikipathways.org/Pathway/WP4673_r119920/WP/Interaction/idfb2588eb "HMGA1" (https://identifiers.org/ensembl/ENSG00000137309) and 
HMGA1" (https://identifiers.org/ensembl/ENSG00000137309)
http://classic.wikipathways.org/instance/WP4673_r119920 http://rdf.wikipathways.org/Pathway/WP4673_r119920/WP/Interaction/idefc85102 "HIST1H4A" (https://identifiers.org/ensembl/ENSG00000278637) and 
HIST1H4A" (https://identifiers.org/ensembl/ENSG00000278637)
http://classic.wikipathways.org/instance/WP4673_r119920 http://rdf.wikipathways.org/Pathway/WP4673_r119920/WP/Interaction/id8a7e8672 "HIST3H3" (https://identifiers.org/ensembl/ENSG00000168148) and 
HIST3H3" (https://identifiers.org/ensembl/ENSG00000168148)
http://classic.wikipathways.org/instance/WP4673_r119920 http://rdf.wikipathways.org/Pathway/WP4673_r119920/WP/Interaction/id1446636f "PRDM9" (https://identifiers.org/ensembl/ENSG00000164256) and 
PRDM9" (https://identifiers.org/ensembl/ENSG00000164256)
http://classic.wikipathways.org/instance/WP4673_r119920 http://rdf.wikipathways.org/Pathway/WP4673_r119920/WP/Interaction/idf9d507f4 "HIST1H4A" (https://identifiers.org/ensembl/ENSG00000278637) and 
HIST1H4A" (https://identifiers.org/ensembl/ENSG00000278637)

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