wikipathways-collection

WikiPathways WP5380

• WikiPathways: WP5380 (classic)
• Species: Homo sapiens
• Scholia: WP5380

  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: 9
  • unknownTypes_knownDatasource: .. all OK!
  • unknownTypes: .x we found 1 problem(s):
    • The following DataNodes have Unknown @Type: 4
  • 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: 1
• 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: 13
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 1
  • 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: all 6 tests 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: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 9

• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/b5485 ()
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/def5f ()
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/eb75f ()
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/e6b38 (7-methylguanosine-containing mRNA cap )
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/a5dea (G protein-coupled receptors)
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/e1d48 (G protein-coupled receptors)
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/f29ae (H2A)
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/a98d2 (dsRNA)
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/a6b01 (ssRNA)

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

Datanodes of unknown type

The following DataNodes have Unknown @Type: 4

• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/e6b38 (7-methylguanosine-containing mRNA cap )
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/ae554 (BRCA1-A complex)
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/a5dea (G protein-coupled receptors)
• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/DataNode/e1d48 (G protein-coupled receptors)

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

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: 1

http://classic.wikipathways.org/instance/WP5380_r134531 F-Actin with datasource Pfam

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

Interactions with Labels

Interactions found that involve Labels: 13

• http://classic.wikipathways.org/instance/WP5380_r134531 “May be involved in the regulation of neuronal survival, differentiation and axonal outgrowth” with graphId bdb14
• http://classic.wikipathways.org/instance/WP5380_r134531 “Function unknown” with graphId e3521
• http://classic.wikipathways.org/instance/WP5380_r134531 “may bind to miRNA hairpins” with graphId f10c3
• http://classic.wikipathways.org/instance/WP5380_r134531 “Lipid droplet degradation” with graphId e3658
• http://classic.wikipathways.org/instance/WP5380_r134531 “Function unknown” with graphId c9328
• http://classic.wikipathways.org/instance/WP5380_r134531 “Facilitates ribosome binding” with graphId f2ed5
• http://classic.wikipathways.org/instance/WP5380_r134531 “acts as a H3K27 mimic increases selectively H3K27me3 when knocked out” with graphId a634a
• http://classic.wikipathways.org/instance/WP5380_r134531 “Controls the packing of microvilli at the apical membrane of epithelial cells” with graphId aa4bf
• http://classic.wikipathways.org/instance/WP5380_r134531 “Involved in autophagy-related processes” with graphId a310e
• http://classic.wikipathways.org/instance/WP5380_r134531 “May play a role in cell-cell adhesion and contact inhibition” with graphId cc3a8
• http://classic.wikipathways.org/instance/WP5380_r134531 “involved in ER secretory pathway” with graphId c245b
• http://classic.wikipathways.org/instance/WP5380_r134531 “Function unknown” with graphId c326e
• http://classic.wikipathways.org/instance/WP5380_r134531 “Desensitization and internalization” with graphId ecb80

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

Possible MIM translocation

Interactions between identical nodes: 1

• http://classic.wikipathways.org/instance/WP5380_r134531 http://rdf.wikipathways.org/Pathway/WP5380_r134531/WP/Interaction/id1370f857 “phosphatidic acids” (https://identifiers.org/chebi/CHEBI:16337) and phosphatidic acids” (https://identifiers.org/chebi/CHEBI:16337)

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