wikipathways-collection

WikiPathways WP5568

• WikiPathways: WP5568 (classic)
• Species: Homo sapiens
• Scholia: WP5568

  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: .. all OK!
  • unknownTypes_Reactome: .. all OK!
  • otherDataSource: .. all OK!
• EnsemblTests: all 4 tests OK!
• GeneTests
  • entrezGeneIdentifiersNotNumber: .. all OK!
  • affyProbeIdentifiersNotCorrect: .. all OK!
  • outdatedIdentifiers: .. all OK!
  • numericHGNCIDs: .. 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: 3
• 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: 14
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 14
  • 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: all 15 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• Sec2PriProjectTests: all 6 tests OK!
• UniProtTests
  • outdatedIdentifiers: .. all OK!
  • deletedIdentifiers: .. all OK!
  • unreviewedIdentifiers: .. all OK!
  • incorrectIdentifiers: .. all OK!
  • allP62805: .x we found 1 problem(s):
    • Potentially imprecise UniProt identifier: 1
• UnicodeTests: all 16 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 147
• Number of assertions: 293
• Number of fails: 5

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 6

• http://classic.wikipathways.org/instance/WP5568_r140346 http://rdf.wikipathways.org/Pathway/WP5568_r140346/DataNode/cae37 (Cell differentiation)
• http://classic.wikipathways.org/instance/WP5568_r140346 http://rdf.wikipathways.org/Pathway/WP5568_r140346/DataNode/ecb41 (Cell reprogramming)
• http://classic.wikipathways.org/instance/WP5568_r140346 http://rdf.wikipathways.org/Pathway/WP5568_r140346/DataNode/ffb94 (Early embryogenesis)
• http://classic.wikipathways.org/instance/WP5568_r140346 http://rdf.wikipathways.org/Pathway/WP5568_r140346/DataNode/c28cd (Embryonic development)
• http://classic.wikipathways.org/instance/WP5568_r140346 http://rdf.wikipathways.org/Pathway/WP5568_r140346/DataNode/d0b5b (Embryonic stem-cell pluripotency)
• http://classic.wikipathways.org/instance/WP5568_r140346 http://rdf.wikipathways.org/Pathway/WP5568_r140346/DataNode/a4eb6 (Organogenesis (neural tube))

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: 3

http://classic.wikipathways.org/instance/WP5568_r140346 H2A with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5568_r140346 H3 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP5568_r140346 H2B with datasource UniProtKB

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

Interactions with Labels

Interactions found that involve Labels: 14

• http://classic.wikipathways.org/instance/WP5568_r140346 “Stimulation” with graphId ce9ca
• http://classic.wikipathways.org/instance/WP5568_r140346 “Activation of process” with graphId a82ae
• http://classic.wikipathways.org/instance/WP5568_r140346 “Intellectual Developmental Disorder with Speech Delay and Dysmorphic Facies” with graphId b7d32
• http://classic.wikipathways.org/instance/WP5568_r140346 “Inhibition” with graphId b7280
• http://classic.wikipathways.org/instance/WP5568_r140346 “Regulation” with graphId c768a
• http://classic.wikipathways.org/instance/WP5568_r140346 “Intellectual Developmental Disorder with Microcephaly and with or Without Ocular Malformations or Hypogonadotropic Hypogonadism” with graphId b59c5
• http://classic.wikipathways.org/instance/WP5568_r140346 “Epilepsy” with graphId b028f
• http://classic.wikipathways.org/instance/WP5568_r140346 “Activation of pathway” with graphId c9010
• http://classic.wikipathways.org/instance/WP5568_r140346 “Coffin-Siris Syndrome 1 “ with graphId f0216
• http://classic.wikipathways.org/instance/WP5568_r140346 “Microphthalmia, Syndromic 3 “ with graphId cf1a8
• http://classic.wikipathways.org/instance/WP5568_r140346 “Septooptic Dysplasia “ with graphId e1326
• http://classic.wikipathways.org/instance/WP5568_r140346 “Binding of gene” with graphId b0402
• http://classic.wikipathways.org/instance/WP5568_r140346 “Associated disease” with graphId c8cea
• http://classic.wikipathways.org/instance/WP5568_r140346 “ACCAAAG” with graphId df5c1

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

Interactions with unconnected points

Interactions with unconnected points: 14

• http://classic.wikipathways.org/instance/WP5568_r140346

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

P62805 matches 14 genes

Potentially imprecise UniProt identifier: 1

• http://classic.wikipathways.org/instance/WP5568_r140346 H4 uses P62805

More details at https://www.wikipathways.org/WikiPathwaysCurator/UniProtTests/allP62805