wikipathways-collection

WikiPathways WP4861

• WikiPathways: WP4861 (classic)
• Species: Homo sapiens
• Scholia: WP4861

  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: 11
  • 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: 2
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests
  • noMetaboliteToNonMetaboliteConversions: .. all OK!
  • noNonMetaboliteToMetaboliteConversions: .. all OK!
  • noGeneProteinConversions: .. all OK!
  • nonNumericIDs: .. all OK!
  • interactionsWithLabels: .. all OK!
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 3
  • 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
  • outdatedHGNCSymbol: .. all OK!
  • outdatedHGNCAccessionNumber: .. all OK!
  • outdatedNCBIIdentifiers: .. all OK!
  • outdatedChEBIIdentifiers: .. all OK!
  • outdatedHMDBIdentifiers: .. all OK!
  • outdatedUniProtKBIdentifiers2: .x we found 1 problem(s):
    • Old UniProtKB identifiers detected: 1
• UniProtTests: all 5 tests OK!
• UnicodeTests: all 17 tests OK!
• WikidataTests: all 4 tests OK!

Summary

• Number of test classes: 22
• Number of tests: 148
• Number of assertions: 295
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 11

• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/c90ec (Amino acid synthesis Antioxidant response Apoptosis)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/e0713 (C/EBP CCAAT enhancer binding protein)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/d0da6 (CRE cAMP response element)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/c085b (ER protein chaperones Lipid biosynthesis ER-associated degradation)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/e9fd9 (ER-associated mRNA)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/ed36d (Global protein translation)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/d43bc (MERS 4a)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/c094e (RIDD)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/a4bee (SARS 8ab)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/dc80b (SARS, IBV infection)
• http://classic.wikipathways.org/instance/WP4861_r140454 http://rdf.wikipathways.org/Pathway/WP4861_r140454/DataNode/cd9a0 (SARS, OC43, MHV, IBV infection)

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: 2

http://classic.wikipathways.org/instance/WP4861_r140454 SARS E with datasource UniProtKB
http://classic.wikipathways.org/instance/WP4861_r140454 PP1 with datasource Wikidata

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

Interactions with unconnected points

Interactions with unconnected points: 3

• http://classic.wikipathways.org/instance/WP4861_r140454

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

UniProtKB identifier has been retracted

Old UniProtKB identifiers detected: 1

• http://classic.wikipathways.org/instance/WP4861_r140454 PPP1R9B has UniProtKB ID D3DTX6 but has been replaced by Q96SB3

More details at https://www.wikipathways.org/WikiPathwaysCurator/Sec2PriProjectTests/outdatedUniProtKBIdentifiers2