wikipathways-collection

WikiPathways WP117

• WikiPathways: WP117 (classic)
• Species: Homo sapiens
• Scholia: WP117

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• DataNodesTests: all 5 tests 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: 14
• GeneralTests: all 15 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• InteractionTests: all 9 tests 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: .x we found 1 problem(s):
    • Old NCBI Gene identifiers detected: 2
  • outdatedChEBIIdentifiers: .. all OK!
  • outdatedHMDBIdentifiers: .. all OK!
  • outdatedUniProtKBIdentifiers2: .x we found 1 problem(s):
    • Old UniProtKB identifiers detected: 1
• UniProtTests
  • outdatedIdentifiers: .. all OK!
  • deletedIdentifiers: .. all OK!
  • unreviewedIdentifiers: .x we found 1 problem(s):
    • Unreviewed UniProt identifiers: 2
  • incorrectIdentifiers: .. all OK!
  • allP62805: .. all OK!
• 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: 4

Fails

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: 14

http://classic.wikipathways.org/instance/WP117_r137227 OR7E35P with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP117_r137227 OR51A1P with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP117_r137227 HSA12 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP117_r137227 Q9H2C7 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP117_r137227 OR1E3P with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP117_r137227 OR7E19P with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP117_r137227 O60411 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP117_r137227 CCR2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP117_r137227 OR7E18P with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP117_r137227 HSA10 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP117_r137227 OR5D3 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP117_r137227 OR1J5 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP117_r137227 P47889 with datasource UniProtKB
http://classic.wikipathways.org/instance/WP117_r137227 Q9BYT4 with datasource UniProtKB

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

NCBI Gene identifier has been retracted

Old NCBI Gene identifiers detected: 2

• http://classic.wikipathways.org/instance/WP117_r137227 CCR2 has NCBI Gene 1231 but has been replaced by 729230
• http://classic.wikipathways.org/instance/WP117_r137227 OR1J5 has NCBI Gene 81370 but has been replaced by 26740

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

UniProtKB identifier has been retracted

Old UniProtKB identifiers detected: 1

• http://classic.wikipathways.org/instance/WP117_r137227 P47889 has UniProtKB ID P47889 but has been replaced by Entry Withdrawn

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

Unreviewed UniProtKB identifiers

Unreviewed UniProt identifiers: 2

• http://classic.wikipathways.org/instance/WP117_r137227 O60411 O60411 is unreviewed, please visit UniProt (https://www.uniprot.org/uniprot/O60411) for (potential) reviewed version;
• http://classic.wikipathways.org/instance/WP117_r137227 OR5D3 O95220 is unreviewed, please visit UniProt (https://www.uniprot.org/uniprot/O95220) for (potential) reviewed version;

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