wikipathways-collection

WikiPathways WP4808

• WikiPathways: WP4808 (classic)
• Species: Homo sapiens
• Scholia: WP4808

  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: 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: 18
  • UnconnectedPoints: .x we found 1 problem(s):
    • Interactions with unconnected points: 5
  • 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: .x we found 1 problem(s):
    • Old NCBI Gene identifiers detected: 1
  • outdatedChEBIIdentifiers: .. all OK!
  • outdatedHMDBIdentifiers: .. all OK!
  • outdatedUniProtKBIdentifiers2: .. all OK!
• 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

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/WP4808_r137050 TNAP with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 18

• http://classic.wikipathways.org/instance/WP4808_r137050 “Hypertrophy” with graphId b7a
• http://classic.wikipathways.org/instance/WP4808_r137050 “WNT signaling canonical / non-canonical” with graphId bed
• http://classic.wikipathways.org/instance/WP4808_r137050 “OMIM:156500 Metaphyseal chondrodysplasia, Schmid type” with graphId f4641
• http://classic.wikipathways.org/instance/WP4808_r137050 “Proliferation” with graphId d5f
• http://classic.wikipathways.org/instance/WP4808_r137050 “Mineralization” with graphId e4d
• http://classic.wikipathways.org/instance/WP4808_r137050 “Gs” with graphId fc068
• http://classic.wikipathways.org/instance/WP4808_r137050 “Vascular invasion” with graphId e31d0
• http://classic.wikipathways.org/instance/WP4808_r137050 “Full differentiation” with graphId fba0c
• http://classic.wikipathways.org/instance/WP4808_r137050 “Dying” with graphId b59
• http://classic.wikipathways.org/instance/WP4808_r137050 “OMIM:271665 Spondylometaepiphyseal dysplasia, short limb-hand type” with graphId b7cc5
• http://classic.wikipathways.org/instance/WP4808_r137050 “OMIM:245150 Keutel syndrome” with graphId c0def
• http://classic.wikipathways.org/instance/WP4808_r137050 “Osteoblastic differentiation” with graphId f20
• http://classic.wikipathways.org/instance/WP4808_r137050 “OMIM:600430 Chromosome 2q37 deletion syndrome” with graphId f8e71
• http://classic.wikipathways.org/instance/WP4808_r137050 “Integrins” with graphId d3b0f
• http://classic.wikipathways.org/instance/WP4808_r137050 “BMPs” with graphId b2d
• http://classic.wikipathways.org/instance/WP4808_r137050 “OMIM:613848 Osteogenesis imperfecta, type X” with graphId aa6b4
• http://classic.wikipathways.org/instance/WP4808_r137050 “OMIM:613073 Metaphyseal anadysplasia 2” with graphId e6bf2
• http://classic.wikipathways.org/instance/WP4808_r137050 “OMIM:614732 Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, and genital anomalies” with graphId f99f8

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

Interactions with unconnected points

Interactions with unconnected points: 5

• http://classic.wikipathways.org/instance/WP4808_r137050

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

NCBI Gene identifier has been retracted

Old NCBI Gene identifiers detected: 1

• http://classic.wikipathways.org/instance/WP4808_r137050 TNAP has NCBI Gene 445341 but has been replaced by Entry Withdrawn

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