wikipathways-collection

WikiPathways WP2912

• WikiPathways: WP2912 (classic)
• Species: Bos taurus

  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!
  • 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: 4
• 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: 6
  • 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 14 tests OK!
• OudatedDataSourcesTests: all 24 tests OK!
• PathwayTests: all 7 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests
  • nonNumericPubMedIDs: .. all OK!
  • unexpectedPubMedIdentifier: .. all OK!
  • zeroPubMedIDs: .. all OK!
  • atLeastOneReference: .x we found 1 problem(s):
    • Found 1 pathways with zero (PubMed) references
  • citesRetractedArticle: .. all OK!
  • outdatedPubMedIdentifiers: .. all 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: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 6

• http://classic.wikipathways.org/instance/WP2912_r107057 http://rdf.wikipathways.org/Pathway/WP2912_r107057/DataNode/e2f12 (Adenosine)
• http://classic.wikipathways.org/instance/WP2912_r107057 http://rdf.wikipathways.org/Pathway/WP2912_r107057/DataNode/eb03a (Arachidonic acid metabolism)
• http://classic.wikipathways.org/instance/WP2912_r107057 http://rdf.wikipathways.org/Pathway/WP2912_r107057/DataNode/ff8a9 (Calcium signal Pathway)
• http://classic.wikipathways.org/instance/WP2912_r107057 http://rdf.wikipathways.org/Pathway/WP2912_r107057/DataNode/ccdff (MHC)
• http://classic.wikipathways.org/instance/WP2912_r107057 http://rdf.wikipathways.org/Pathway/WP2912_r107057/DataNode/fba9a (MHC)
• http://classic.wikipathways.org/instance/WP2912_r107057 http://rdf.wikipathways.org/Pathway/WP2912_r107057/DataNode/f24c9 (PKG)

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: 4

http://classic.wikipathways.org/instance/WP2912_r107057 PPP1R12B with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2912_r107057 PLCB3 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2912_r107057 phospholipase A2 with datasource Entrez Gene
http://classic.wikipathways.org/instance/WP2912_r107057 CALML6 with datasource Entrez Gene

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

Interactions with Labels

Interactions found that involve Labels: 6

• http://classic.wikipathways.org/instance/WP2912_r107057 “Crossbreidge” with graphId b756c
• http://classic.wikipathways.org/instance/WP2912_r107057 “RELAXCATION” with graphId b0cea
• http://classic.wikipathways.org/instance/WP2912_r107057 “Reduction of intracellular Ca2+ concentration” with graphId a9371
• http://classic.wikipathways.org/instance/WP2912_r107057 “Depolarization” with graphId f1346
• http://classic.wikipathways.org/instance/WP2912_r107057 “Intravasal pressure /stretch” with graphId a0852
• http://classic.wikipathways.org/instance/WP2912_r107057 “Hyperpolarization” with graphId b85a4

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

At least one reference

Found 1 pathways with zero (PubMed) references

• http://classic.wikipathways.org/instance/WP2912_r107057 ‘Vascular smooth muscle contraction’ in Bos taurus has zero references;

More details at https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference