wikipathways-collection

WikiPathways WP2578

• WikiPathways: WP2578 (classic)
• Species: Caenorhabditis elegans

  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: 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: 4
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 38
  • 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: all 6 tests 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/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/DataNode/b42c4 (BiP/ GRP78)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/DataNode/c255f (BiP/ GRP78)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/DataNode/d13ed (BiP/ GRP78)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/DataNode/eb96f (Development)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/DataNode/b6535 (ER homeostasis)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/DataNode/ea7ab (Translation)

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: 1

http://classic.wikipathways.org/instance/WP2578_r135395 ABU-1 with datasource WormBase

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

Interactions with Labels

Interactions found that involve Labels: 4

• http://classic.wikipathways.org/instance/WP2578_r135395 “ER Stress (unfolded proteins)” with graphId e8aa5
• http://classic.wikipathways.org/instance/WP2578_r135395 “Environmental stress (e.g. heat, hypoxia, pathogens)” with graphId c6a54
• http://classic.wikipathways.org/instance/WP2578_r135395 “21 genes induced by PEK-1” with graphId c3248
• http://classic.wikipathways.org/instance/WP2578_r135395 “139 genes induced by IRE-1/XBP-1 pathway” with graphId ff1a5

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

Possible MIM translocation

Interactions between identical nodes: 38

• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf41d3b1f “uggt-1” (https://identifiers.org/ensembl/WBGene00018604) and uggt-1” (https://identifiers.org/ensembl/WBGene00018604)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf41d3b1f “uggt-1” (https://identifiers.org/ensembl/WBGene00018604) and UGGT-1” (https://identifiers.org/ensembl/WBGene00018604)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf41d3b1f “UGGT-1” (https://identifiers.org/ensembl/WBGene00018604) and uggt-1” (https://identifiers.org/ensembl/WBGene00018604)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf41d3b1f “UGGT-1” (https://identifiers.org/ensembl/WBGene00018604) and UGGT-1” (https://identifiers.org/ensembl/WBGene00018604)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf124f596 “ATF-6” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf124f596 “ATF-6” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf124f596 “ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf124f596 “ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id406b6290 “PEK-1” (https://identifiers.org/ensembl/WBGene00003970) and PEK-1” (https://identifiers.org/ensembl/WBGene00003970)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id1f0c3ef5 “apy-1” (https://identifiers.org/ensembl/WBGene00017244) and apy-1” (https://identifiers.org/ensembl/WBGene00017244)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id1f0c3ef5 “apy-1” (https://identifiers.org/ensembl/WBGene00017244) and APY-1” (https://identifiers.org/ensembl/WBGene00017244)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id1f0c3ef5 “APY-1” (https://identifiers.org/ensembl/WBGene00017244) and apy-1” (https://identifiers.org/ensembl/WBGene00017244)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id1f0c3ef5 “APY-1” (https://identifiers.org/ensembl/WBGene00017244) and APY-1” (https://identifiers.org/ensembl/WBGene00017244)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ida52039d9 “ATF-6” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ida52039d9 “ATF-6” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ida52039d9 “ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ida52039d9 “ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idccbf72f4 “ATF-6” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idccbf72f4 “ATF-6” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idccbf72f4 “ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idccbf72f4 “ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222) and ATF-6 bZip domain” (https://identifiers.org/ensembl/WBGene00000222)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id5b58735 “HSP-4/ BiP/GRP78” (https://identifiers.org/ensembl/WBGene00002008) and HSP-4/ BiP/GRP78” (https://identifiers.org/ensembl/WBGene00002008)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id5b58735 “HSP-4/ BiP/GRP78” (https://identifiers.org/ensembl/WBGene00002008) and hsp-4” (https://identifiers.org/ensembl/WBGene00002008)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id5b58735 “hsp-4” (https://identifiers.org/ensembl/WBGene00002008) and HSP-4/ BiP/GRP78” (https://identifiers.org/ensembl/WBGene00002008)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/id5b58735 “hsp-4” (https://identifiers.org/ensembl/WBGene00002008) and hsp-4” (https://identifiers.org/ensembl/WBGene00002008)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ide4929131 “CRT-1” (https://identifiers.org/ensembl/WBGene00000802) and CRT-1” (https://identifiers.org/ensembl/WBGene00000802)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ide4929131 “CRT-1” (https://identifiers.org/ensembl/WBGene00000802) and crt-1” (https://identifiers.org/ensembl/WBGene00000802)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ide4929131 “crt-1” (https://identifiers.org/ensembl/WBGene00000802) and CRT-1” (https://identifiers.org/ensembl/WBGene00000802)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/ide4929131 “crt-1” (https://identifiers.org/ensembl/WBGene00000802) and crt-1” (https://identifiers.org/ensembl/WBGene00000802)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idf0dbc297 “IRE-1” (https://identifiers.org/ensembl/WBGene00002147) and IRE-1” (https://identifiers.org/ensembl/WBGene00002147)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idb5e95ca “UGGT-2” (https://identifiers.org/ensembl/WBGene00009178) and UGGT-2” (https://identifiers.org/ensembl/WBGene00009178)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idb5e95ca “UGGT-2” (https://identifiers.org/ensembl/WBGene00009178) and uggt-2” (https://identifiers.org/ensembl/WBGene00009178)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idb5e95ca “uggt-2” (https://identifiers.org/ensembl/WBGene00009178) and UGGT-2” (https://identifiers.org/ensembl/WBGene00009178)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/idb5e95ca “uggt-2” (https://identifiers.org/ensembl/WBGene00009178) and uggt-2” (https://identifiers.org/ensembl/WBGene00009178)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/iddd3b1699 “xbp-1 mRNA” (https://identifiers.org/ensembl/WBGene00006959) and xbp-1 mRNA” (https://identifiers.org/ensembl/WBGene00006959)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/iddd3b1699 “xbp-1 mRNA” (https://identifiers.org/ensembl/WBGene00006959) and XBP-1” (https://identifiers.org/ensembl/WBGene00006959)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/iddd3b1699 “XBP-1” (https://identifiers.org/ensembl/WBGene00006959) and xbp-1 mRNA” (https://identifiers.org/ensembl/WBGene00006959)
• http://classic.wikipathways.org/instance/WP2578_r135395 http://rdf.wikipathways.org/Pathway/WP2578_r135395/WP/Interaction/iddd3b1699 “XBP-1” (https://identifiers.org/ensembl/WBGene00006959) and XBP-1” (https://identifiers.org/ensembl/WBGene00006959)

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