lipidmaps-wp-curation

WikiPathways WP2533

• WikiPathways: WP2533 (classic)
• Species: Homo sapiens
• Scholia: WP2533
• WPRDF file: wp/Human/WP2533.ttl
• GPMLRDF file: wp/gpml/Human/WP2533.ttl
• SBML file: sbml/WP2533.sbml (SVG) (conversion notes)

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: all 5 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 1 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: 11
  • possibleTranslocations: .x we found 1 problem(s):
    • Interactions between identical nodes: 4
  • noProteinProteinConversions: .. all OK!
  • incorrectKEGGIdentifiers: .. all OK!
• KEGGMetaboliteTests: all 2 tests OK!
• LIPIDMAPSTests
  • retiredIdentifiers: .. all OK!
  • onlyLIPIDMAPS: .x we found 1 problem(s):
    • Expected a LIPID MAPS identifier, but found other identifiers: 59
• MetaboliteStructureTests: all 1 tests OK!
• MetabolitesTests: all 14 tests OK!
• OudatedDataSourcesTests: all 9 tests OK!
• PathwayTests: all 11 tests OK!
• ProteinsTests: all 2 tests OK!
• PubChemMetabolitesTests: all 3 tests OK!
• ReferencesTests: all 6 tests OK!
• UniProtTests: all 5 tests OK!
• WikidataTests: all 14 tests OK!

Summary

• Number of test classes: 21
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 4

Fails

Data nodes without an identifier

The following DataNodes have no identifier: 6

• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/DataNode/b1e34 (1,2-diacyl-sn-glycero-3-phospho-(1’-sn-glycero-phosphate) (PGP))
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/DataNode/ef20e (Acyl group)
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/DataNode/e8b46 (H₂O)
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/DataNode/a5f9b (O₂ + NADH + H+)
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/DataNode/af0fe (PPi)
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/DataNode/b9d3a (Pi)

More details at https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier

Interactions with unconnected points

Interactions with unconnected points: 11

• http://classic.wikipathways.org/instance/WP2533_rr139678

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

Possible MIM translocation

Interactions between identical nodes: 4

• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/WP/Interaction/ccbb7 “1-alkyl-2-acyl-sn-glycero-3-phosphocholine (Plasmanylcholine)” (https://identifiers.org/chebi/CHEBI:36702) and 1-alkyl-2-acyl-sn-glycero-3-phosphocholine (Plasmanylcholine)” (https://identifiers.org/chebi/CHEBI:36702)
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/WP/Interaction/ccbb7 “1-alkyl-2-acyl-sn-glycero-3-phosphocholine (Plasmanylcholine)” (https://identifiers.org/chebi/CHEBI:36702) and 1-alkyl-sn-glycero-3-phosphocholine (Lyso PAF)” (https://identifiers.org/chebi/CHEBI:36702)
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/WP/Interaction/ccbb7 “1-alkyl-sn-glycero-3-phosphocholine (Lyso PAF)” (https://identifiers.org/chebi/CHEBI:36702) and 1-alkyl-2-acyl-sn-glycero-3-phosphocholine (Plasmanylcholine)” (https://identifiers.org/chebi/CHEBI:36702)
• http://classic.wikipathways.org/instance/WP2533_r139678 http://rdf.wikipathways.org/Pathway/WP2533_rr139678/WP/Interaction/ccbb7 “1-alkyl-sn-glycero-3-phosphocholine (Lyso PAF)” (https://identifiers.org/chebi/CHEBI:36702) and 1-alkyl-sn-glycero-3-phosphocholine (Lyso PAF)” (https://identifiers.org/chebi/CHEBI:36702)

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

Only LIPID MAPS identifiers

Expected a LIPID MAPS identifier, but found other identifiers: 59

http://classic.wikipathways.org/instance/WP2533_rr139678 Phosphocholine (Choline-P) has 1014 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Ethanolamine phosphate has 1015 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Phosphorylethanolamine has 1015 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Pi has 1061 from PubChem-substance but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 CDP-ethanolamine has 123727 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Cytidine diphosphate ethanolamine (CDP-ethanolamine) has 123727 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 H₂O has 15377 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 2 H₂O has 16240 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-alkyl-2-acyl-sn-glycerol has 17756737 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Choline has 305 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 3 (S-adenosyl-methionine) has 34756 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 S-Adenosylmethionine (AdoMet) has 34756 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 NADH + H+ has 439153 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 3 (S-adenosylhomocysteine) has 439155 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 S-Adenosylhomocysteine (AdoHcy) has 439155 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Acetyl-CoA has 444493 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 PPi has 45212 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1D-myo-Inositol-1-P has 5288642 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-Alkyldihydroxyacetone phosphate (Octanoyl DHAP) has 53481029 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 NADPH + H+ has 5884 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 NADP (Coenzyme II) has 5886 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 NAD+ (Coenzyme I) has 5892 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Serine has 5951 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 ATP has 5957 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Adenosine triphosphate (ATP) has 5957 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 ADP has 6022 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Adenosine diphosphate (ADP) has 6022 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 CMP has 6131 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Cytidine monophosphate (CMP) has 6131 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 CTP has 6176 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Cytidine triphosphate (CTP) has 6176 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Dihydroxyacetone phosphate has 668 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 CoA-SH has 6816 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Coenzyme A (CoA-SH) has 6816 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Ethanolamine has 700 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Glycerol-3-P has 7048686 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 sn-glycerol-3-phosphate (glycerol-3-P) has 7048686 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Glycerol has 753 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Inositol has 892 from PubChem-compound but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-Alkyl-sn-glycerol has CHEBI:15850 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-Alkyl-2-acetyl-sn-glycerol has CHEBI:16291 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-Alkyl-sn-glycerol 3-phosphate has CHEBI:17106 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-alkenyl-2-acylglycero- phosphoethanolamine has CHEBI:17476 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-Alkyl-2-acetyl-sn-glycerol 3-phosphate has CHEBI:17555 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-Alkenyl-2-acyl- glycerophosphocholine has CHEBI:17810 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Acyl coenzyme A (Acyl-CoA) has CHEBI:17984 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Acyl-CoA has CHEBI:17984 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Phosphatidylinositol-4,5-bisphosphate [PIP2(4',5')] has CHEBI:18348 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Cardiolipin (DPG, CL) has CHEBI:28494 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-alkyl-2-acyl-sn-glycero-3-phosphocholine (Plasmanylcholine) has CHEBI:36702 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-alkyl-sn-glycero-3-phosphocholine (Lyso PAF) has CHEBI:36702 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine (Platelet Activating Factor, PAF) has CHEBI:36707 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-alkyl-2-acyl-sn-glycero- 3-phosphoethanolamine has CHEBI:36712 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-alkyl-2-acyl-sn-glycerol 3-phosphate (Plasmanic acid) has CHEBI:37296 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 CDP-choline has CHEBI:49086 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Phosphatidylinositol-4-phosphate (PIP) has CHEBI:58178 from ChEBI but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 D-Glucose-6-P has HMDB0003498 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 1-Acyl dihydroxyacetone phosphate (Acyl-DHAP) has HMDB0011750 from HMDB but expected a LIPID MAPS identifier
http://classic.wikipathways.org/instance/WP2533_rr139678 Shark liver oil has Q4380845 from Wikidata but expected a LIPID MAPS identifier

More details at https://www.wikipathways.org/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS