sr24-curation

WikiPathways WP4784

• WikiPathways: WP4784 (classic)
• Species: Homo sapiens
• Scholia: WP4784

  Tests

• CASMetabolitesTests: all 2 tests OK!
• ChEBIMetabolitesTests: all 5 tests OK!
• ChemSpiderTests: all 2 tests OK!
• CovidDiseaseMapsTests
  • interactionsWithoutReferences: .x we found 1 problem(s):
    • Interactions without literature references: 34
  • missingHGNC: .. all OK!
• DataNodesTests: all 5 tests OK!
• EnsemblTests: all 5 tests OK!
• GeneTests: all 4 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 2 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests: all 6 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
  • metaboliteAlsoOtherType: .. all OK!
  • casNumbersNotMarkedAsMetabolite: .. all OK!
  • chemspiderIDsNotMarkedAsMetabolite: .. all OK!
  • HMDBIDsNotMarkedAsMetabolite: .. all OK!
  • KEGGIDsNotMarkedAsMetabolite: .. all OK!
  • metabolitesWithAnEnsembleID: .. all OK!
  • metabolitesWithAnEntrezGeneID: .. all OK!
  • metabolitesWithDbButNoIdentifier: .. all OK!
  • metabolitesWithIdentifierButNoDb: .. all OK!
  • ChEBIIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
  • PubChemIDsNotNumbers: .. all OK!
  • PubChemSubstanceIDsNotNumbers: .. all OK!
  • tooManyInChIKeys: .x we found 1 problem(s):
    • Non-zero count of metabolites with more than one InChIKey: 2
• 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
  • keggWithoutMapping: .. all OK!
  • pubchemCIDWithoutMapping: .. all OK!
  • hmdbWithoutMapping: .. all OK!
  • casWithoutMapping: .. all OK!
  • wikDataTypo: .. all OK!
  • duplicateWikidataMappings: .. all OK!
  • wikidataIdentifiersWrong: .. all OK!
  • chemspiderCIDWithoutMapping: .. all OK!
  • lipidMapsWithoutMapping: .. all OK!
  • kNApSAcKWithoutMapping: .. all OK!
  • replaceWikipedia: .. all OK!
  • chebiWithoutMapping_Reactome: .. all OK!
  • chebiWithoutMapping: .x we found 1 problem(s):
    • ChEBI identifiers without Wikidata mappings: 2
  • inchikeyWithoutMapping: .. all OK!
  • retiredIdentifiers: .. all OK!

Summary

• Number of test classes: 23
• Number of tests: 140
• Number of assertions: 281
• Number of fails: 4

Fails

Interactions without references

Interactions without literature references: 34

• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id1126db9c
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/idbc60baf4
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id262c22a9
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id4cb20e14
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id231f3742
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id3a160615
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id953cd359
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id9352d435
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id3bc4867b
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id4e4293dd
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/idb5b28b50
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id60daebd3
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id24f327d
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id5877efd3
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/daa2b
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id18e10d3f
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id282d297
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/iddae07d44
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id950944a
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id53fa5c89
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id8bf24cc5
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id6c986edf
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id368221f1
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id6641570c
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/idaa870ae9
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/idf02814e8
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id893d736b
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/idc8295a55
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id4b994c8c
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/idceb8f07f
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id1ae2c86c
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id87a84cd1
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/idb9a2a75c
• http://classic.wikipathways.org/instance/WP4784_r136159 -> http://rdf.wikipathways.org/Pathway/WP4784_r136159/WP/Interaction/id63b6a533

More details at https://www.wikipathways.org/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences

Interactions with Labels

Interactions found that involve Labels: 6

• http://classic.wikipathways.org/instance/WP4784_r136159 “Glycosylated proteoglycan” with graphId f9593
• http://classic.wikipathways.org/instance/WP4784_r136159 “Proteoglycan core synthesized in rough endoplasmic reticulum” with graphId a2815
• http://classic.wikipathways.org/instance/WP4784_r136159 “Newly synthesized proteoglycan” with graphId c8c96
• http://classic.wikipathways.org/instance/WP4784_r136159 “Sulfation of proteoglycan” with graphId a01a9
• http://classic.wikipathways.org/instance/WP4784_r136159 “Sulfur-containing amino acid metabolism” with graphId faf4d
• http://classic.wikipathways.org/instance/WP4784_r136159 “Newly synthesized proteoglycan” with graphId f1c48

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

Too many InChIKeys for the used identifier

Non-zero count of metabolites with more than one InChIKey: 2

• http://classic.wikipathways.org/instance/WP4784_r136159 has: UDP xylose (CHEBI:16082) with InChIKeys: DQQDLYVHOTZLOR-OCIMBMBZSA-N, XWZCZWKUGIQPJD-UHFFFAOYSA-N
• http://classic.wikipathways.org/instance/WP4784_r136159 has: UMP (CHEBI:16695) with InChIKeys: DJJCXFVJDGTHFX-XVFCMESISA-N, DJJCXFVJDGTHFX-UHFFFAOYSA-N

More details at https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/tooManyInChIKeys

ChEBI identifier without a match in Wikidata

ChEBI identifiers without Wikidata mappings: 2

• https://identifiers.org/chebi/CHEBI:24769 (L-Iduronic acid) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4784_r136159
• https://identifiers.org/chebi/CHEBI:4178 (D-glucuronic acid) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4784_r136159

More details at https://www.wikipathways.org/WikiPathwaysCurator/WikidataTests/chebiWithoutMapping