imd-pathway-curation

WikiPathways WP4271

• WikiPathways: WP4271 (classic)
• Species: Homo sapiens
• Scholia: WP4271

  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: all 4 tests OK!
• GeneralTests: all 15 tests OK!
• HMDBMetabolitesTests: all 1 tests OK!
• HMDBSecMetabolitesTests: all 3 tests OK!
• IEMPathwayTests
  • allMetabolitesInteract: .x we found 1 problem(s):
    • Found metabolites without interaction: 6
  • metabolicConversions: .. all OK!
  • catalystsWithCommonDataSource: .. all OK!
  • metabolicConversionIdentifiersCommon: .. all OK!
  • diseasesHaveIdentifiers: .x we found 1 problem(s):
    • Likely diseases without identifiers: 1
  • omimIdentifiers: .x we found 1 problem(s):
    • OMIM links should start with “https://omim.org/entry/”: 13
• 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: 1
  • 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 9 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: 22
• Number of tests: 120
• Number of assertions: 241
• Number of fails: 5

Fails

IEMPathwayTests.allMetabolitesInteract

Found metabolites without interaction: 6

https://identifiers.org/wikipathways/WP4271 has an metabolite not linked to an interaction: NADP+
https://identifiers.org/wikipathways/WP4271 has an metabolite not linked to an interaction: 2 * SAH
https://identifiers.org/wikipathways/WP4271 has an metabolite not linked to an interaction: 2 * SAM
https://identifiers.org/wikipathways/WP4271 has an metabolite not linked to an interaction: MTHF
https://identifiers.org/wikipathways/WP4271 has an metabolite not linked to an interaction: Methionine
https://identifiers.org/wikipathways/WP4271 has an metabolite not linked to an interaction: THF

IEMPathwayTests.diseasesHaveIdentifiers

Likely diseases without identifiers: 1

https://identifiers.org/wikipathways/WP4271 "Adenosylcobalamin and methylcobalamin synthesis defect cblJ" does not have an identifier

IEMPathwayTests.omimIdentifiers

OMIM links should start with “https://omim.org/entry/”: 13

https://identifiers.org/wikipathways/WP4271 "Methionine synthase deficiency cblE" has unexpected OMIM href: https://omim.org/236270
https://identifiers.org/wikipathways/WP4271 "Adenosylcobalamin synthesis defect cblA" has unexpected OMIM href: https://omim.org/251100
https://identifiers.org/wikipathways/WP4271 "Adenosylcobalamin and methylcobalamin synthesis defect cblD-MMA/HC" has unexpected OMIM href: https://omim.org/277410
https://identifiers.org/wikipathways/WP4271 "Adenosylcobalamin synthesis defect cblD-MMA" has unexpected OMIM href: https://omim.org/277410
https://identifiers.org/wikipathways/WP4271 "Adenosylcobalamin and methylcobalamin synthesis defect cblC" has unexpected OMIM href: https://omim.org/277400
https://identifiers.org/wikipathways/WP4271 "Transcobalamin receptor defect" has unexpected OMIM href: https://omim.org/613646
https://identifiers.org/wikipathways/WP4271 "Intrinsic factor  deficiency" has unexpected OMIM href: https://omim.org/261000
https://identifiers.org/wikipathways/WP4271 "Methionine synthase deficiency cblG" has unexpected OMIM href: https://omim.org/250940
https://identifiers.org/wikipathways/WP4271 "Haptocorrin deficiency" has unexpected OMIM href: https://omim.org/193090
https://identifiers.org/wikipathways/WP4271 "Adenosylcobalamin and methylcobalamin synthesis defect cblF" has unexpected OMIM href: https://omim.org/277380
https://identifiers.org/wikipathways/WP4271 "Amnionless deficiency" has unexpected OMIM href: https://omim.org/261100
https://identifiers.org/wikipathways/WP4271 "Adenosylcobalamin synthesis defect cblD-HC" has unexpected OMIM href: https://omim.org/277410
https://identifiers.org/wikipathways/WP4271 "Cubilin deficiency" has unexpected OMIM href: https://omim.org/261100

InteractionTests.interactionsWithLabels

Interactions found that involve Labels: 1

http://classic.wikipathways.org/instance/WP4271_r128221 "Tissue" with graphId a967a

ChEBI identifier without a match in Wikidata

ChEBI identifiers without Wikidata mappings: 2

https://identifiers.org/chebi/CHEBI:28115 (Cofactor) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4271_r128221 ; 
https://identifiers.org/chebi/CHEBI:28115 (Methylcobalamin) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP4271_r128221 ; 

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