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egonwegonw
committedMar 17, 2025·
New validation results
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‎index2.md

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‎reports/WP1495.json

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{
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"schemaVersion": 1,
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"label": "curation",
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"message": "3 issues",
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"color": "orange"
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"message": "1 issue",
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"color": "yellow"
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}

‎reports/WP1495.md

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* ChemSpiderTests: all 2 tests OK!
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* DataNodesTests
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* dataNodesWithoutIdentifier: .x we found 1 problem(s):
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* [The following DataNodes have no identifier: 7](#d2d32fa6)
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* [The following DataNodes have no identifier: 4](#d2d32fa3)
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* unknownTypes_knownDatasource: .. all OK!
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* unknownTypes: .. all OK!
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* unknownTypes_Reactome: .. all OK!
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* KEGGMetaboliteTests: all 2 tests OK!
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* LIPIDMAPSTests: all 1 tests OK!
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* MetaboliteStructureTests: all 1 tests OK!
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* MetabolitesTests
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* ChEBIIDsNotMarkedAsMetabolite: .. all OK!
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* HMDBIDsNotMarkedAsMetabolite: .. all OK!
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* KEGGIDsNotMarkedAsMetabolite: .. all OK!
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* PubChemIDsNotMarkedAsMetabolite: .. all OK!
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* PubChemIDsNotNumbers: .. all OK!
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* PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
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* PubChemSubstanceIDsNotNumbers: .. all OK!
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* achiralAminoAcids: .x we found 1 problem(s):
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* [Metabolites with ChEBI identifiers of achiral amino acids: 1](#9c17608e)
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* casNumbersNotMarkedAsMetabolite: .. all OK!
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* chemspiderIDsNotMarkedAsMetabolite: .. all OK!
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* metaboliteAlsoOtherType: .. all OK!
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* metabolitesWithAnEnsembleID: .. all OK!
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* metabolitesWithAnEntrezGeneID: .. all OK!
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* metabolitesWithDbButNoIdentifier: .. all OK!
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* metabolitesWithIdentifierButNoDb: .. all OK!
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* MetabolitesTests: all 15 tests OK!
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* OudatedDataSourcesTests: all 24 tests OK!
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* PathwayTests: all 8 tests OK!
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* ProteinsTests: all 2 tests OK!
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* PubChemMetabolitesTests: all 3 tests OK!
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* ReferencesTests
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* nonNumericPubMedIDs: .. all OK!
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* unexpectedPubMedIdentifier: .. all OK!
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* zeroPubMedIDs: .. all OK!
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* atLeastOneReference: .x we found 1 problem(s):
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* [Found 1 pathways with zero (PubMed) references](#d0a459f0)
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* citesRetractedArticle: .. all OK!
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* outdatedPubMedIdentifiers: .. all OK!
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* ReferencesTests: all 6 tests OK!
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* UniProtTests: all 5 tests OK!
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* WikidataTests: all 4 tests OK!
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* Number of test classes: 20
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* Number of tests: 120
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* Number of assertions: 241
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* Number of fails: 3
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* Number of fails: 1
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## Fails
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<a name="d2d32fa6" />
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<a name="d2d32fa3" />
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## Data nodes without an identifier
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The following DataNodes have no identifier: 7
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The following DataNodes have no identifier: 4
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) http://rdf.wikipathways.org/Pathway/WP1495_r138046/DataNode/b002e (FAD)
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) http://rdf.wikipathways.org/Pathway/WP1495_r138046/DataNode/fc69f (FADH2)
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) http://rdf.wikipathways.org/Pathway/WP1495_r138046/DataNode/ac46e (H2O)
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) http://rdf.wikipathways.org/Pathway/WP1495_r138046/DataNode/a7732 (H2O2)
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) http://rdf.wikipathways.org/Pathway/WP1495_r138046/DataNode/cfe83 (NH3)
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) http://rdf.wikipathways.org/Pathway/WP1495_r138046/DataNode/e2ab1 (O2)
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) http://rdf.wikipathways.org/Pathway/WP1495_r138046/DataNode/c5660 (a-Ketoglutarate)
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* [http://classic.wikipathways.org/instance/WP1495_r138124](http://classic.wikipathways.org/instance/WP1495_r138124) http://rdf.wikipathways.org/Pathway/WP1495_r138124/DataNode/b002e (FAD)
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* [http://classic.wikipathways.org/instance/WP1495_r138124](http://classic.wikipathways.org/instance/WP1495_r138124) http://rdf.wikipathways.org/Pathway/WP1495_r138124/DataNode/fc69f (FADH2)
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* [http://classic.wikipathways.org/instance/WP1495_r138124](http://classic.wikipathways.org/instance/WP1495_r138124) http://rdf.wikipathways.org/Pathway/WP1495_r138124/DataNode/cfe83 (NH3)
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* [http://classic.wikipathways.org/instance/WP1495_r138124](http://classic.wikipathways.org/instance/WP1495_r138124) http://rdf.wikipathways.org/Pathway/WP1495_r138124/DataNode/c5660 (a-Ketoglutarate)
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More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier](https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier)
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<a name="9c17608e" />
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## Identifier used of a amino acid with undefined stereochemistry
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Metabolites with ChEBI identifiers of achiral amino acids: 1
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```
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http://classic.wikipathways.org/instance/WP1495_r138046 Serine CHEBI:17822
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```
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More details at [https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/achiralAminoAcids](https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/achiralAminoAcids)
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<a name="d0a459f0" />
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## At least one reference
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Found 1 pathways with zero (PubMed) references
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* [http://classic.wikipathways.org/instance/WP1495_r138046](http://classic.wikipathways.org/instance/WP1495_r138046) 'Glycine metabolism' in Homo sapiens has zero references;
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More details at [https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)
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‎reports/WP2563.json

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{
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"schemaVersion": 1,
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"label": "curation",
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"message": "2 issues",
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"message": "1 issue",
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"color": "yellow"
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}

‎reports/WP2563.md

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* KEGGMetaboliteTests: all 2 tests OK!
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* LIPIDMAPSTests: all 1 tests OK!
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* MetaboliteStructureTests: all 1 tests OK!
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* MetabolitesTests
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* ChEBIIDsNotMarkedAsMetabolite: .. all OK!
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* HMDBIDsNotMarkedAsMetabolite: .. all OK!
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* KEGGIDsNotMarkedAsMetabolite: .. all OK!
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* PubChemIDsNotMarkedAsMetabolite: .. all OK!
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* PubChemIDsNotNumbers: .. all OK!
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* PubChemSubstanceIDsNotMarkedAsMetabolite: .. all OK!
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* PubChemSubstanceIDsNotNumbers: .. all OK!
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* achiralAminoAcids: .x we found 1 problem(s):
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* [Metabolites with ChEBI identifiers of achiral amino acids: 1](#9c17608e)
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* casNumbersNotMarkedAsMetabolite: .. all OK!
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* chemspiderIDsNotMarkedAsMetabolite: .. all OK!
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* metaboliteAlsoOtherType: .. all OK!
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* metabolitesWithAnEnsembleID: .. all OK!
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* metabolitesWithAnEntrezGeneID: .. all OK!
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* metabolitesWithDbButNoIdentifier: .. all OK!
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* metabolitesWithIdentifierButNoDb: .. all OK!
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* MetabolitesTests: all 15 tests OK!
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* OudatedDataSourcesTests: all 24 tests OK!
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* PathwayTests: all 8 tests OK!
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* ProteinsTests: all 2 tests OK!
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* Number of test classes: 20
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* Number of tests: 120
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* Number of assertions: 241
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* Number of fails: 2
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* Number of fails: 1
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## Fails
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The following genes with an identifier have been found but that do not have a mapping to Ensembl: 4
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```
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http://classic.wikipathways.org/instance/WP2563_r87715 KDH with datasource UniProtKB
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http://classic.wikipathways.org/instance/WP2563_r87715 GDH with datasource UniProtKB
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http://classic.wikipathways.org/instance/WP2563_r87715 GarA with datasource UniProtKB
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http://classic.wikipathways.org/instance/WP2563_r87715 gltB with datasource UniProtKB
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http://classic.wikipathways.org/instance/WP2563_r138126 KDH with datasource UniProtKB
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http://classic.wikipathways.org/instance/WP2563_r138126 GDH with datasource UniProtKB
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http://classic.wikipathways.org/instance/WP2563_r138126 GarA with datasource UniProtKB
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http://classic.wikipathways.org/instance/WP2563_r138126 gltB with datasource UniProtKB
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```
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More details at [https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping](https://www.wikipathways.org/WikiPathwaysCurator/GeneTests/genesWithoutEnsemblMapping)
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<a name="9c17608e" />
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## Identifier used of a amino acid with undefined stereochemistry
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Metabolites with ChEBI identifiers of achiral amino acids: 1
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```
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http://classic.wikipathways.org/instance/WP2563_r87715 Glutamine CHEBI:28300
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```
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More details at [https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/achiralAminoAcids](https://www.wikipathways.org/WikiPathwaysCurator/MetabolitesTests/achiralAminoAcids)
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‎reports/WP37.json

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{
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"schemaVersion": 1,
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"label": "curation",
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"message": "2 issues",
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"message": "1 issue",
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"color": "yellow"
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}

‎reports/WP37.md

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* GeneTests: all 5 tests OK!
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* GeneralTests: all 15 tests OK!
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* HMDBSecMetabolitesTests: all 3 tests OK!
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* InteractionTests
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* noMetaboliteToNonMetaboliteConversions: .. all OK!
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* noNonMetaboliteToMetaboliteConversions: .. all OK!
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* noGeneProteinConversions: .. all OK!
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* nonNumericIDs: .. all OK!
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* interactionsWithLabels: .. all OK!
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* possibleTranslocations: .x we found 1 problem(s):
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* [Interactions between identical nodes: 2](#1c118207)
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* noProteinProteinConversions: .. all OK!
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* incorrectKEGGIdentifiers: .. all OK!
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* InteractionTests: all 8 tests OK!
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* KEGGMetaboliteTests: all 2 tests OK!
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* LIPIDMAPSTests: all 1 tests OK!
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* MetaboliteStructureTests: all 1 tests OK!
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* Number of test classes: 20
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* Number of tests: 120
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* Number of assertions: 241
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* Number of fails: 2
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* Number of fails: 1
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## Fails
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<a name="1c118207" />
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## Possible MIM translocation
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Interactions between identical nodes: 2
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* [http://classic.wikipathways.org/instance/WP37_r117902](http://classic.wikipathways.org/instance/WP37_r117902) [http://rdf.wikipathways.org/Pathway/WP37_r117902/WP/Interaction/ea2db](http://rdf.wikipathways.org/Pathway/WP37_r117902/WP/Interaction/ea2db) "Il1a" ([https://identifiers.org/ensembl/ENSMUSG00000027399](https://identifiers.org/ensembl/ENSMUSG00000027399)) and
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Il1a" ([https://identifiers.org/ensembl/ENSMUSG00000027399](https://identifiers.org/ensembl/ENSMUSG00000027399))
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* [http://classic.wikipathways.org/instance/WP37_r117902](http://classic.wikipathways.org/instance/WP37_r117902) [http://rdf.wikipathways.org/Pathway/WP37_r117902/WP/Interaction/cb469](http://rdf.wikipathways.org/Pathway/WP37_r117902/WP/Interaction/cb469) "Il1b" ([https://identifiers.org/ensembl/ENSMUSG00000027398](https://identifiers.org/ensembl/ENSMUSG00000027398)) and
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Il1b" ([https://identifiers.org/ensembl/ENSMUSG00000027398](https://identifiers.org/ensembl/ENSMUSG00000027398))
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More details at [https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations](https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations)
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<a name="d0a459f0" />
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## At least one reference
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Found 1 pathways with zero (PubMed) references
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* [http://classic.wikipathways.org/instance/WP37_r117902](http://classic.wikipathways.org/instance/WP37_r117902) 'IL-1 signaling pathway' in Mus musculus has zero references;
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* [http://classic.wikipathways.org/instance/WP37_r138122](http://classic.wikipathways.org/instance/WP37_r138122) 'IL-1 signaling pathway' in Mus musculus has zero references;
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More details at [https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)

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