From 6f7a167514cd94e906557c3092ac757ec3b120ab Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 7 Nov 2024 09:37:05 +0100 Subject: [PATCH] Reports --- index.md | 5 +- reports/WP4156.json | 6 + reports/WP4156.md | 188 ++++++++++++++++++++++++++ reports/WP4156.txt | 1 + reports/WP5173.json | 6 + reports/WP5173.md | 166 +++++++++++++++++++++++ reports/WP5173.txt | 1 + reports/WP5176.json | 6 + reports/WP5176.md | 316 ++++++++++++++++++++++++++++++++++++++++++++ reports/WP5176.txt | 1 + reports/WP5178.json | 6 + reports/WP5178.md | 189 ++++++++++++++++++++++++++ reports/WP5178.txt | 1 + 13 files changed, 891 insertions(+), 1 deletion(-) create mode 100644 reports/WP4156.json create mode 100644 reports/WP4156.md create mode 100644 reports/WP4156.txt create mode 100644 reports/WP5173.json create mode 100644 reports/WP5173.md create mode 100644 reports/WP5173.txt create mode 100644 reports/WP5176.json create mode 100644 reports/WP5176.md create mode 100644 reports/WP5176.txt create mode 100644 reports/WP5178.json create mode 100644 reports/WP5178.md create mode 100644 reports/WP5178.txt diff --git a/index.md b/index.md index 9a6934c..84e63ac 100644 --- a/index.md +++ b/index.md @@ -1,4 +1,7 @@ # Validation Reports -* [reports/WP4.md](reports/WP4.md) ⨯ +* [reports/WP4156.md](reports/WP4156.md) pathway status +* [reports/WP5173.md](reports/WP5173.md) pathway status +* [reports/WP5176.md](reports/WP5176.md) pathway status +* [reports/WP5178.md](reports/WP5178.md) pathway status diff --git a/reports/WP4156.json b/reports/WP4156.json new file mode 100644 index 0000000..de237e9 --- /dev/null +++ b/reports/WP4156.json @@ -0,0 +1,6 @@ +{ + "schemaVersion": 1, + "label": "curation", + "message": "3 errors", + "color": "red" +} diff --git a/reports/WP4156.md b/reports/WP4156.md new file mode 100644 index 0000000..b841dc3 --- /dev/null +++ b/reports/WP4156.md @@ -0,0 +1,188 @@ + +# WikiPathways WP4156 + +* WikiPathways: [WP4156](https://identifiers.org/wikipathways:WP4156) +* Scholia: [WP4156](https://scholia.toolforge.org/wikipathways/WP4156) +* WPRDF file: [wp/Human/WP4156.ttl](../wp/Human/WP4156.ttl) +* GPMLRDF file: [wp/gpml/Human/WP4156.ttl](../wp/gpml/Human/WP4156.ttl) +* SBML file: [sbml/WP4156.sbml](../sbml/WP4156.sbml) ([SVG](../sbml/WP4156.svg)) ([conversion notes](../sbml/WP4156.txt)) + +## Tests +* CASMetabolitesTests: all 2 tests OK! +* ChEBIMetabolitesTests: all 4 tests OK! +* ChemSpiderTests: all 2 tests OK! +* CovidDiseaseMapsTests + * interactionsWithoutReferences: .x we found 1 problem(s): + * [Interactions without literature references: 62](#9701cd7e) + * missingHGNC: .. all OK! +* DataNodesTests: all 5 tests OK! +* EnsemblTests: all 5 tests OK! +* GeneTests: all 4 tests OK! +* GeneralTests: all 13 tests OK! +* HMDBMetabolitesTests: all 2 tests OK! +* HMDBSecMetabolitesTests: all 3 tests OK! +* InteractionTests: all 8 tests 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: 32](#d0bfb6b8) +* MetaboliteStructureTests: all 2 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: 1](#a4e4037e) +* OudatedDataSourcesTests: all 7 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 15 tests OK! + + +## Summary + +* Number of test classes: 22 +* Number of tests: 116 +* Number of assertions: 234 +* Number of fails: 3 + +## Fails + + + +## CovidDiseaseMapsTests.interactionsWithoutReferences + +Interactions without literature references: 62 +``` +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idaf49de82 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idcfec2bee +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idc7ad578 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id210ea6b1 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idc3ff3f1c +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idd98f6358 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id277f5b5a +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/iddf08bbd6 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id6b39a446 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id9ef7cfc3 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id3c540fa2 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/ideb9fcede +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idcd230f57 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idb7ed86f6 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/c1a93 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idaa1af98f +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/bcf5c +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/f32e5 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id2c686da2 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id9c5562ef +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/ComplexBinding/a765a +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idd7741aaf +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/f78df +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/ComplexBinding/a69e0 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/c06ac +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id1eb5096c +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/cefac +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id24333043 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idf156bc02 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/fe1d8 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/ida9b8e551 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/ide9604c01 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id94aadbf8 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id4876ba83 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/b111a +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idb70c8a5b +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/ca689 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/a780c +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idd348c017 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id790b1035 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/c454a +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/ide4d37224 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id68d7effb +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idab741d7e +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id70f3fdfe +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id3c385ad3 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idd28db677 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/a76fc +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id7326c6e +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id218a73f5 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id5b2cfbca +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idb61b60ed +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id32c71291 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id1826379 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id4e503ef6_2 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/ida371d2ff +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idc788ccbe +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id4e503ef6_1 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idcb6f2385 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/idfc3d6f39 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/f7ae9 +http://classic.wikipathways.org/instance/WP4156_r128201 -> http://rdf.wikipathways.org/Pathway/WP4156_r128201/WP/Interaction/id93f579bc +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences](https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences) + + + +## LIPIDMAPSTests.onlyLIPIDMAPS + +Expected a LIPID MAPS identifier, but found other identifiers: 32 +``` +http://classic.wikipathways.org/instance/WP4156_r128201 oxo-PH4 has 135398702 from PubChem-compound but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 PTP has CHEBI:136564 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 O2 has CHEBI:15379 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 SAM has CHEBI:15414 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 HO-BH4 has CHEBI:15642 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 MHPG has CHEBI:1576 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 melatonin has CHEBI:16796 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 N-acetylserotonin has CHEBI:17697 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 VMA has CHEBI:20106 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Phe has CHEBI:28044 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Serotonin has CHEBI:28790 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 BH4 has CHEBI:30436 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 norepinephrine has CHEBI:33569 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 GTP has CHEBI:37565 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 q-BH2 has CHEBI:43120 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 5-OH-Trp has CHEBI:58266 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 NH2TP has CHEBI:58462 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 3-OMD has CHEBI:82913 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Epinephrine has HMDB0000068 from HMDB but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 5HIAA has HMDB0000763 from HMDB but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Dopamine has Q170304 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Phenyl-alanine has Q170545 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Trp has Q181003 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 tyr has Q188017 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 sepiapterin has Q2271580 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Primapterin has Q26261687 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 NADPH has Q26841327 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 L-DOPA has Q300989 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Biopterin has Q41793745 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 7,8-BH2 has Q5276421 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 HVA has Q903566 from Wikidata but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP4156_r128201 Neopterin has Q908292 from Wikidata but expected a LIPID MAPS identifier +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS](https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS) + + + +## MetabolitesTests.tooManyInChIKeys + +Non-zero count of metabolites with more than one InChIKey: 1 +``` +http://classic.wikipathways.org/instance/WP4156_r128201 (example) has: q-BH2 CHEBI:43120 with InChIKeys: ZHQJVZLJDXWFFX-RPDRRWSUSA-N, ZHQJVZLJDXWFFX-UHFFFAOYSA-N +``` + diff --git a/reports/WP4156.txt b/reports/WP4156.txt new file mode 100644 index 0000000..2194786 --- /dev/null +++ b/reports/WP4156.txt @@ -0,0 +1 @@ +status=⨯ diff --git a/reports/WP5173.json b/reports/WP5173.json new file mode 100644 index 0000000..ede8c45 --- /dev/null +++ b/reports/WP5173.json @@ -0,0 +1,6 @@ +{ + "schemaVersion": 1, + "label": "curation", + "message": "5 errors", + "color": "red" +} diff --git a/reports/WP5173.md b/reports/WP5173.md new file mode 100644 index 0000000..458eb08 --- /dev/null +++ b/reports/WP5173.md @@ -0,0 +1,166 @@ + +# WikiPathways WP5173 + +* WikiPathways: [WP5173](https://identifiers.org/wikipathways:WP5173) +* Scholia: [WP5173](https://scholia.toolforge.org/wikipathways/WP5173) +* WPRDF file: [wp/Human/WP5173.ttl](../wp/Human/WP5173.ttl) +* GPMLRDF file: [wp/gpml/Human/WP5173.ttl](../wp/gpml/Human/WP5173.ttl) +* SBML file: [sbml/WP5173.sbml](../sbml/WP5173.sbml) ([SVG](../sbml/WP5173.svg)) ([conversion notes](../sbml/WP5173.txt)) + +## Tests +* CASMetabolitesTests: all 2 tests OK! +* ChEBIMetabolitesTests: all 4 tests OK! +* ChemSpiderTests: all 2 tests OK! +* CovidDiseaseMapsTests + * interactionsWithoutReferences: .x we found 1 problem(s): + * [Interactions without literature references: 12](#9701cce3) + * missingHGNC: .. all OK! +* DataNodesTests: all 5 tests OK! +* EnsemblTests: all 5 tests OK! +* GeneTests: all 4 tests OK! +* GeneralTests: all 13 tests OK! +* HMDBMetabolitesTests: all 2 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: 13](#fe97a8bb) + * possibleTranslocations: .x we found 1 problem(s): + * [Interactions between identical nodes: 2](#1c118207) + * 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: 10](#d0bfb678) +* MetaboliteStructureTests + * atLeastFifteenMetabolites: .x we found 1 problem(s): + * Expected true but found false + * isPartOfAPathway: .. all OK! +* MetabolitesTests: all 15 tests OK! +* OudatedDataSourcesTests: all 7 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 15 tests OK! + + +## Summary + +* Number of test classes: 22 +* Number of tests: 116 +* Number of assertions: 234 +* Number of fails: 5 + +## Fails + + + +## CovidDiseaseMapsTests.interactionsWithoutReferences + +Interactions without literature references: 12 +``` +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/d5868 +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/ac8fc +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/e0131 +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a84b2_1 +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/e5a6a +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a4ae6 +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a84b2_2 +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/fe651 +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f16aa +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f0f1e +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f075d +http://classic.wikipathways.org/instance/WP5173_r134383 -> http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/c030e +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences](https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences) + + + +## InteractionTests.interactionsWithLabels + +Interactions found that involve Labels: 13 +``` +http://classic.wikipathways.org/instance/WP5173_r134383 "Polyglucosan body myopathy 2" with graphId b5440 +http://classic.wikipathways.org/instance/WP5173_r134383 "Congenital disorder of glycosylation, +type It" with graphId de139 +http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage disease 0, muscle" with graphId fbaa3 +http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage +disease VI" with graphId ae5e6 +http://classic.wikipathways.org/instance/WP5173_r134383 "Galactokinase deficiency" with graphId d2625 +http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage disease XV" with graphId abc2c +http://classic.wikipathways.org/instance/WP5173_r134383 "Polyglucosan body neuropathy" with graphId eba21 +http://classic.wikipathways.org/instance/WP5173_r134383 "Uridine diphosphate +galactose-4-epimerase +deficiency" with graphId c9ff6 +http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage disease 0, liver" with graphId f124e +http://classic.wikipathways.org/instance/WP5173_r134383 "Galactosaemia" with graphId a8706 +http://classic.wikipathways.org/instance/WP5173_r134383 "Glycogen storage +disease IV" with graphId aaa50 +http://classic.wikipathways.org/instance/WP5173_r134383 "Fanconi-Bickel syndrome" with graphId fd3d0 +http://classic.wikipathways.org/instance/WP5173_r134383 "Intestinal glucose-galactose +malabsorption" with graphId d61c1 +``` + + + +## InteractionTests.possibleTranslocations + +Interactions between identical nodes: 2 +``` +http://classic.wikipathways.org/instance/WP5173_r134383 http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/a4ae6 "Galactose" (https://identifiers.org/chebi/CHEBI:28260) and +Galactose" (https://identifiers.org/chebi/CHEBI:28260) +http://classic.wikipathways.org/instance/WP5173_r134383 http://rdf.wikipathways.org/Pathway/WP5173_r134383/WP/Interaction/f075d "Galactose" (https://identifiers.org/chebi/CHEBI:28260) and +Galactose" (https://identifiers.org/chebi/CHEBI:28260) +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations](https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations) + + + +## LIPIDMAPSTests.onlyLIPIDMAPS + +Expected a LIPID MAPS identifier, but found other identifiers: 10 +``` +http://classic.wikipathways.org/instance/WP5173_r134383 Glycogen (n+1) has 9005-79-2 from CAS but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 D-galactonate has CHEBI:12931 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 Glucose-1-phosphate has CHEBI:16077 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 Galactose-1-phosphate has CHEBI:17973 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 UDP-glucose has CHEBI:18066 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 Glycogen has CHEBI:28087 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 Galactose has CHEBI:28260 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 UDP-galactose has CHEBI:67119 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 Galactitol has HMDB0000107 from HMDB but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5173_r134383 Glucose-6-phosphate has HMDB0001401 from HMDB but expected a LIPID MAPS identifier +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS](https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS) + + + +## MetaboliteStructureTests.atLeastFifteenMetabolites + +Unexpectedly low metabolite count: 10 + +``` +[["mb"], +["https://identifiers.org/chebi/CHEBI:17973"], +["https://identifiers.org/cas/9005-79-2"], +["https://identifiers.org/chebi/CHEBI:28087"], +["https://identifiers.org/hmdb/HMDB0000107"], +["https://identifiers.org/chebi/CHEBI:18066"], +["https://identifiers.org/chebi/CHEBI:28260"], +["https://identifiers.org/chebi/CHEBI:67119"], +["https://identifiers.org/chebi/CHEBI:12931"], +["https://identifiers.org/chebi/CHEBI:16077"], +["https://identifiers.org/hmdb/HMDB0001401"] +] +``` + diff --git a/reports/WP5173.txt b/reports/WP5173.txt new file mode 100644 index 0000000..2194786 --- /dev/null +++ b/reports/WP5173.txt @@ -0,0 +1 @@ +status=⨯ diff --git a/reports/WP5176.json b/reports/WP5176.json new file mode 100644 index 0000000..d4f6cbf --- /dev/null +++ b/reports/WP5176.json @@ -0,0 +1,6 @@ +{ + "schemaVersion": 1, + "label": "curation", + "message": "7 errors", + "color": "red" +} diff --git a/reports/WP5176.md b/reports/WP5176.md new file mode 100644 index 0000000..eb31c9a --- /dev/null +++ b/reports/WP5176.md @@ -0,0 +1,316 @@ + +# WikiPathways WP5176 + +* WikiPathways: [WP5176](https://identifiers.org/wikipathways:WP5176) +* Scholia: [WP5176](https://scholia.toolforge.org/wikipathways/WP5176) +* WPRDF file: [wp/Human/WP5176.ttl](../wp/Human/WP5176.ttl) +* GPMLRDF file: [wp/gpml/Human/WP5176.ttl](../wp/gpml/Human/WP5176.ttl) +* SBML file: [sbml/WP5176.sbml](../sbml/WP5176.sbml) ([SVG](../sbml/WP5176.svg)) ([conversion notes](../sbml/WP5176.txt)) + +## Tests +* CASMetabolitesTests: all 2 tests OK! +* ChEBIMetabolitesTests: all 4 tests OK! +* ChemSpiderTests: all 2 tests OK! +* CovidDiseaseMapsTests + * interactionsWithoutReferences: .x we found 1 problem(s): + * [Interactions without literature references: 36](#9701cd25) + * missingHGNC: .. all OK! +* DataNodesTests + * dataNodesWithoutIdentifier: .x we found 1 problem(s): + * [The following DataNodes have no identifier: 1](#d2d32fa0) + * unknownTypes_knownDatasource: .. all OK! + * unknownTypes: .. all OK! + * unknownTypes_Reactome: .. all OK! + * otherDataSource: .. all OK! +* EnsemblTests: all 5 tests OK! +* GeneTests: all 4 tests OK! +* GeneralTests: all 13 tests OK! +* HMDBMetabolitesTests: all 2 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: 23](#fe97a8da) + * possibleTranslocations: .x we found 1 problem(s): + * [Interactions between identical nodes: 18](#661ebef2) + * 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: 45](#d0bfb6da) +* MetaboliteStructureTests: all 2 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: 10](#f79c6c72) +* OudatedDataSourcesTests: all 7 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: .x we found 1 problem(s): + * [HMDB identifiers without Wikidata mappings: 2](#8860e69c) + * 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: .. all OK! + * hmdbWithoutMapping: .. all OK! + * retiredIdentifiers: .. all OK! + + +## Summary + +* Number of test classes: 22 +* Number of tests: 116 +* Number of assertions: 234 +* Number of fails: 7 + +## Fails + + + +## CovidDiseaseMapsTests.interactionsWithoutReferences + +Interactions without literature references: 36 +``` +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf6fc40c0 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/d6e0a +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/b1016 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id5146a5f2 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id7dc4b6b3 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id7163f5cd +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idd570d3dd +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id16ef543 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc140a77b +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/ide7aec33e +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idb48f7124 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc113f090 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/d2fc6 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id74ac6806 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id9b1e8d5e +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/c0013 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/ida7fdfba6 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/iddd131e99 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id2452e40d +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idb319f660 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id614ebc +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id57a6c794 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/fa787 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id65daa818 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idb2b8e9c2 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id208b5bc7 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7bb1b1e +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id96a4f2d4 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idbbfdd88e +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/iddca38220 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id1d5900d8 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/f79f6 +http://classic.wikipathways.org/instance/WP5176_r128232 -> http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idd35e240a +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences](https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences) + + + +## DataNodesTests.dataNodesWithoutIdentifier + +The following DataNodes have no identifier: 1 +``` +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/DataNode/a89f4 (Bilirubin disposal) +``` + + + +## InteractionTests.interactionsWithLabels + +Interactions found that involve Labels: 23 +``` +http://classic.wikipathways.org/instance/WP5176_r128232 "AMACR deficiency" with graphId c5b2c +http://classic.wikipathways.org/instance/WP5176_r128232 "Bile acid amidation defect" with graphId c5d24 +http://classic.wikipathways.org/instance/WP5176_r128232 "ABCB11 deficiency" with graphId ea3c9 +http://classic.wikipathways.org/instance/WP5176_r128232 "ATP8B1 deficiency" with graphId d7f7d +http://classic.wikipathways.org/instance/WP5176_r128232 "3β-Dehydrogenase +deficiency" with graphId bbe71 +http://classic.wikipathways.org/instance/WP5176_r128232 "Sterol 27-hydroxylase deficiency" with graphId a7126 +http://classic.wikipathways.org/instance/WP5176_r128232 "3β-Dehydrogenase deficiency" with graphId b0872 +http://classic.wikipathways.org/instance/WP5176_r128232 "OATP1B1 disease" with graphId ce805 +http://classic.wikipathways.org/instance/WP5176_r128232 "Sterol 27-hydroxylase deficiency" with graphId dd5ab +http://classic.wikipathways.org/instance/WP5176_r128232 "Bile acid amidation defect" with graphId b9802 +http://classic.wikipathways.org/instance/WP5176_r128232 "D-bifunctional protein deficiency" with graphId aa859 +http://classic.wikipathways.org/instance/WP5176_r128232 "Congenital bile acid synthesis defect 6" with graphId b5ee6 +http://classic.wikipathways.org/instance/WP5176_r128232 "OATP1B3 disease" with graphId a0972 +http://classic.wikipathways.org/instance/WP5176_r128232 "5β-Reductase deficiency" with graphId c9359 +http://classic.wikipathways.org/instance/WP5176_r128232 "ABCB4 deficiency" with graphId aee45 +http://classic.wikipathways.org/instance/WP5176_r128232 "Cholesterol 7α-hydroxylase deficiency" with graphId a293f +http://classic.wikipathways.org/instance/WP5176_r128232 "Congenital bile +acid synthesis +defect type 5" with graphId ab185 +http://classic.wikipathways.org/instance/WP5176_r128232 "Sterol carrier protein 2 deficiency " with graphId d3833 +http://classic.wikipathways.org/instance/WP5176_r128232 "ABCC2 deficiency" with graphId cc569 +http://classic.wikipathways.org/instance/WP5176_r128232 "5β-Reductase deficiency" with graphId bbeac +http://classic.wikipathways.org/instance/WP5176_r128232 "Bile acid-CoA ligase deficiency" with graphId c0ad7 +http://classic.wikipathways.org/instance/WP5176_r128232 "Spastic Paraplegia 5A" with graphId e61d9 +http://classic.wikipathways.org/instance/WP5176_r128232 "Bile acid-CoA +ligase deficiency" with graphId d0e4e +``` + + + +## InteractionTests.possibleTranslocations + +Interactions between identical nodes: 18 +``` +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf6fc40c0 "glycocholate" (https://identifiers.org/chebi/CHEBI:29746) and +glycocholate" (https://identifiers.org/chebi/CHEBI:29746) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id5146a5f2 "Phosphatidylserine" (https://identifiers.org/chebi/CHEBI:18303) and +Phosphatidylserine" (https://identifiers.org/chebi/CHEBI:18303) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada "Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) and +Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada "Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) and +taurocholate" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and +Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idc7133ada "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and +taurocholate" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e "Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) and +Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e "Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) and +taurocholate" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and +Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id8dde6d9e "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and +taurocholate" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/c0013 "glycocholate" (https://identifiers.org/chebi/CHEBI:29746) and +glycocholate" (https://identifiers.org/chebi/CHEBI:29746) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f "Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) and +Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f "Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) and +taurocholate" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and +Taurocholic acid" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idf77f787f "taurocholate" (https://identifiers.org/chebi/CHEBI:36257) and +taurocholate" (https://identifiers.org/chebi/CHEBI:36257) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/id57a6c794 "phosphatidylcholines" (https://identifiers.org/chebi/CHEBI:49183) and +phosphatidylcholines" (https://identifiers.org/chebi/CHEBI:49183) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/fa787 "Bilirubin glucuronide" (https://identifiers.org/chebi/CHEBI:16427) and +Bilirubin glucuronide" (https://identifiers.org/chebi/CHEBI:16427) +http://classic.wikipathways.org/instance/WP5176_r128232 http://rdf.wikipathways.org/Pathway/WP5176_r128232/WP/Interaction/idbbfdd88e "Bile acid" (https://identifiers.org/chebi/CHEBI:36277) and +Bile acid" (https://identifiers.org/chebi/CHEBI:36277) +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations](https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations) + + + +## LIPIDMAPSTests.onlyLIPIDMAPS + +Expected a LIPID MAPS identifier, but found other identifiers: 45 +``` +http://classic.wikipathways.org/instance/WP5176_r128232 cholyl-CoA has CHEBI:15519 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 cholesterol has CHEBI:16113 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Bilirubin glucuronide has CHEBI:16427 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-al has CHEBI:16466 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 5beta-cholestane-3alpha,7alpha,12alpha-triol has CHEBI:16496 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Taurochenodeoxycholic acid has CHEBI:16525 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha-dihydroxy-5beta-cholestan-26-oic acid has CHEBI:16577 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 5beta-cholestane-3alpha,7alpha,12alpha,26-tetrol has CHEBI:17278 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 7-alpha-Hydroxycholesterol has CHEBI:17500 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Glycocholic acid has CHEBI:17687 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 27-Hydroxycholesterol has CHEBI:17703 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 7alpha-Hydroxy-4-cholesten-3-one has CHEBI:17899 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Phosphatidylserine has CHEBI:18303 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-oic acid has CHEBI:18402 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 7alpha,12alpha-dihydroxy-5beta-cholestan-3-one has CHEBI:2288 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 7alpha-hydroxy-5beta-cholestan-3-one has CHEBI:2290 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3α,7α,12α-trihydroxy-24-oxo-5β-cholestan-26-oyl-CoA has CHEBI:27379 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha-Dihydroxy-5beta-cholest-24-enoyl-CoA has CHEBI:27393 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha-dihydroxy-5beta-cholestan-26-al has CHEBI:27428 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholest-24-enoyl-CoA has CHEBI:27505 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 5beta-cholestane-3alpha,7alpha-diol has CHEBI:28047 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 7alpha,12alpha-Dihydroxy-4-cholesten-3-one has CHEBI:28477 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 5beta-cholestane-3alpha,7alpha,26-triol has CHEBI:28540 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Chenodeoxycholoyl-CoA has CHEBI:28701 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 glycocholate has CHEBI:29746 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 cholate has CHEBI:29747 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 chenodeoxycholate(1-) has CHEBI:36234 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Taurocholic acid has CHEBI:36257 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 taurocholate has CHEBI:36257 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Glycochenodeoxycholic acid has CHEBI:36274 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Bile acid has CHEBI:36277 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 (25R)-3alpha,7alpha,12alpha-Trihydroxy-5beta-cholestan-26-oyl-CoA has CHEBI:37642 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 (25S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA has CHEBI:37643 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 7alpha,26-dihydroxy-5beta-cholestan-3-one has CHEBI:48778 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 7alpha,26-dihydroxycholest-4-en-3-one has CHEBI:48825 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 phosphatidylcholines has CHEBI:49183 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 Taurine has CHEBI:507393 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy -5beta-cholestan-26-oyl-CoA has CHEBI:52050 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3beta-Hydroxy-5-cholestenoic acid has CHEBI:81014 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestan-26-oyl-CoA has CHEBI:87704 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3beta,7alpha-Dihydroxy-5-cholestenoate has HMDB0012454 from HMDB but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 5beta-Cholestane-3alpha,7alpha,27-triol has HMDB0060138 from HMDB but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 (25R)-3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA has HMDB0060304 from HMDB but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 (25S)-3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA has HMDB0060306 from HMDB but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5176_r128232 3alpha,7alpha,24-trihydroxy -5beta-cholestan-26-oyl-CoA has Q27103111 from Wikidata but expected a LIPID MAPS identifier +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS](https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS) + + + +## MetabolitesTests.tooManyInChIKeys + +Non-zero count of metabolites with more than one InChIKey: 10 +``` +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: cholyl-CoA CHEBI:15519 with InChIKeys: ZKWNOTQHFKYUNU-JGCIYWTLSA-N, ZKWNOTQHFKYUNU-TVKZAFKCSA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: Bilirubin glucuronide CHEBI:16427 with InChIKeys: ARBDURHEPGRPSR-LCNKTQGVSA-N, ARBDURHEPGRPSR-GEADQAOESA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: Taurochenodeoxycholic acid CHEBI:16525 with InChIKeys: AODPIQQILQLWGS-OBRSLYEHSA-N, BHTRKEVKTKCXOH-BJLOMENOSA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: 7alpha-hydroxy-5beta-cholestan-3-one CHEBI:2290 with InChIKeys: HWOOALPDOJHOPO-SENDYOAPSA-N, HWOOALPDOJHOPO-YREUSXKVSA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: 3α,7α,12α-trihydroxy-24-oxo-5β-cholestan-26-oyl-CoA CHEBI:27379 with InChIKeys: AWLXQJGPNLCTLM-XFQWJXLTSA-N, AWLXQJGPNLCTLM-YFXOTMPNSA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: 3alpha,7alpha-Dihydroxy-5beta-cholest-24-enoyl-CoA CHEBI:27393 with InChIKeys: SEBZZAWTQNNGPK-YOKOLYSVSA-N, SEBZZAWTQNNGPK-ZAVIOYSRSA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: 3alpha,7alpha-dihydroxy-5beta-cholestan-26-al CHEBI:27428 with InChIKeys: YWGOKHMOJTZGBN-SBOSHUFNSA-N, YWGOKHMOJTZGBN-UGMUFZQESA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholest-24-enoyl-CoA CHEBI:27505 with InChIKeys: QVDPWQVOSKJUES-WYOYJMLVSA-N, QVDPWQVOSKJUES-SQEGORTJSA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: 7alpha,12alpha-Dihydroxy-4-cholesten-3-one CHEBI:28477 with InChIKeys: UQPYXHJTHPHOMM-NIBOIBLTSA-N, VJGNBLOGSXHTLR-JFXJTJEYSA-N +http://classic.wikipathways.org/instance/WP5176_r128232 (example) has: 5beta-cholestane-3alpha,7alpha,26-triol CHEBI:28540 with InChIKeys: OQIJRBFRXGIHMI-UGMUFZQESA-N, OQIJRBFRXGIHMI-KZQGXEQDSA-N +``` + + + +## WikidataTests.hmdbWithoutMapping + +HMDB identifiers without Wikidata mappings: 2 +``` +https://identifiers.org/hmdb/HMDB0060138 (5beta-Cholestane-3alpha,7alpha,27-triol) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5176_r128232 ; +https://identifiers.org/hmdb/HMDB0060306 ((25S)-3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA) does not have a Wikidata mapping in http://classic.wikipathways.org/instance/WP5176_r128232 ; +``` + diff --git a/reports/WP5176.txt b/reports/WP5176.txt new file mode 100644 index 0000000..2194786 --- /dev/null +++ b/reports/WP5176.txt @@ -0,0 +1 @@ +status=⨯ diff --git a/reports/WP5178.json b/reports/WP5178.json new file mode 100644 index 0000000..31a8ab0 --- /dev/null +++ b/reports/WP5178.json @@ -0,0 +1,6 @@ +{ + "schemaVersion": 1, + "label": "curation", + "message": "4 errors", + "color": "red" +} diff --git a/reports/WP5178.md b/reports/WP5178.md new file mode 100644 index 0000000..0c208d5 --- /dev/null +++ b/reports/WP5178.md @@ -0,0 +1,189 @@ + +# WikiPathways WP5178 + +* WikiPathways: [WP5178](https://identifiers.org/wikipathways:WP5178) +* Scholia: [WP5178](https://scholia.toolforge.org/wikipathways/WP5178) +* WPRDF file: [wp/Human/WP5178.ttl](../wp/Human/WP5178.ttl) +* GPMLRDF file: [wp/gpml/Human/WP5178.ttl](../wp/gpml/Human/WP5178.ttl) +* SBML file: [sbml/WP5178.sbml](../sbml/WP5178.sbml) ([SVG](../sbml/WP5178.svg)) ([conversion notes](../sbml/WP5178.txt)) + +## Tests +* CASMetabolitesTests: all 2 tests OK! +* ChEBIMetabolitesTests: all 4 tests OK! +* ChemSpiderTests: all 2 tests OK! +* CovidDiseaseMapsTests + * interactionsWithoutReferences: .x we found 1 problem(s): + * [Interactions without literature references: 21](#9701cd01) + * missingHGNC: .. all OK! +* DataNodesTests: all 5 tests OK! +* EnsemblTests: all 5 tests OK! +* GeneTests: all 4 tests OK! +* GeneralTests: all 13 tests OK! +* HMDBMetabolitesTests: all 2 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: 23](#fe97a8da) + * possibleTranslocations: .x we found 1 problem(s): + * [Interactions between identical nodes: 10](#661ebeea) + * 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: 16](#d0bfb67e) +* MetaboliteStructureTests: all 2 tests OK! +* MetabolitesTests: all 15 tests OK! +* OudatedDataSourcesTests: all 7 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 15 tests OK! + + +## Summary + +* Number of test classes: 22 +* Number of tests: 116 +* Number of assertions: 234 +* Number of fails: 4 + +## Fails + + + +## CovidDiseaseMapsTests.interactionsWithoutReferences + +Interactions without literature references: 21 +``` +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idac4df07f +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id4a0403c5 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id7072e443_2 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idbd4d1a2a +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id7072e443_1 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idb199c6df +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idb8f00d5f +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idbf2ba389 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id834409db +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id4ba3a08f +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id87617ee3 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id131d5722 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id20c278e1 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idfaf3d965 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idbbd3b96c +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id786f82e3 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idf6e74140 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/ide7bc322 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id3a7d5881 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id92a3d684 +http://classic.wikipathways.org/instance/WP5178_r134494 -> http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id2943e1d0 +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences](https://wikipathways.github.io/WikiPathwaysCurator/CovidDiseaseMapsTests/interactionsWithoutReferences) + + + +## InteractionTests.interactionsWithLabels + +Interactions found that involve Labels: 23 +``` +http://classic.wikipathways.org/instance/WP5178_r134494 "Hexokinase deficiency" with graphId b592e +http://classic.wikipathways.org/instance/WP5178_r134494 "" with graphId d7103 +http://classic.wikipathways.org/instance/WP5178_r134494 "conversion" with graphId f7775 +http://classic.wikipathways.org/instance/WP5178_r134494 "Phosphoglucomutase 1 +deficiency" with graphId bd5eb +http://classic.wikipathways.org/instance/WP5178_r134494 "Aldolase B +deficiency" with graphId b7faa +http://classic.wikipathways.org/instance/WP5178_r134494 "Triosephosphate isomerase +deficiency" with graphId c3189 +http://classic.wikipathways.org/instance/WP5178_r134494 "connection to +disease" with graphId a96b3 +http://classic.wikipathways.org/instance/WP5178_r134494 "" with graphId a09d4 +http://classic.wikipathways.org/instance/WP5178_r134494 "Fanconi-Bickel syndrome" with graphId b262a +http://classic.wikipathways.org/instance/WP5178_r134494 "HMSNR" with graphId b8b74 +http://classic.wikipathways.org/instance/WP5178_r134494 "Glycerate kinase +deficiency" with graphId b83c3 +http://classic.wikipathways.org/instance/WP5178_r134494 "Intestinal glucose-galactose +malabsorption" with graphId aaf8e +http://classic.wikipathways.org/instance/WP5178_r134494 "Glucose phosphate isomerase +deficiency" with graphId b9270 +http://classic.wikipathways.org/instance/WP5178_r134494 "" with graphId f708f +http://classic.wikipathways.org/instance/WP5178_r134494 "alternative conversion or conversion +in alternative entry" with graphId db4d3 +http://classic.wikipathways.org/instance/WP5178_r134494 "Ketohexokinase +deficiency" with graphId e55be +http://classic.wikipathways.org/instance/WP5178_r134494 "NEDVIBA" with graphId e6b46 +http://classic.wikipathways.org/instance/WP5178_r134494 "Fructose-1,6-biphosphatase +deficiency" with graphId f3427 +http://classic.wikipathways.org/instance/WP5178_r134494 "" with graphId a6339 +http://classic.wikipathways.org/instance/WP5178_r134494 "Catalysis" with graphId a7fac +http://classic.wikipathways.org/instance/WP5178_r134494 "Glucose-6-phosphatase +deficiency" with graphId b1b23 +http://classic.wikipathways.org/instance/WP5178_r134494 "Sorbitol dehydrogenase deficiency +with peripheral neuropathy" with graphId ef2de +http://classic.wikipathways.org/instance/WP5178_r134494 "Retinitis pigmentosa 79" with graphId ffa6b +``` + + + +## InteractionTests.possibleTranslocations + +Interactions between identical nodes: 10 +``` +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idb199c6df "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and +Glucose" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idb199c6df "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and +Glc" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idb199c6df "Glc" (https://identifiers.org/chebi/CHEBI:17234) and +Glucose" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/idb199c6df "Glc" (https://identifiers.org/chebi/CHEBI:17234) and +Glc" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id131d5722 "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and +Glucose" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id131d5722 "Glucose" (https://identifiers.org/chebi/CHEBI:17234) and +Glc" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id131d5722 "Glc" (https://identifiers.org/chebi/CHEBI:17234) and +Glucose" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id131d5722 "Glc" (https://identifiers.org/chebi/CHEBI:17234) and +Glc" (https://identifiers.org/chebi/CHEBI:17234) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id20c278e1 "Sorbitol" (https://identifiers.org/chebi/CHEBI:30911) and +Sorbitol" (https://identifiers.org/chebi/CHEBI:30911) +http://classic.wikipathways.org/instance/WP5178_r134494 http://rdf.wikipathways.org/Pathway/WP5178_r134494/WP/Interaction/id92a3d684 "Fructose" (https://identifiers.org/chebi/CHEBI:28645) and +Fructose" (https://identifiers.org/chebi/CHEBI:28645) +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations](https://wikipathways.github.io/WikiPathwaysCurator/InteractionTests/possibleTranslocations) + + + +## LIPIDMAPSTests.onlyLIPIDMAPS + +Expected a LIPID MAPS identifier, but found other identifiers: 16 +``` +http://classic.wikipathways.org/instance/WP5178_r134494 Frc-1-P has CHEBI:138881 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 pyruvate has CHEBI:15361 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Glc-1-P has CHEBI:16077 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Dihydroxyacetone-P has CHEBI:16108 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 D-glycerate has CHEBI:16659 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Glyceraldehyde has CHEBI:17378 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 2-P-Glycerate has CHEBI:17835 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Sucrose has CHEBI:17992 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Glycogen has CHEBI:28087 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Fructose has CHEBI:28645 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Glyceraldehyde-3-P has CHEBI:29052 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Sorbitol has CHEBI:30911 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Frc-1,6-P2 has CHEBI:32966 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Glc 6-P has CHEBI:4170 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Frc-6-P has CHEBI:57634 from ChEBI but expected a LIPID MAPS identifier +http://classic.wikipathways.org/instance/WP5178_r134494 Glc-6-P has CHEBI:58225 from ChEBI but expected a LIPID MAPS identifier +``` + +More details at [https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS](https://wikipathways.github.io/WikiPathwaysCurator/LIPIDMAPSTests/onlyLIPIDMAPS) + diff --git a/reports/WP5178.txt b/reports/WP5178.txt new file mode 100644 index 0000000..2194786 --- /dev/null +++ b/reports/WP5178.txt @@ -0,0 +1 @@ +status=⨯