New validation results

wikipathways · Oct 10, 2024 · 01c43bf · 01c43bf
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diff --git a/index2.md b/index2.md
diff --git a/pathways.txt b/pathways.txt
@@ -1203,6 +1203,7 @@ WP441
 WP442
 WP445
 WP4462
+WP4463
 WP4466
 WP4474
 WP4478

diff --git a/reports/WP253.md b/reports/WP253.md
@@ -48,7 +48,7 @@
 
 Found 1 pathways with zero (PubMed) references
 
-* [http://classic.wikipathways.org/instance/WP253_r107251](http://classic.wikipathways.org/instance/WP253_r107251) 'Glycolysis' in Saccharomyces cerevisiae has zero references; 
+* [http://classic.wikipathways.org/instance/WP253_r135640](http://classic.wikipathways.org/instance/WP253_r135640) 'Glycolysis' in Saccharomyces cerevisiae has zero references; 
 
 
 More details at [https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)

diff --git a/reports/WP36.md b/reports/WP36.md
@@ -48,7 +48,7 @@
 
 Found 1 pathways with zero (PubMed) references
 
-* [http://classic.wikipathways.org/instance/WP36_r124941](http://classic.wikipathways.org/instance/WP36_r124941) 'De novo biosynthesis of pyrimidine deoxyribonucleotides' in Saccharomyces cerevisiae has zero references; 
+* [http://classic.wikipathways.org/instance/WP36_r135637](http://classic.wikipathways.org/instance/WP36_r135637) 'De novo biosynthesis of pyrimidine deoxyribonucleotides' in Saccharomyces cerevisiae has zero references; 
 
 
 More details at [https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)

diff --git a/reports/WP423.md b/reports/WP423.md
@@ -48,7 +48,7 @@
 
 Found 1 pathways with zero (PubMed) references
 
-* [http://classic.wikipathways.org/instance/WP423_r117348](http://classic.wikipathways.org/instance/WP423_r117348) 'Threonine and methionine biosynthesis' in Saccharomyces cerevisiae has zero references; 
+* [http://classic.wikipathways.org/instance/WP423_r135629](http://classic.wikipathways.org/instance/WP423_r135629) 'Threonine and methionine biosynthesis' in Saccharomyces cerevisiae has zero references; 
 
 
 More details at [https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)

diff --git a/reports/WP4463.json b/reports/WP4463.json
@@ -0,0 +1,6 @@
+{
+  "schemaVersion": 1,
+  "label": "curation",
+  "message": "2 issues",
+  "color": "red"
+}
diff --git a/reports/WP4463.md b/reports/WP4463.md
@@ -0,0 +1,89 @@
+<img style="float: right; width: 200px" src="https://upload.wikimedia.org/wikipedia/commons/thumb/8/83/Wplogo_with_text_500.png/640px-Wplogo_with_text_500.png" />
+# WikiPathways WP4463
+
+* WikiPathways: [WP4463](https://wikipathways.org/pathways/WP4463) ([classic](https://classic.wikipathways.org/instance/WP4463))
+* Species: Homo sapiens
+* Scholia: [WP4463](https://scholia.toolforge.org/wikipathways/WP4463)
+## Tests
+* CASMetabolitesTests: all 2 tests OK!
+* ChEBIMetabolitesTests: all 5 tests OK!
+* ChemSpiderTests: all 2 tests OK!
+* DataNodesTests
+    * dataNodesWithoutIdentifier: .x we found 1 problem(s):
+        * [The following DataNodes have no identifier: 8](#d2d32fa7)
+    * unknownTypes_knownDatasource: .. all OK!
+    * unknownTypes: .. all OK!
+    * unknownTypes_Reactome: .. all OK!
+    * otherDataSource: .. all OK!
+* EnsemblTests: all 4 tests OK!
+* GeneTests: all 4 tests OK!
+* GeneralTests: all 15 tests OK!
+* HMDBSecMetabolitesTests: all 3 tests OK!
+* InteractionTests
+    * noMetaboliteToNonMetaboliteConversions: .. all OK!
+    * noNonMetaboliteToMetaboliteConversions: .. all OK!
+    * noGeneProteinConversions: .. all OK!
+    * nonNumericIDs: .. all OK!
+    * interactionsWithLabels: .. all OK!
+    * possibleTranslocations: .x we found 1 problem(s):
+        * [Interactions between identical nodes: 4](#1c118209)
+    * 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 24 tests OK!
+* PathwayTests: all 7 tests OK!
+* ProteinsTests: all 2 tests OK!
+* PubChemMetabolitesTests: all 3 tests OK!
+* ReferencesTests: all 6 tests OK!
+* UniProtTests: all 5 tests OK!
+* WikidataTests: all 4 tests OK!
+
+
+## Summary
+
+* Number of test classes: 20
+* Number of tests: 117
+* Number of assertions: 235
+* Number of fails: 2
+
+## Fails
+
+<a name="d2d32fa7" />
+
+## Data nodes without an identifier
+
+The following DataNodes have no identifier: 8
+
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/d86c4 (AC)
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/e62f2 (AC)
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/b2e9c (LDL)
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/aabe0 (Receptor?)
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/c8981 (Receptor?)
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/d49bb (Receptor?)
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/d8aef (Receptor?)
+* [http://classic.wikipathways.org/instance/WP4463_r135645](http://classic.wikipathways.org/instance/WP4463_r135645) http://rdf.wikipathways.org/Pathway/WP4463_r135645/DataNode/e8fa2 (Receptor?)
+
+
+More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier](https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier)
+
+<a name="1c118209" />
+
+## Possible MIM translocation
+
+Interactions between identical nodes: 4
+```
+http://classic.wikipathways.org/instance/WP4463_r135645 http://rdf.wikipathways.org/Pathway/WP4463_r135645/WP/Interaction/id8a3eebc4 "Cholesterol" (https://identifiers.org/chebi/CHEBI:16113) and 
+Cholesterol" (https://identifiers.org/chebi/CHEBI:16113)
+http://classic.wikipathways.org/instance/WP4463_r135645 http://rdf.wikipathways.org/Pathway/WP4463_r135645/WP/Interaction/idf4fbde59 "Androstenedione" (https://identifiers.org/chebi/CHEBI:16422) and 
+Androstenedione" (https://identifiers.org/chebi/CHEBI:16422)
+http://classic.wikipathways.org/instance/WP4463_r135645 http://rdf.wikipathways.org/Pathway/WP4463_r135645/WP/Interaction/cc022 "Testosterone" (https://identifiers.org/chebi/CHEBI:17347) and 
+Testosterone" (https://identifiers.org/chebi/CHEBI:17347)
+http://classic.wikipathways.org/instance/WP4463_r135645 http://rdf.wikipathways.org/Pathway/WP4463_r135645/WP/Interaction/cedc1 "Progesterone" (https://identifiers.org/chebi/CHEBI:17026) and 
+Progesterone" (https://identifiers.org/chebi/CHEBI:17026)
+```
+
+More details at [https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations](https://www.wikipathways.org/WikiPathwaysCurator/InteractionTests/possibleTranslocations)
+
diff --git a/reports/WP472.md b/reports/WP472.md
@@ -48,7 +48,7 @@
 
 Found 1 pathways with zero (PubMed) references
 
-* [http://classic.wikipathways.org/instance/WP472_r117324](http://classic.wikipathways.org/instance/WP472_r117324) 'Phosphatidic acid and phospholipid biosynthesis' in Saccharomyces cerevisiae has zero references; 
+* [http://classic.wikipathways.org/instance/WP472_r135643](http://classic.wikipathways.org/instance/WP472_r135643) 'Phosphatidic acid and phospholipid biosynthesis' in Saccharomyces cerevisiae has zero references; 
 
 
 More details at [https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference](https://www.wikipathways.org/WikiPathwaysCurator/ReferencesTests/atLeastOneReference)

diff --git a/reports/WP92.json b/reports/WP92.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "success",
-  "color": "brightgreen"
+  "message": "1 issue",
+  "color": "red"
 }
diff --git a/reports/WP92.md b/reports/WP92.md
@@ -19,7 +19,10 @@
 * MetabolitesTests: all 14 tests OK!
 * OudatedDataSourcesTests: all 24 tests OK!
 * PathwayTests: all 7 tests OK!
-* ProteinsTests: all 2 tests OK!
+* ProteinsTests
+    * wrongBrendaFormat: .. all OK!
+    * wrongEnzymeNomenclatureFormat: .x we found 1 problem(s):
+        * [Enzyme Nomenclature identifiers with the wrong format: 1](#2e095de1)
 * PubChemMetabolitesTests: all 3 tests OK!
 * ReferencesTests: all 6 tests OK!
 * UniProtTests: all 5 tests OK!
@@ -31,7 +34,16 @@
 * Number of test classes: 20
 * Number of tests: 117
 * Number of assertions: 235
-* Number of fails: 0
+* Number of fails: 1
 
 ## Fails
 
+<a name="2e095de1" />
+
+## ProteinsTests.wrongEnzymeNomenclatureFormat
+
+Enzyme Nomenclature identifiers with the wrong format: 1
+```
+http://classic.wikipathways.org/instance/WP92_r135633 -> EC 2.7.4.6, EC 2.7.4.6
+ ```
+
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@@ Expand Up / @@ -1203,6 +1203,7 @@ WP441 @@
     WP442
     WP445
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     WP4466
     WP4474
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