New validation results

wikipathways · Aug 6, 2024 · c4a165e · c4a165e
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diff --git a/index2.md b/index2.md
diff --git a/reports/WP4787.md b/reports/WP4787.md
@@ -51,25 +51,25 @@
 
 Interactions found that involve Labels: 19
 ```
-http://classic.wikipathways.org/instance/WP4787_r135074 "Mesenchymal progenitor /
+http://classic.wikipathways.org/instance/WP4787_r135101 "Deletion of OSX" with graphId dffd9
+http://classic.wikipathways.org/instance/WP4787_r135101 "Osteoblast" with graphId c2507
+http://classic.wikipathways.org/instance/WP4787_r135101 "Osteocyte" with graphId d893f
+http://classic.wikipathways.org/instance/WP4787_r135101 "Chondrocyte" with graphId ed28d
+http://classic.wikipathways.org/instance/WP4787_r135101 "Chondroblast" with graphId e3d35
+http://classic.wikipathways.org/instance/WP4787_r135101 "Calvarian bones, clavicles" with graphId d9440
+http://classic.wikipathways.org/instance/WP4787_r135101 "Osteoblast" with graphId eed50
+http://classic.wikipathways.org/instance/WP4787_r135101 "SOX9+" with graphId d5eca
+http://classic.wikipathways.org/instance/WP4787_r135101 "RUNX2+" with graphId b9988
+http://classic.wikipathways.org/instance/WP4787_r135101 "Osteo-chondro progenitor" with graphId ea262
+http://classic.wikipathways.org/instance/WP4787_r135101 "Mesenchymal progenitor /
 Mesenchymal stem cell" with graphId db64d
-http://classic.wikipathways.org/instance/WP4787_r135074 "Myogenic lineage" with graphId dbca1
-http://classic.wikipathways.org/instance/WP4787_r135074 "Deletion of OSX" with graphId dffd9
-http://classic.wikipathways.org/instance/WP4787_r135074 "Osteoblast" with graphId c2507
-http://classic.wikipathways.org/instance/WP4787_r135074 "SOX9+" with graphId d5eca
-http://classic.wikipathways.org/instance/WP4787_r135074 "RUNX2+" with graphId b9988
-http://classic.wikipathways.org/instance/WP4787_r135074 "RUNX2+, OSX+" with graphId c27f3
-http://classic.wikipathways.org/instance/WP4787_r135074 "Perichondral cell" with graphId de89e
-http://classic.wikipathways.org/instance/WP4787_r135074 "Osteo-chondro progenitor" with graphId ea262
-http://classic.wikipathways.org/instance/WP4787_r135074 "Chondrocyte" with graphId ed28d
-http://classic.wikipathways.org/instance/WP4787_r135074 "Chondroblast" with graphId e3d35
-http://classic.wikipathways.org/instance/WP4787_r135074 "Preosteoblast" with graphId ff887
-http://classic.wikipathways.org/instance/WP4787_r135074 "Osteocyte" with graphId d893f
-http://classic.wikipathways.org/instance/WP4787_r135074 "Osteoblast" with graphId eed50
-http://classic.wikipathways.org/instance/WP4787_r135074 "Hypertrophic chondrocyte" with graphId f9554
-http://classic.wikipathways.org/instance/WP4787_r135074 "Deletion of beta-catenin gene" with graphId fa75d
-http://classic.wikipathways.org/instance/WP4787_r135074 "Axial skeleton, extremities" with graphId bc86b
-http://classic.wikipathways.org/instance/WP4787_r135074 "Calvarian bones, clavicles" with graphId d9440
-http://classic.wikipathways.org/instance/WP4787_r135074 "Adipogenic lineage" with graphId a576b
+http://classic.wikipathways.org/instance/WP4787_r135101 "RUNX2+, OSX+" with graphId c27f3
+http://classic.wikipathways.org/instance/WP4787_r135101 "Perichondral cell" with graphId de89e
+http://classic.wikipathways.org/instance/WP4787_r135101 "Preosteoblast" with graphId ff887
+http://classic.wikipathways.org/instance/WP4787_r135101 "Deletion of beta-catenin gene" with graphId fa75d
+http://classic.wikipathways.org/instance/WP4787_r135101 "Myogenic lineage" with graphId dbca1
+http://classic.wikipathways.org/instance/WP4787_r135101 "Adipogenic lineage" with graphId a576b
+http://classic.wikipathways.org/instance/WP4787_r135101 "Axial skeleton, extremities" with graphId bc86b
+http://classic.wikipathways.org/instance/WP4787_r135101 "Hypertrophic chondrocyte" with graphId f9554
 ```
 
diff --git a/reports/WP4861.md b/reports/WP4861.md
@@ -48,25 +48,25 @@
 
 The following DataNodes have no identifier: 11
 
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/c90ec (Amino acid synthesis
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/c90ec (Amino acid synthesis
 Antioxidant response
 Apoptosis)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/e0713 (C/EBP
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/e0713 (C/EBP
 CCAAT enhancer binding protein)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/d0da6 (CRE
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/d0da6 (CRE
 cAMP response element)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/c085b (ER protein chaperones
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/c085b (ER protein chaperones
 Lipid biosynthesis
 ER-associated degradation)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/e9fd9 (ER-associated
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/e9fd9 (ER-associated
 mRNA)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/ed36d (Global protein
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/ed36d (Global protein
 translation)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/d43bc (MERS 4a)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/c094e (RIDD)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/a4bee (SARS 8ab)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/dc80b (SARS, IBV infection)
-* [http://classic.wikipathways.org/instance/WP4861_r124658](http://classic.wikipathways.org/instance/WP4861_r124658) http://rdf.wikipathways.org/Pathway/WP4861_r124658/DataNode/cd9a0 (SARS, OC43,
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/d43bc (MERS 4a)
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/c094e (RIDD)
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/a4bee (SARS 8ab)
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/dc80b (SARS, IBV infection)
+* [http://classic.wikipathways.org/instance/WP4861_r135076](http://classic.wikipathways.org/instance/WP4861_r135076) http://rdf.wikipathways.org/Pathway/WP4861_r135076/DataNode/cd9a0 (SARS, OC43,
 MHV, IBV infection)
 
 

diff --git a/reports/WP4906.json b/reports/WP4906.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "5 issues",
+  "message": "2 issues",
   "color": "red"
 }
diff --git a/reports/WP4906.md b/reports/WP4906.md
@@ -6,45 +6,18 @@
 * Scholia: [WP4906](https://scholia.toolforge.org/wikipathways/WP4906)
 ## Tests
 * CASMetabolitesTests: all 2 tests OK!
-* ChEBIMetabolitesTests
-    * secondaryChEBIIdentifiers: .. all OK!
-    * faultyChEBIIdentifiers: .. all OK!
-    * chebiDataTypo: . all OK!
-    * faultyChEBIChEBIIdentifiers: x we found 1 problem(s):
-        * [Faulty ChEBI identifiers detected: 2](#eb2972d0)
-    * neutralIons: .. all 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: 2](#d2d32fa1)
+        * [The following DataNodes have no identifier: 3](#d2d32fa2)
     * unknownTypes_knownDatasource: .. all OK!
     * unknownTypes: .. all OK!
     * unknownTypes_Reactome: .. all OK!
     * otherDataSource: .. all OK!
 * EnsemblTests: all 4 tests OK!
-* GeneTests
-    * entrezGeneIdentifiersNotNumber: .x we found 1 problem(s):
-        * [Entrez Gene identifiers that are not numbers: 1](#39c5c867)
-    * affyProbeIdentifiersNotCorrect: .. all OK!
-    * outdatedIdentifiers: .... all OK!
-    * nonNumericHGNCAccessionNumbers: .. all OK!
-* GeneralTests
-    * curationAndHypothetical: .. all OK!
-    * curationAndNeedsWork: .. all OK!
-    * curationAndReactome: .. all OK!
-    * dataNodeWithoutGraphId: .. all OK!
-    * duplicateTitles: .. all OK!
-    * emptyDataSources: . all OK!
-    * emptyLabelOfNodeWithIdentifier: .x we found 1 problem(s):
-        * [Data nodes with an identifier but empty label: 1](#a07a01aa)
-    * groupsHaveDetail: .. all OK!
-    * noTags: .. all OK!
-    * nullDataSources: .. all OK!
-    * stockComments: .. all OK!
-    * titlesShortEnough: .. all OK!
-    * undefinedDataSources: .. all OK!
-    * undefinedIdentifier: .. all OK!
-    * weirdCharacterTitles: .. all OK!
+* GeneTests: all 4 tests OK!
+* GeneralTests: all 15 tests OK!
 * HMDBSecMetabolitesTests: all 3 tests OK!
 * InteractionTests
     * noMetaboliteToNonMetaboliteConversions: .. all OK!
@@ -74,56 +47,29 @@
 * Number of test classes: 20
 * Number of tests: 117
 * Number of assertions: 235
-* Number of fails: 5
+* Number of fails: 2
 
 ## Fails
 
-<a name="eb2972d0" />
-
-## ChEBIMetabolitesTests.faultyChEBIChEBIIdentifiers
-
-Faulty ChEBI identifiers detected: 2
-```
-http://classic.wikipathways.org/instance/WP4906_r135034 CoA has a faulty identifier ChEBI:57287 (it should be a number or start with "CHEBI:")
-http://classic.wikipathways.org/instance/WP4906_r135034 S-palmitoyl-L-cysteine residue of a protein has a faulty identifier ChEBI:74151 (it should be a number or start with "CHEBI:")
-```
-
-<a name="d2d32fa1" />
+<a name="d2d32fa2" />
 
 ## Data nodes without an identifier
 
-The following DataNodes have no identifier: 2
+The following DataNodes have no identifier: 3
 
-* [http://classic.wikipathways.org/instance/WP4906_r135034](http://classic.wikipathways.org/instance/WP4906_r135034) http://rdf.wikipathways.org/Pathway/WP4906_r135034/DataNode/b40ed ()
-* [http://classic.wikipathways.org/instance/WP4906_r135034](http://classic.wikipathways.org/instance/WP4906_r135034) http://rdf.wikipathways.org/Pathway/WP4906_r135034/DataNode/e2c2d ()
+* [http://classic.wikipathways.org/instance/WP4906_r135075](http://classic.wikipathways.org/instance/WP4906_r135075) http://rdf.wikipathways.org/Pathway/WP4906_r135075/DataNode/ae61e ()
+* [http://classic.wikipathways.org/instance/WP4906_r135075](http://classic.wikipathways.org/instance/WP4906_r135075) http://rdf.wikipathways.org/Pathway/WP4906_r135075/DataNode/b40ed ()
+* [http://classic.wikipathways.org/instance/WP4906_r135075](http://classic.wikipathways.org/instance/WP4906_r135075) http://rdf.wikipathways.org/Pathway/WP4906_r135075/DataNode/e2c2d ()
 
 
 More details at [https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier](https://www.wikipathways.org/WikiPathwaysCurator/DataNodesTests/dataNodesWithoutIdentifier)
 
-<a name="39c5c867" />
-
-## GeneTests.entrezGeneIdentifiersNotNumber
-
-Entrez Gene identifiers that are not numbers: 1
-```
-http://classic.wikipathways.org/instance/WP4906_r135034 -> , unkown
- ```
-
-<a name="a07a01aa" />
-
-## GeneralTests.emptyLabelOfNodeWithIdentifier
-
-Data nodes with an identifier but empty label: 1
-```
-https://identifiers.org/ncbigene/unkown (), http://classic.wikipathways.org/instance/WP4906_r135034
-```
-
 <a name="630d2678" />
 
 ## InteractionTests.interactionsWithLabels
 
 Interactions found that involve Labels: 1
 ```
-http://classic.wikipathways.org/instance/WP4906_r135034 "unknown function" with graphId f7b7a
+http://classic.wikipathways.org/instance/WP4906_r135075 "unknown function" with graphId f7b7a
 ```