New validation results (and 2 new pathways)

wikipathways · Jan 19, 2024 · 6006bd9 · 6006bd9
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diff --git a/pathways.txt b/pathways.txt
@@ -1432,7 +1432,9 @@ WP501
 WP5023
 WP5024
 WP5025
+WP5026
 WP5027
+WP5028
 WP5029
 WP502
 WP5030

diff --git a/reports/WP3679.json b/reports/WP3679.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "2 issues",
+  "message": "1 issue",
   "color": "red"
 }
diff --git a/reports/WP3679.md b/reports/WP3679.md
@@ -17,8 +17,7 @@
     * noNonMetaboliteToMetaboliteConversions: .. all OK!
     * noGeneProteinConversions: .. all OK!
     * nonNumericIDs: .. all OK!
-    * interactionsWithLabels: .x we found 1 problem(s):
-        * [Interactions found that involve Labels: 2](#630d2679)
+    * interactionsWithLabels: .. all OK!
     * possibleTranslocations: .x we found 1 problem(s):
         * [Interactions between identical nodes: 3](#1c118208)
     * noProteinProteinConversions: .. all OK!
@@ -41,31 +40,21 @@
 * Number of test classes: 20
 * Number of tests: 97
 * Number of assertions: 196
-* Number of fails: 2
+* Number of fails: 1
 
 ## Fails
 
-<a name="630d2679" />
-
-## InteractionTests.interactionsWithLabels
-
-Interactions found that involve Labels: 2
-```
-http://classic.wikipathways.org/instance/WP3679_rr117678 "endocannabinoids" with graphId a50e8
-http://classic.wikipathways.org/instance/WP3679_rr117678 "endocannabinoids" with graphId f0fac
-```
-
 <a name="1c118208" />
 
 ## InteractionTests.possibleTranslocations
 
 Interactions between identical nodes: 3
 ```
-http://classic.wikipathways.org/instance/WP3679_rr117678 http://rdf.wikipathways.org/Pathway/WP3679_rr117678/WP/Interaction/ida4f5458d "Ca 2+" (https://identifiers.org/chebi/CHEBI:29108) and 
+http://classic.wikipathways.org/instance/WP3679_rr127931 http://rdf.wikipathways.org/Pathway/WP3679_rr127931/WP/Interaction/ida4f5458d "Ca 2+" (https://identifiers.org/chebi/CHEBI:29108) and 
 Ca 2+" (https://identifiers.org/chebi/CHEBI:29108)
-http://classic.wikipathways.org/instance/WP3679_rr117678 http://rdf.wikipathways.org/Pathway/WP3679_rr117678/WP/Interaction/id9071c85b "Ca 2+" (https://identifiers.org/chebi/CHEBI:29108) and 
+http://classic.wikipathways.org/instance/WP3679_rr127931 http://rdf.wikipathways.org/Pathway/WP3679_rr127931/WP/Interaction/iddcb9dd99 "Ca 2+" (https://identifiers.org/chebi/CHEBI:29108) and 
 Ca 2+" (https://identifiers.org/chebi/CHEBI:29108)
-http://classic.wikipathways.org/instance/WP3679_rr117678 http://rdf.wikipathways.org/Pathway/WP3679_rr117678/WP/Interaction/iddcb9dd99 "Ca 2+" (https://identifiers.org/chebi/CHEBI:29108) and 
+http://classic.wikipathways.org/instance/WP3679_rr127931 http://rdf.wikipathways.org/Pathway/WP3679_rr127931/WP/Interaction/id9071c85b "Ca 2+" (https://identifiers.org/chebi/CHEBI:29108) and 
 Ca 2+" (https://identifiers.org/chebi/CHEBI:29108)
 ```
 

diff --git a/reports/WP3845.md b/reports/WP3845.md
@@ -23,7 +23,7 @@
     * noGeneProteinConversions: .. all OK!
     * nonNumericIDs: .. all OK!
     * interactionsWithLabels: .x we found 1 problem(s):
-        * [Interactions found that involve Labels: 3](#630d267a)
+        * [Interactions found that involve Labels: 2](#630d2679)
     * possibleTranslocations: .. all OK!
     * noProteinProteinConversions: .. all OK!
     * incorrectKEGGIdentifiers: .. all OK!
@@ -55,18 +55,17 @@
 
 The following DataNodes have no identifier: 2
 ```
-http://classic.wikipathways.org/instance/WP3845_rr123396 http://rdf.wikipathways.org/Pathway/WP3845_rr123396/DataNode/c5788 (Cell Adhesion)
-http://classic.wikipathways.org/instance/WP3845_rr123396 http://rdf.wikipathways.org/Pathway/WP3845_rr123396/DataNode/bd8ac (Unknown)
+http://classic.wikipathways.org/instance/WP3845_rr127900 http://rdf.wikipathways.org/Pathway/WP3845_rr127900/DataNode/c5788 (Cell Adhesion)
+http://classic.wikipathways.org/instance/WP3845_rr127900 http://rdf.wikipathways.org/Pathway/WP3845_rr127900/DataNode/bd8ac (Unknown)
 ```
 
-<a name="630d267a" />
+<a name="630d2679" />
 
 ## InteractionTests.interactionsWithLabels
 
-Interactions found that involve Labels: 3
+Interactions found that involve Labels: 2
 ```
-http://classic.wikipathways.org/instance/WP3845_rr123396 "NOTCH intra-cellular domain" with graphId a9a94
-http://classic.wikipathways.org/instance/WP3845_rr123396 "NOTCH non-canonical targets" with graphId fb0ee
-http://classic.wikipathways.org/instance/WP3845_rr123396 "NOTCH extra-cellular domain" with graphId ec254
+http://classic.wikipathways.org/instance/WP3845_rr127900 "NICD" with graphId e9cb1
+http://classic.wikipathways.org/instance/WP3845_rr127900 "NOTCH non-canonical targets" with graphId fb0ee
 ```
 
diff --git a/reports/WP3863.md b/reports/WP3863.md
@@ -50,9 +50,9 @@
 
 Interactions found that involve Labels: 3
 ```
-http://classic.wikipathways.org/instance/WP3863_rr121717 "Proliferation, differentiation, 
+http://classic.wikipathways.org/instance/WP3863_rr127932 "DNA" with graphId f792a
+http://classic.wikipathways.org/instance/WP3863_rr127932 "Superantigen (SEB)" with graphId fb17e
+http://classic.wikipathways.org/instance/WP3863_rr127932 "Proliferation, differentiation, 
 immune response" with graphId db9f7
-http://classic.wikipathways.org/instance/WP3863_rr121717 "Superantigen (SEB)" with graphId fb17e
-http://classic.wikipathways.org/instance/WP3863_rr121717 "DNA" with graphId f792a
 ```
 
diff --git a/reports/WP3872.md b/reports/WP3872.md
@@ -7,17 +7,21 @@
 * CASMetabolitesTests: all 2 tests OK!
 * ChEBIMetabolitesTests: all 4 tests OK!
 * ChemSpiderTests: all 2 tests OK!
-* DataNodesTests
-    * dataNodesWithoutIdentifier: .x we found 1 problem(s):
-        * [The following DataNodes have no identifier: 4](#d2d32fa3)
-    * unknownTypes_knownDatasource: .. all OK!
-    * unknownTypes: .. all OK!
-    * unknownTypes_Reactome: .. all OK!
+* DataNodesTests: all 4 tests OK!
 * EnsemblTests: all 4 tests OK!
 * GeneTests: all 4 tests OK!
 * GeneralTests: all 13 tests OK!
 * HMDBSecMetabolitesTests: all 3 tests OK!
-* InteractionTests: all 8 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: 4](#630d267b)
+    * possibleTranslocations: .. all OK!
+    * noProteinProteinConversions: .. all OK!
+    * incorrectKEGGIdentifiers: .. all OK!
 * KEGGMetaboliteTests: all 2 tests OK!
 * LIPIDMAPSTests: all 1 tests OK!
 * MetaboliteStructureTests: all 1 tests OK!
@@ -40,16 +44,15 @@
 
 ## Fails
 
-<a name="d2d32fa3" />
+<a name="630d267b" />
 
-## DataNodesTests.dataNodesWithoutIdentifier
+## InteractionTests.interactionsWithLabels
 
-The following DataNodes have no identifier: 4
+Interactions found that involve Labels: 4
 ```
-http://classic.wikipathways.org/instance/WP3872_rr123397 http://rdf.wikipathways.org/Pathway/WP3872_rr123397/DataNode/ee150 (BCL-2 family)
-http://classic.wikipathways.org/instance/WP3872_rr123397 http://rdf.wikipathways.org/Pathway/WP3872_rr123397/DataNode/d33be (Growth Factor Receptors)
-http://classic.wikipathways.org/instance/WP3872_rr123397 http://rdf.wikipathways.org/Pathway/WP3872_rr123397/DataNode/c6dab (siRNA A6
-)
-http://classic.wikipathways.org/instance/WP3872_rr123397 http://rdf.wikipathways.org/Pathway/WP3872_rr123397/DataNode/b97c9 (siRNA B4)
+http://classic.wikipathways.org/instance/WP3872_rr127930 "Growth Factor Receptors" with graphId e6378
+http://classic.wikipathways.org/instance/WP3872_rr127930 "siRNA Integrin A6" with graphId c2aa2
+http://classic.wikipathways.org/instance/WP3872_rr127930 "siRNA PIK3CA" with graphId d2502
+http://classic.wikipathways.org/instance/WP3872_rr127930 "siRNA Integrin B4" with graphId c96bb
 ```
 
diff --git a/reports/WP3873.md b/reports/WP3873.md
@@ -7,17 +7,21 @@
 * CASMetabolitesTests: all 2 tests OK!
 * ChEBIMetabolitesTests: all 4 tests OK!
 * ChemSpiderTests: all 2 tests OK!
-* DataNodesTests
-    * dataNodesWithoutIdentifier: .x we found 1 problem(s):
-        * [The following DataNodes have no identifier: 2](#d2d32fa1)
-    * unknownTypes_knownDatasource: .. all OK!
-    * unknownTypes: .. all OK!
-    * unknownTypes_Reactome: .. all OK!
+* DataNodesTests: all 4 tests OK!
 * EnsemblTests: all 4 tests OK!
 * GeneTests: all 4 tests OK!
 * GeneralTests: all 13 tests OK!
 * HMDBSecMetabolitesTests: all 3 tests OK!
-* InteractionTests: all 8 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: 1](#630d2678)
+    * possibleTranslocations: .. all OK!
+    * noProteinProteinConversions: .. all OK!
+    * incorrectKEGGIdentifiers: .. all OK!
 * KEGGMetaboliteTests: all 2 tests OK!
 * LIPIDMAPSTests: all 1 tests OK!
 * MetaboliteStructureTests: all 1 tests OK!
@@ -40,13 +44,12 @@
 
 ## Fails
 
-<a name="d2d32fa1" />
+<a name="630d2678" />
 
-## DataNodesTests.dataNodesWithoutIdentifier
+## InteractionTests.interactionsWithLabels
 
-The following DataNodes have no identifier: 2
+Interactions found that involve Labels: 1
 ```
-http://classic.wikipathways.org/instance/WP3873_rr123360 http://rdf.wikipathways.org/Pathway/WP3873_rr123360/DataNode/c7312 (Chemosensetivity)
-http://classic.wikipathways.org/instance/WP3873_rr123360 http://rdf.wikipathways.org/Pathway/WP3873_rr123360/DataNode/ee91a (Tumorigenesis)
+http://classic.wikipathways.org/instance/WP3873_rr127936 "Tumorigenesis" with graphId d7179
 ```
 
diff --git a/reports/WP3875.md b/reports/WP3875.md
@@ -50,8 +50,8 @@
 
 Interactions found that involve Labels: 3
 ```
-http://classic.wikipathways.org/instance/WP3875_rr117657 "Origin Firing" with graphId c740a
-http://classic.wikipathways.org/instance/WP3875_rr117657 "Replisome Stability" with graphId eb3a5
-http://classic.wikipathways.org/instance/WP3875_rr117657 "Cell Arrest Cycle" with graphId f3cbb
+http://classic.wikipathways.org/instance/WP3875_rr127928 "Cell Arrest Cycle" with graphId f3cbb
+http://classic.wikipathways.org/instance/WP3875_rr127928 "Origin Firing" with graphId c740a
+http://classic.wikipathways.org/instance/WP3875_rr127928 "Replisome Stability" with graphId eb3a5
 ```
 
diff --git a/reports/WP3877.md b/reports/WP3877.md
@@ -46,7 +46,7 @@
 
 The following DataNodes have no identifier: 2
 ```
-http://classic.wikipathways.org/instance/WP3877_rr117828 http://rdf.wikipathways.org/Pathway/WP3877_rr117828/DataNode/a02c4 (CRE)
-http://classic.wikipathways.org/instance/WP3877_rr117828 http://rdf.wikipathways.org/Pathway/WP3877_rr117828/DataNode/b06ac (TLR11)
+http://classic.wikipathways.org/instance/WP3877_rr127906 http://rdf.wikipathways.org/Pathway/WP3877_rr127906/DataNode/a02c4 (CRE)
+http://classic.wikipathways.org/instance/WP3877_rr127906 http://rdf.wikipathways.org/Pathway/WP3877_rr127906/DataNode/b06ac (TLR11)
 ```
 
diff --git a/reports/WP3878.json b/reports/WP3878.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "curation",
-  "message": "2 issues",
+  "message": "3 issues",
   "color": "red"
 }
diff --git a/reports/WP3878.md b/reports/WP3878.md
@@ -9,12 +9,17 @@
 * 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!
 * EnsemblTests: all 4 tests OK!
-* GeneTests: all 4 tests OK!
+* GeneTests
+    * entrezGeneIdentifiersNotNumber: .. all OK!
+    * affyProbeIdentifiersNotCorrect: .. all OK!
+    * outdatedIdentifiers: ...x we found 1 problem(s):
+        * [Found integer HGNC symbols (did you mean 'HGNC Accession number'?): 1](#7c6b1fb0)
+    * nonNumericHGNCAccessionNumbers: .. all OK!
 * GeneralTests: all 13 tests OK!
 * HMDBSecMetabolitesTests: all 3 tests OK!
 * InteractionTests
@@ -23,7 +28,7 @@
     * noGeneProteinConversions: .. all OK!
     * nonNumericIDs: .. all OK!
     * interactionsWithLabels: .x we found 1 problem(s):
-        * [Interactions found that involve Labels: 6](#630d267d)
+        * [Interactions found that involve Labels: 4](#630d267b)
     * possibleTranslocations: .. all OK!
     * noProteinProteinConversions: .. all OK!
     * incorrectKEGGIdentifiers: .. all OK!
@@ -45,31 +50,39 @@
 * Number of test classes: 20
 * Number of tests: 97
 * Number of assertions: 196
-* Number of fails: 2
+* Number of fails: 3
 
 ## Fails
 
-<a name="d2d32fa1" />
+<a name="d2d32fa2" />
 
 ## DataNodesTests.dataNodesWithoutIdentifier
 
-The following DataNodes have no identifier: 2
+The following DataNodes have no identifier: 3
 ```
-http://classic.wikipathways.org/instance/WP3878_rr123399 http://rdf.wikipathways.org/Pathway/WP3878_rr123399/DataNode/adc8e (uH2A)
-http://classic.wikipathways.org/instance/WP3878_rr123399 http://rdf.wikipathways.org/Pathway/WP3878_rr123399/DataNode/f0698 (uH2B)
+http://classic.wikipathways.org/instance/WP3878_rr127927 http://rdf.wikipathways.org/Pathway/WP3878_rr127927/DataNode/b8df3 (DNA repair)
+http://classic.wikipathways.org/instance/WP3878_rr127927 http://rdf.wikipathways.org/Pathway/WP3878_rr127927/DataNode/c98f2 (PPP activation)
+http://classic.wikipathways.org/instance/WP3878_rr127927 http://rdf.wikipathways.org/Pathway/WP3878_rr127927/DataNode/bf7fa (Pathway)
 ```
 
-<a name="630d267d" />
+<a name="7c6b1fb0" />
+
+## GeneTests.outdatedIdentifiers
+
+Found integer HGNC symbols (did you mean 'HGNC Accession number'?): 1
+```
+http://classic.wikipathways.org/instance/WP3878_rr127927 H2AX has 4739
+```
+
+<a name="630d267b" />
 
 ## InteractionTests.interactionsWithLabels
 
-Interactions found that involve Labels: 6
+Interactions found that involve Labels: 4
 ```
-http://classic.wikipathways.org/instance/WP3878_rr123399 "CSR" with graphId f1315
-http://classic.wikipathways.org/instance/WP3878_rr123399 "V(D)J" with graphId c43f9
-http://classic.wikipathways.org/instance/WP3878_rr123399 "DNA Damage " with graphId dfa16
-http://classic.wikipathways.org/instance/WP3878_rr123399 "Hypotonic Stress " with graphId ac954
-http://classic.wikipathways.org/instance/WP3878_rr123399 "Oxidative Stress" with graphId be0d2
-http://classic.wikipathways.org/instance/WP3878_rr123399 "Autophagy" with graphId dd00c
+http://classic.wikipathways.org/instance/WP3878_rr127927 "V(D)J" with graphId c43f9
+http://classic.wikipathways.org/instance/WP3878_rr127927 "Hypotonic Stress " with graphId ac954
+http://classic.wikipathways.org/instance/WP3878_rr127927 "DNA Damage " with graphId dfa16
+http://classic.wikipathways.org/instance/WP3878_rr127927 "CSR" with graphId f1315
 ```
 
diff --git a/reports/WP3879.md b/reports/WP3879.md
@@ -9,7 +9,7 @@
 * 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: 1](#d2d32fa0)
     * unknownTypes_knownDatasource: .. all OK!
     * unknownTypes: .. all OK!
     * unknownTypes_Reactome: .. all OK!
@@ -23,7 +23,7 @@
     * noGeneProteinConversions: .. all OK!
     * nonNumericIDs: .. all OK!
     * interactionsWithLabels: .x we found 1 problem(s):
-        * [Interactions found that involve Labels: 6](#630d267d)
+        * [Interactions found that involve Labels: 4](#630d267b)
     * possibleTranslocations: .. all OK!
     * noProteinProteinConversions: .. all OK!
     * incorrectKEGGIdentifiers: .. all OK!
@@ -49,27 +49,25 @@
 
 ## Fails
 
-<a name="d2d32fa1" />
+<a name="d2d32fa0" />
 
 ## DataNodesTests.dataNodesWithoutIdentifier
 
-The following DataNodes have no identifier: 2
+The following DataNodes have no identifier: 1
 ```
-http://classic.wikipathways.org/instance/WP3879_rr123400 http://rdf.wikipathways.org/Pathway/WP3879_rr123400/DataNode/bc30f (Cap-Independent Translation Initiation of p27 mRNA Through its 5'UTR)
-http://classic.wikipathways.org/instance/WP3879_rr123400 http://rdf.wikipathways.org/Pathway/WP3879_rr123400/DataNode/de848 (Cap-Independent Translation Initiation of p27 mRNA Through its 5'UTR)
+http://classic.wikipathways.org/instance/WP3879_rr127903 http://rdf.wikipathways.org/Pathway/WP3879_rr127903/DataNode/bc30f (Cap-Independent Translation Initiation 
+of p27 mRNA Through its 5'UTR)
 ```
 
-<a name="630d267d" />
+<a name="630d267b" />
 
 ## InteractionTests.interactionsWithLabels
 
-Interactions found that involve Labels: 6
+Interactions found that involve Labels: 4
 ```
-http://classic.wikipathways.org/instance/WP3879_rr123400 "PI3K" with graphId d48c9
-http://classic.wikipathways.org/instance/WP3879_rr123400 "AMP/ATP Ratio" with graphId eae0b
-http://classic.wikipathways.org/instance/WP3879_rr123400 "Hypomethylation of 5' mRNA cap" with graphId a697f
-http://classic.wikipathways.org/instance/WP3879_rr123400 "Receptor Tyrosine Kinases" with graphId f55ba
-http://classic.wikipathways.org/instance/WP3879_rr123400 "Prevention of Cancer" with graphId d7ec4
-http://classic.wikipathways.org/instance/WP3879_rr123400 "Prevention of Cancer" with graphId f3f7d
+http://classic.wikipathways.org/instance/WP3879_rr127903 "AMP/ATP Ratio" with graphId eae0b
+http://classic.wikipathways.org/instance/WP3879_rr127903 "Receptor Tyrosine Kinases" with graphId f55ba
+http://classic.wikipathways.org/instance/WP3879_rr127903 "Hypomethylation of 5' mRNA cap" with graphId a697f
+http://classic.wikipathways.org/instance/WP3879_rr127903 "Prevention of Cancer" with graphId d7ec4
 ```
 
diff --git a/reports/WP5026.json b/reports/WP5026.json
@@ -0,0 +1,6 @@
+{
+  "schemaVersion": 1,
+  "label": "curation",
+  "message": "2 issues",
+  "color": "red"
+}