[GL_RefAnnotTable] Add database versions, fix go.db version

Author: torres-alexis

GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A.md

@@ -151,7 +151,7 @@ The default columns in the annotation table are:
 | org.Sc.sgd.db   | 3.19.1  | [https://bioconductor.org/packages/release/data/annotation/html/org.Sc.sgd.db.html](https://www.bioconductor.org/packages/release/data/annotation/html/org.Sc.sgd.db.html) |
 | AnnotationForge | 1.46.0  | [https://bioconductor.org/packages/AnnotationForge](https://bioconductor.org/packages/AnnotationForge) |
 | biomaRt         |  2.60.1  | [https://bioconductor.org/packages/biomaRt](https://bioconductor.org/packages/biomaRt) |
-| GO.db           |  2.0.0  | [https://bioconductor.org/packages/GO.db](https://bioconductor.org/packages/GO.db) |
+| GO.db           |  3.19.1  | [https://bioconductor.org/packages/GO.db](https://bioconductor.org/packages/GO.db) |
 
 ---
 
@@ -164,8 +164,12 @@ The default columns in the annotation table are:
 > - Plants: Ensembl plants release 59
 > - Bacteria: Ensembl bacteria release 59  
 >  
-> **PANTHER:**  18.0  
-> > *Note: The values in the 'name' column of [GL-DPPD-7110-A_annotations.csv](GL-DPPD-7110-A_annotations.csv) (e.g., MOUSE, HUMAN, ARABIDOPSIS) are derived from the short names used in PANTHER. These short names are subject to change.*
+> **Database Versions:**
+> - STRINGdb: 12.0  
+> - PANTHERdb: 18.0  
+> - GO.db: 2.1 (used only when creating a local org.db R package)  
+>  
+> > *Note: The values in the 'name' column of [GL-DPPD-7110-A_annotations.csv](GL-DPPD-7110-A_annotations.csv) (e.g., HUMAN, MOUSE, RAT) are derived from the short names used in PANTHER. These short names are subject to change.*  
 
 ---
 

GeneLab_Reference_Annotations/Workflow_Documentation/GL_RefAnnotTable-A/CHANGELOG.md

@@ -10,9 +10,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added  
 
 - Added software: 
-    - AnnotationForge version 1.46.0.  
-    - biomaRt version 2.60.1.  
-    - GO.db version 2.0.0.  
+    - AnnotationForge version 1.46.0    
+    - biomaRt version 2.60.1  
+    - GO.db version 3.19.1  
 - Added support for:
     - Bacillus subtilis, subsp. subtilis 168  
     - Brachypodium distachyon  
@@ -48,11 +48,11 @@ Bioconductor. Used for:
     - Plants: Ensembl plants release 59
     - Bacteria: Ensembl bacteria release 59
 - Updated software:
-    - tidyverse version updated from 1.3.2 to 2.0.0.  
-    - STRINGdb version updated from 2.8.4 to 2.16.0.   
-    - PANTHER.db version updated from 1.0.11 to 1.0.12. 
-    - rtracklayer version updated from 1.56.1 to 1.64.0.
-    - Bioconductor version updated from 3.15.1 to 3.19.1.  
+    - tidyverse version updated from 1.3.2 to 2.0.0  
+    - STRINGdb version updated from 2.8.4 to 2.16.0   
+    - PANTHER.db version updated from 1.0.11 to 1.0.12 
+    - rtracklayer version updated from 1.56.1 to 1.64.0
+    - Bioconductor version updated from 3.15.1 to 3.19.1  
 - Removed org.EcK12.eg.db and replaced it with a locally created annotations 
 database, as it is no longer available on Bioconductor
 - Changed the first argument of GL-DPPD-7110-A_build-genome-annots-tab.R from