Merge pull request #2306 from geneontology/issue-2237-goref-cleanup

Final removal of GO_REF Markdown files

.github/workflows/refresh-readmes.yaml

@@ -15,13 +15,10 @@ jobs:
       - name: run make on rules
         working-directory: ./metadata/rules/
         run: make -B README.md
-      - name: run make on gorefs
-        working-directory: ./metadata/gorefs
-        run: make -B README.md
       - uses: stefanzweifel/git-auto-commit-action@v4
         name: commit READMEs
         with:
-          commit_message: refreshing goref and rules README.md files
+          commit_message: refreshing rules README.md file
           commit_user_email: [email protected]
           # Please do the dirty check, don't skip
           skip_dirty_check: false

metadata/db-xrefs.yaml

@@ -971,7 +971,7 @@
 - database: GO_REF
   name: Gene Ontology Database references
   generic_urls:
-    - http://current.geneontology.org/metadata/gorefs/index.html
+    - http://geneontology.org/gorefs
   entity_types:
     - type_name: entity
       type_id: BET:0000000

metadata/gorefs.yaml

@@ -1522,19 +1522,17 @@
   authors: Mouse Genome Informatics scientific curators and FlyBase
   year: 2014
 - id: GO_REF:0000096
-  title: Automated transfer of experimentally-verified manual GO annotation data to
-    close orthologs.
-  description: |-
-    Mouse Genome Database (MGD), The HUGO Gene Nomenclature Committee (HGNC), and
-    Rat Genome Database (RGD) have extensive procedures in place, overseen by expert
-    curation, to establish orthology relationships between their genes. The Experimentally
-    based annotations annotated by each group (IDA, IMP IPI, IGI, and EXP) are used
-    to provide annotations  to the respective mouse and rat orthologs, and given the
-    ISO evidence code and an entry in the inferred_from field to indicate the orthologous
-    entity.
-  authors: Mouse Genome Informatics scientific curators
+  title: Automated transfer of experimentally-verified manual GO annotation data to 
+    mouse-rat orthologs.
+  description: |-
+    The Alliance of Genome Resources (https://www.alliancegenome.org/) has procedures in 
+    place to establish orthology relationships between genes. The experimentally-based 
+    annotations (IDA, IMP IPI, IGI, and EXP) annotated by Rat Genome Database (RGD) and 
+    The Mouse Genome Database (MGD) are used to provide annotations to the respective 
+    mouse and rat orthologs, and given the ISO evidence code and an entry in the "With 
+    (or) From" field to indicate the orthologous entity.
+  authors: The Gene Ontology Consortium
   external_accession:
-    - J:164563
     - J:155856
     - RGD:1624291
   year: 2014
@@ -1943,15 +1941,15 @@
   year: 2023
   is_obsolete: false
 - id: GO_REF:0000119
-  title: Automated transfer of experimentally-verified manual GO annotation data to
-    mouse-human orthologs
-  description: |-
-    The Alliance of Genome Resources (https://www.alliancegenome.org/) has procedures
-    in place to establish orthology relationships between genes. The experimentally-based
-    annotations (IDA, IMP IPI, IGI, and EXP) for human genes  generated by the GOA
-    pipeline are used to provide annotations to the respective mouse orthologs, and
-    given the ISO evidence code and an entry in the inferred_from field to indicate
-    the orthologous entity.
+  title: Automated transfer of experimentally-verified manual GO annotation data to 
+    mouse-human orthologs.
+  description: |-
+    The Alliance of Genome Resources (https://www.alliancegenome.org/) has procedures in 
+    place to establish orthology relationships between genes. The experimentally-based 
+    annotations (IDA, IMP IPI, IGI, and EXP) for human genes generated by the GOA pipeline 
+    are used to provide annotations to the respective mouse orthologs, and given the ISO 
+    evidence code and an entry in the "With (or) From" field to indicate the orthologous 
+    entity.
   authors: The Gene Ontology Consortium
   year: 2023
   external_accession: