codes ...

ga4gh-beacon · Feb 7, 2025 · 145f64c · 145f64c
1 parent ec6a011
commit 145f64c
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 1 deletion.
diff --git a/docs/terms-and-values.md b/docs/terms-and-values.md
@@ -64,6 +64,15 @@ as well as a dedicated vocabulary derived from EFO terminology.
 
 * for CNV queries use the EFO terms for relative copy number changes for either
   `copyChange` or `variantType` parameters, depending on the Beacon version
+* in Beacon v2+ the `copyChange` parameter MUST use a primaryCode representing one of:
+    - EFO:0030069: complete genomic loss    
+    - EFO:0020073: high-level loss    
+    - EFO:0030068: low-level loss    
+    - EFO:0030067: loss    
+    - EFO:0030064: regional base ploidy    
+    - EFO:0030070: gain    
+    - EFO:0030071: low-level gain    
+    - EFO:0030072: high-level gain    
 * for other types of variations `variantType` according to query documentation and
   emerging examples
 * `variantType` might be replaced during future development

diff --git a/mkdocs.yaml b/mkdocs.yaml
@@ -15,7 +15,7 @@ nav:
   - Beacon v2 Query Solutions: generated/requestProfiles_g_variant
   - Beacon v2+ Query Proposals: generated/requestProfiles_VQSrequest
   - Parameter Definitions: generated/requestParameterComponents
-  - Query Types: query-types
+  # - Query Types: query-types
   - Genomic Coordinates: genomic-coordinates-mappings
   - Recommended Terms: terms-and-values
   - Query Schema Source Files: https://github.com/ga4gh-beacon/variant-query-types/tree/main/schemas