Merge pull request #960 from OHDSI/manual_changes_29_02_2024

Add new concept_classes for OMOP Genomic; modify vocabulary_name

working/manual_changes/2024/2024-02-29.sql

@@ -0,0 +1,52 @@
+--Update of content to complement OMOP Genomic February 2024 release
+
+--1. Add new concept classes
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewConceptClass(
+    pConcept_class_id       =>'Structural Variant',
+    pConcept_class_name     =>'Variant at the DNA level not attributable to a single gene, including a karyotype'
+);
+END $_$;
+
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewConceptClass(
+    pConcept_class_id       =>'Gene Protein Variant',
+    pConcept_class_name     =>'Variant at the protein level for a gene'
+);
+END $_$;
+
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewConceptClass(
+    pConcept_class_id       =>'Gene Variant',
+    pConcept_class_name     =>'Variant of unspecified modality at the gene level'
+);
+END $_$;
+
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewConceptClass(
+    pConcept_class_id       =>'Gene DNA Variant',
+    pConcept_class_name     =>'Variant at the DNA level attributable to a gene'
+);
+END $_$;
+
+DO $_$
+BEGIN
+  PERFORM vocabulary_pack.AddNewConceptClass(
+    pConcept_class_id       =>'Gene RNA Variant',
+    pConcept_class_name     =>'Variant at the transcript (RNA) level for a gene'
+);
+END $_$;
+
+
+--2. Modify vocabulary
+UPDATE vocabulary
+SET vocabulary_name = 'OMOP Genomic vocabulary of known variants involved in disease'
+WHERE vocabulary_id = 'OMOP Genomic';
+
+UPDATE concept
+SET concept_name = 'OMOP Genomic vocabulary of known variants involved in disease'
+WHERE concept_id = 33002;