Changes between Version 16 and Version 17 of i2b2 HowTo Create an Ontology

Timestamp:

06/07/16 15:34:46 (8 years ago)

Author:

Richard Bramley

Comment:

--

i2b2 HowTo Create an Ontology

@@ -13 +13 @@
   - `@OntologyBaseNode` is the name of the root node for the ontology, e.g., 'EMISPrimaryCareData'
   - `@OntologyDescription` is a short description of the ontology, e.g., 'EMIS Primary Care Data from GEM'
-3. Execute the stored procedure `[dbo].[CreateOntologyInStudy] @OntologyID, @MetaDatabaseName, @DataDatabaseName` for each project that requires the ontology
- - Where:
-  - `@OntologyID` is the ID returned by the previous stored procedure.
-  - `@MetaDatabaseName` is the name of the i2b2 meta database where the ontology should be created, e.g., 'project_MetaData'
-  - `@DataDatabaseName` is the name of the i2b2 data database where the ontology should be created, e.g., 'project_Data'
-4. Amend the stored procedure `[dbo].[LoadAllOntologiesIntoConceptDimension]` in the i2b2 data database to add the import of the codes into the `concept_dimension`.
- - The line should be of the form: `EXEC dbo.LoadOntologyIntoConceptDimension {Ontology ID};`, where `OntologyID` is the ID of the ontology created above.
-5. Create a stored procedure to import the ontology codes into the i2b2 meta database.  The procedure should follow the form:
-{{{
-CREATE PROC [dbo].[Update{Ontology Name}] AS
-DELETE FROM dbo.{Ontology Table Name};
-
-INSERT INTO     dbo.{Ontology Table Name}
-SELECT [C_HLEVEL]
-      ,[C_FULLNAME]
-      ,[C_NAME]
-      ,[C_SYNONYM_CD]
-      ,[C_VISUALATTRIBUTES]
-      ,[C_TOTALNUM]
-      ,[C_BASECODE]
-      ,[C_METADATAXML]
-      ,[C_FACTTABLECOLUMN]
-      ,[C_TABLENAME]
-      ,[C_COLUMNNAME]
-      ,[C_COLUMNDATATYPE]
-      ,[C_OPERATOR]
-      ,[C_DIMCODE]
-      ,[C_COMMENT]
-      ,[C_TOOLTIP]
-      ,[UPDATE_DATE]
-      ,[DOWNLOAD_DATE]
-      ,[IMPORT_DATE]
-      ,[SOURCESYSTEM_CD]
-      ,[VALUETYPE_CD]
-          ,[m_applied_path]
-          ,[m_exclusive_cd]
-          ,[C_PATH]
-          ,[C_SYMBOL]
-  FROM [i2b2ClinDataIntegration].[dbo].[i2b2Ontology]
-  WHERE OntologyID = {Ontology ID}
-}}}
- - Where:
-  - `Ontology Name` is the name used for the ontology above
-  - `Ontology Table Name` is the name of the ontology table created in the i2b2 meta database.
-  - `OntologyID` is the ID of the ontology created above
+3. Create records in the table `OntologyUsage` in the `i2b2ClinDataIntegration` database for each study that will use the ontology.  The `StudyName` is the unique portion of the i2b2 database names, for example `i2b2_app03_{studyName}_data`.
+4. Run the command `EXECUTE [i2b2ClinDataIntegration].[dbo].[UpdateOntologyConceptCodes];`
 
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