i2b2 HowTo Create an Ontology

Tags: i2b2 HowTo

Procedure

1. Log into the server UHLSQLBRICCSDB\UHLBRICCSDB and database i2b2ClinDataIntegration
2. Execute the stored procedure [dbo].[CreateEmptyOntology](@OntologyName, @Prefix, @SourceSystem, @OntologyBaseNode, @OntologyDescription)
   • Where:
     • @OntologyName is the name of the ontology and must not contain spaces, e.g., 'EMISPrimaryCareData'
     • @Prefix is the prefix for the concept codes and must not contain spaces, e.g., 'EMISPCD'
     • @SourceSystem is the system from which the data is being copied, e.g., 'Gem Risk Stratification'
     • @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

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