Changes between Version 6 and Version 7 of i2b2 HowTo Create an Ontology

Timestamp:

03/13/14 11:41:56 (10 years ago)

Author:

Richard Bramley

Comment:

--

i2b2 HowTo Create an Ontology

@@ -119 +119 @@
 
 DECLARE @OntologyName VARCHAR(50), -- The name of the ontology, e.g. 'Onyx'
-                @Prefix VARCHAR(10), -- The prefix for the concept code, e.g. 'ONX'
-                @OntologyDescription VARCHAR(100), -- A nice description, e.g. 'BRICCS Onyx Questionnaire'
-                @OntologyBaseNode VARCHAR(50), -- The name of the base node of the tree within i2b2, e.g. 'Onyx'
-                @SourceSystem VARCHAR(50), -- The system from where the data came, e.g. 'BRICCS Onyx'
-                @MetaDatabaseName VARCHAR(50), -- The name of the Meta Database in which to create the Ontology, e.g. 'i2b2_b1_metadata'
-                @DataDatabaseName VARCHAR(50) -- The name of the Data Database in which to create the Ontology, e.g. 'i2b2_b1_data'
-                
-SET @OntologyName = 'TestCiviCRM' -- Must not contain spaces
-SET @Prefix = 'TestGenCV'
-SET @OntologyDescription = 'TestGenvasc Study Details from CiviCRM'
-SET @OntologyBaseNode = 'TestCiviCRM'
-SET @SourceSystem = 'TestGenvasc CiviCRM'
-SET @MetaDatabaseName = 'i2b2_b1_metadata'
-SET @DataDatabaseName = 'i2b2_b1_data'
+                @Prefix VARCHAR(10), -- The prefix for the concept code, e.g. 'ONX'
+                @OntologyDescription VARCHAR(100), -- A nice description, e.g. 'BRICCS Onyx Questionnaire'
+                @OntologyBaseNode VARCHAR(50), -- The name of the base node of the tree within i2b2, e.g. 'Onyx'
+                @SourceSystem VARCHAR(50), -- The system from where the data came, e.g. 'BRICCS Onyx'
+                @MetaDatabaseName VARCHAR(50), -- The name of the Meta Database in which to create the Ontology, e.g. 'i2b2_b1_metadata'
+                @DataDatabaseName VARCHAR(50) -- The name of the Data Database in which to create the Ontology, e.g. 'i2b2_b1_data'
+                
+SET @OntologyName = 'PrimaryCareData' -- Must not contain spaces
+SET @Prefix = 'PCD'
+SET @OntologyDescription = 'Primary Care Data from GEM'
+SET @OntologyBaseNode = 'PrimaryCareData'
+SET @SourceSystem = 'Gem Risk Stratification'
+SET @MetaDatabaseName = 'i2b2_app03_genvasc_MetaData'
+SET @DataDatabaseName = 'i2b2_app03_genvasc_Data'
 
 ----------------------------------------------------------------
@@ -179 +179 @@
 SET @UpgradeOntology1_6A = '
     ALTER TABLE ' + @OntologyName + '
-        ADD m_applied_path varchar(700) NULL
+        ADD m_applied_path varchar(700) NULL
     ;
     
     ALTER TABLE ' + @OntologyName + '
-        ADD m_exclusion_cd varchar(25) NULL
+        ADD m_exclusion_cd varchar(25) NULL
     ;
     
     ALTER TABLE ' + @OntologyName + '
-        ADD     C_PATH  VARCHAR(700)   NULL
+        ADD     C_PATH  VARCHAR(700)   NULL
     ;
     
     ALTER TABLE ' + @OntologyName + '
-        ADD     C_SYMBOL VARCHAR(50)    NULL
+        ADD     C_SYMBOL VARCHAR(50)    NULL
     ;
 '
@@ -201 +201 @@
 
     ALTER TABLE ' + @OntologyName + '
-        ALTER COLUMN [m_applied_path] varchar(700) NOT NULL
-    ;
-        
+        ALTER COLUMN [m_applied_path] varchar(700) NOT NULL
+    ;
+        
     CREATE INDEX ' + @OntologyName + '_META_FULLNAME_IDX ON ' + @OntologyName + '(C_FULLNAME);
     
-    CREATE INDEX ' + @OntologyName + '_META_APPLIED_PATH_IDX ON ' + @OntologyName + '(M_APPLIED_PATH);  
+    CREATE INDEX ' + @OntologyName + '_META_APPLIED_PATH_IDX ON ' + @OntologyName + '(M_APPLIED_PATH);  
 '
 
@@ -248 +248 @@
 INSERT INTO [i2b2ClinDataIntegration].[dbo].[Ontology] ([Name],[Prefix],[SourceSystem])
 VALUES (
-                        @OntologyName
+                        @OntologyName
            ,@Prefix
            ,@SourceSystem);
@@ -258 +258 @@
 INSERT INTO [i2b2ClinDataIntegration].[dbo].[OntologyCode] ([ParentID],[OntologyID],[Code],[Name],[OntologyNodeTypeCode],[OntologyNodeStatusCode],[Editable],[MetaDataTypeCode],[MetaUnits])
 VALUES (
-                        NULL
+                        NULL
            ,@OntologyID
            ,1
@@ -267 +267 @@
            ,NULL
            ,NULL
-        );
-
+        );
+*/
 -- Insert the base code into the Ontology table
 DECLARE @TCreateBaseInOntologyTable VARCHAR(MAX)
@@ -274 +274 @@
    USE ' + @MetaDatabaseName + '; 
    
-   INSERT INTO  Onyxv2
+   INSERT INTO  ' + @OntologyName + '
    SELECT [C_HLEVEL]
       ,[C_FULLNAME]