= i2b2 Create an Ontology

The procedure to create the tables for a new ontology.

1. Create the ontology table in the Meta Database

[1] Name of the ontology, e.g. 'ONYX'

{{{#!sql

  CREATE TABLE {Ontology Name from [1]}
   (	"C_HLEVEL" INT			NOT NULL, 
	"C_FULLNAME" VARCHAR(700)	NOT NULL, 
	"C_NAME" VARCHAR(2000)		NOT NULL, 
	"C_SYNONYM_CD" CHAR(1)		NOT NULL, 
	"C_VISUALATTRIBUTES" CHAR(3)	NOT NULL, 
	"C_TOTALNUM" INT			NULL, 
	"C_BASECODE" VARCHAR(50)	NULL, 
	"C_METADATAXML" TEXT		NULL, 
	"C_FACTTABLECOLUMN" VARCHAR(50)	NOT NULL, 
	"C_TABLENAME" VARCHAR(50)	NOT NULL, 
	"C_COLUMNNAME" VARCHAR(50)	NOT NULL, 
	"C_COLUMNDATATYPE" VARCHAR(50)	NOT NULL, 
	"C_OPERATOR" VARCHAR(10)	NOT NULL, 
	"C_DIMCODE" VARCHAR(700)	NOT NULL, 
	"C_COMMENT" TEXT			NULL, 
	"C_TOOLTIP" VARCHAR(900)	NULL, 
	"UPDATE_DATE" DATETIME		NOT NULL, 
	"DOWNLOAD_DATE" DATETIME	NULL, 
	"IMPORT_DATE" DATETIME	NULL, 
	"SOURCESYSTEM_CD" VARCHAR(50)	NULL, 
	"VALUETYPE_CD" VARCHAR(50)	NULL
   ) ;

}}}

2. Create a Scheme

A scheme is the prefix for a concept code.  Not exactly sure what it is used for, but hey ho.  You create one like this:

[2] Scheme name, e.g. 'CBO'
[3] Descriptive name for ontology, e.g. 'Onyx Ontology'

{{{#!sql

INSERT INTO SCHEMES(C_KEY, C_NAME, C_DESCRIPTION)
  VALUES('{Scheme name from [2]}:', '{Scheme name from [2]}', '{Descriptive name for ontology from [3]}');

}}}

3. Tell i2b2 about the new ontology

[4] Base path for ontology, e.g. '\onyx\'

{{{#!sql

INSERT INTO TABLE_ACCESS(C_TABLE_CD, C_TABLE_NAME, C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_DIMTABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, C_ENTRY_DATE, C_CHANGE_DATE, C_STATUS_CD, C_PROTECTED_ACCESS, VALUETYPE_CD)
  VALUES('{Ontology Name from [1]}', '{Ontology Name from [1]}', 0, '{Base path for ontology [4]}', '{Descriptive name for ontology [3]}', 'N', 'CA', NULL, NULL, NULL, 'concept_cd', 'concept_dimension', 'concept_path', 'T', 'LIKE', '{Base path for ontology [4]}', NULL, '{Descriptive name for ontology [3]}', NULL, NULL, NULL, 'N', NULL);

}}}

4. Create ontology hierarchy and Concept codes

This is beyond the scope of this page.  In order to stop the UI from giving an error when you click on the root note, you can create the root node in the ontology table.

{{{#!sql

INSERT INTO {Ontology Name from [1]}
           ([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])
     VALUES
           (0
           ,'{Base path for ontology [4]}'
           ,'{Descriptive name for ontology [3]}'
           ,'N'
           ,'CA'
           ,NULL
           ,NULL
           ,NULL
           ,'concept_cd'
           ,'concept_dimension'
           ,'concept_path'
           ,'N'
           ,'LIKE'
           ,'{Base path for ontology [4]}'
           ,NULL
           ,'{Descriptive name for ontology [3]}'
           ,GETDATE()
           ,NULL
           ,NULL
           ,'{A suitable source perhaps Ontology description from [3]}'
           ,NULL)
GO

}}}

Or run this script - Edit the parameters first

{{{#!sql

DECLARE @OntologyName VARCHAR(50), -- The name of the ontology, e.g. 'Onyx'
		@Prefix VARCHAR(10), -- The prefic 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'

----------------------------------------------------------------
-------------- T H E   A C T U A L   S C R I P T ---------------
----------------------------------------------------------------

--
-- CREATE ONTOLOGY TABLE
--

DECLARE @TCreateOntologyTable VARCHAR(MAX)
SET @TCreateOntologyTable = '
   USE ' + @MetaDatabaseName + '; 
   
   CREATE TABLE ' + @OntologyName + '
   (    "C_HLEVEL" INT                  NOT NULL, 
        "C_FULLNAME" VARCHAR(700)       NOT NULL, 
        "C_NAME" VARCHAR(2000)          NOT NULL, 
        "C_SYNONYM_CD" CHAR(1)          NOT NULL, 
        "C_VISUALATTRIBUTES" CHAR(3)    NOT NULL, 
        "C_TOTALNUM" INT                    NULL, 
        "C_BASECODE" VARCHAR(50)        NULL, 
        "C_METADATAXML" TEXT            NULL, 
        "C_FACTTABLECOLUMN" VARCHAR(50) NOT NULL, 
        "C_TABLENAME" VARCHAR(50)       NOT NULL, 
        "C_COLUMNNAME" VARCHAR(50)      NOT NULL, 
        "C_COLUMNDATATYPE" VARCHAR(50)  NOT NULL, 
        "C_OPERATOR" VARCHAR(10)        NOT NULL, 
        "C_DIMCODE" VARCHAR(700)        NOT NULL, 
        "C_COMMENT" TEXT                    NULL, 
        "C_TOOLTIP" VARCHAR(900)        NULL, 
        "UPDATE_DATE" DATETIME          NOT NULL, 
        "DOWNLOAD_DATE" DATETIME        NULL, 
        "IMPORT_DATE" DATETIME  NULL, 
        "SOURCESYSTEM_CD" VARCHAR(50)   NULL, 
        "VALUETYPE_CD" VARCHAR(50)      NULL
   ) ;'
   
EXEC (@TCreateOntologyTable);

-- Upgrade ontology table to version 1.6

DECLARE @UpgradeOntology1_6A VARCHAR(MAX)
DECLARE @UpgradeOntology1_6B VARCHAR(MAX)

SET @UpgradeOntology1_6A = '
    ALTER TABLE ' + @OntologyName + '
	ADD m_applied_path varchar(700) NULL
    ;
    
    ALTER TABLE ' + @OntologyName + '
	ADD m_exclusion_cd varchar(25) NULL
    ;
    
    ALTER TABLE ' + @OntologyName + '
	ADD	C_PATH	VARCHAR(700)   NULL
    ;
    
    ALTER TABLE ' + @OntologyName + '
	ADD	C_SYMBOL VARCHAR(50)	NULL
    ;
'

SET @UpgradeOntology1_6B = '
    UPDATE ' + @OntologyName + '
    SET m_applied_path = ''@''
    ;

    ALTER TABLE ' + @OntologyName + '
	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);	
'

EXEC (@UpgradeOntology1_6A);
EXEC (@UpgradeOntology1_6B);

--
-- CREATE SCHEME
--

DECLARE @TCreateScheme VARCHAR(MAX)
SET @TCreateScheme = '
   USE ' + @MetaDatabaseName + '; 
   
   INSERT INTO SCHEMES(C_KEY, C_NAME, C_DESCRIPTION)
   VALUES(''' + @Prefix + ':'', ''' + @Prefix + ''', ''' + @OntologyDescription + ''');'
   
EXEC (@TCreateScheme);

--
-- CREATE TABLE ACCESS
--

DECLARE @TCreateTableAccess VARCHAR(MAX)
SET @TCreateTableAccess = '
   USE ' + @MetaDatabaseName + '; 
   
   INSERT INTO TABLE_ACCESS(C_TABLE_CD, C_TABLE_NAME, C_HLEVEL, C_FULLNAME, C_NAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOTALNUM, C_BASECODE, C_METADATAXML, C_FACTTABLECOLUMN, C_DIMTABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_OPERATOR, C_DIMCODE, C_COMMENT, C_TOOLTIP, C_ENTRY_DATE, C_CHANGE_DATE, C_STATUS_CD, C_PROTECTED_ACCESS, VALUETYPE_CD)
   VALUES(''' + @OntologyName +  ''', ''' + @OntologyName + ''', 0, ''\' + @OntologyBaseNode + '\'', ''' + @OntologyDescription + ''', ''N'', ''CA'', NULL, NULL, NULL, ''concept_cd'', ''concept_dimension'', ''concept_path'', ''T'', ''LIKE'', ''\' + @OntologyBaseNode + '\'', NULL, ''' + @OntologyDescription + ''', NULL, NULL, NULL, ''N'', NULL);';
   
EXEC (@TCreateTableAccess);

--
-- CREATE THE BASE FOR THE ONTOLOGY
--

DECLARE @OntologyID INT

-- Create the Ontology

INSERT INTO [i2b2ClinDataIntegration].[dbo].[Ontology] ([Name],[Prefix],[SourceSystem])
VALUES (
			@OntologyName
           ,@Prefix
           ,@SourceSystem);

SET @OntologyID = SCOPE_IDENTITY();

-- Create the ontology base code

INSERT INTO [i2b2ClinDataIntegration].[dbo].[OntologyCode] ([ParentID],[OntologyID],[Code],[Name],[OntologyNodeTypeCode],[OntologyNodeStatusCode],[Editable],[MetaDataTypeCode],[MetaUnits])
VALUES (
			NULL
           ,@OntologyID
           ,1
           ,@OntologyBaseNode
           ,'C'
           ,'A'
           ,0
           ,NULL
           ,NULL
	);

-- Insert the base code into the Ontology table
DECLARE @TCreateBaseInOntologyTable VARCHAR(MAX)
SET @TCreateBaseInOntologyTable = '
   USE ' + @MetaDatabaseName + '; 
   
   INSERT INTO	Onyxv2
   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]
  FROM [i2b2ClinDataIntegration].[dbo].[i2b2Ontology]
  WHERE OntologyID = ' + CONVERT(VARCHAR(10), @OntologyID);
   
EXEC (@TCreateBaseInOntologyTable);

-- Insert the base code into the Concept Table
DECLARE @TCreateBaseConceptTable VARCHAR(MAX)
SET @TCreateBaseConceptTable = '
   USE ' + @DataDatabaseName + '; 
   
INSERT INTO concept_dimension
SELECT 
      [concept_path]
      ,[concept_cd]
      ,[name_char]
      ,[concept_blob]
      ,[update_date]
      ,[download_date]
      ,[import_date]
      ,[sourcesystem_cd]
      ,[UPLOAD_ID]
  FROM [i2b2ClinDataIntegration].[dbo].[i2b2OntologyConceptCodes]
  WHERE OntologyID = ' +  + CONVERT(VARCHAR(10), @OntologyID);
   
EXEC (@TCreateBaseConceptTable);

----------------------------------------------------------------
------- E N D   O F   T H E   A C T U A L   S C R I P T --------
----------------------------------------------------------------

}}}