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'

  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'

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\'

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.

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