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We are working on the full integration of Fractalis into tranSMART 19.0. This is a work in progress, involving new ETL interfaces between ttranSMART and Fractalis.
Database schemas
tranSMART and i2b2
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Where columns are date or time values in i2b2 and string values in transmart, they have been corrected to the appropriate date or time values. Initial testing found no conflicts in ETL procedures.
Column widths have been defined to be the same size across multiple tables (e.g. subject_id). Local installations are free to increase these sizes if they require longer strings but should beware of potential impact on database performance.
Required columns are updated in transmart so taht that any column columns required by i2b2 in a common tabel table are also required in transmart. One date needed to be defined in ETL procedures using an obvious default valukevalue. No other impacts have been noted in initial testing.
Triggers are required for some tables in i2b2. Although postgres can be configured automatically to increment unique identifiers for new rows in a table, the i2b2 code may include a call to increment a named sequence to generate a unique id value when a row is inserted. This necessitates defining a sequence with this name and using the same sequence in a trigger function to maintain database integrity.
Integers in portgres postgres are defined as type 'int' unless extremely large large values are expected. Values that can exceed 1 billion are defined as type 'bigint'.
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- i2b2hive
- i2b2imdata
- i2b2pm
- i2b2workdata
Though not used (currently) by tranSMART the aim is to create a database that can be populated and used as an i2b2 platform.
New I2b2 Tablespaces
I2b2 does not define tablespaces by default. A set of tablespace names were agreed with the i2b2-transmart developers for implementation in the tranSMART shcemaschema.
All i2b2 tables are in tablespace I2B2 and all i2b2 indices are in tablespace I2B2_INDEX, .
These reflect the tablespaces TRANSMART and INDX used fpor for the transmart-specific tables and indexes.
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Earlier tranSMART releases defined 3 additional tablespaces: biomart, deapp and search_app. These were no longer used - though they were cteated created with a new database.
They have been removed from tranSMART 19.0. For this release they are ignored by tranSMART code
New tables have been added to the schemas used by tranSMART 16.3.
Support for transmart_batch on Oracle is included by default. In tranSMARt tranSMART 16.3 this had to be installed before transmart_batch could be used with an Oracle database.
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