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The database includes new schemas (i2b2hive, i2b2imdata, i2b2pm, i2b2workdata) to support a full i2b2 database. All i2b2-specific tables have their initial contents defined as for a standard i2b2 installation.

Schema amapp

Tables defining metadata terms for Browse tab annotation. New terms for Study and Program are defined.

Schema biomart


Schema biomart_stage


Schema biomart_user


Schema deapp


Schema fmapp


Schema galaxy



Schema i2b2demodata

The default password for this user/role is changed to the i2b2 defauilt 'demouser'.


Schema i2b2hive

This standard i2b2 schema is new to tranSMART in 19.1.

Preloaded with the same metadata as a new i2b2 installation.

Schema i2b2imdata

This standard i2b2 schema is new to tranSMART in 19.1.

Schema i2b2metadata

The default password for this user/role is changed to the i2b2 defauilt 'demouser'.

Schema i2b2pm

This standard i2b2 schema is new to tranSMART in 19.1.

Preloaded with the same metadata as a new i2b2 installation.

Schema i2b2workdata

This standard i2b2 schema is new to tranSMART in 19.1.

Schema searchapp

Search keyword data is updated.

Schema tm_cz


Schema tm_lz


Schema tm_wz


Schema ts_batch


Data dictionaries

The pre-loaded metadata from Entrez (genes for human and mouse) and Medline (disease MeSH terms) has been updated.

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New placeholders are provided for org.transmart.i2b2.view.enable to enable viewing i2b2 data, and for com.recomdata.transmartIntro and com.recomdata.transmartWelcome to display alternative HTML text on the Browse and Login pages. transmartInto replaces the default Browse tab introductory text. transmartWelcome is an additional paragraph that appears below.

Database comparison script

The ora-pg-compare.pl script is extended to compare PostgresQL and Oracle database definitions for tranSMART and i2b2.

This script is used to keep database definitions for both platforms tranSMART and i2b2 in sync.

Scripts

Installation

Install scripts

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