How BIRN is organized

• BIRN Executive Committee
• Key Personnel
• Participating Institutions

What BIRN offers

• BIRN CC Tools Primer
• fBIRN Tools Primer
• mBIRN Tools Primer
• Mouse BIRN Tools Primer
• BIRN Data Repository

Who uses BIRN

• BIRN Coordinating Center
• Function BIRN
• Morphometry BIRN
• Mouse BIRN

Affiliated Sites

• NCRR
• NIH-CIT
• NDAR
• NA-MIC
• UK e-Science

BIRN Glossary

Copyright

Human Imaging Database (HID)

This extensible database management system has been developed and implemented to address the problems associated with managing the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories, and throughout clinical imaging communities at large. This system is comprised of three core components:

• The Human Clinical and Imaging Database (HID)
• An intuitive web based user interface (HID GUI)
• Clinical Assement Layout Manager (CALM)

The database is composed of an extensible schema and structured core. The core database contains a hierarchical description of an experiment and how experimental protocols relate to this hierarchy. Each descriptor in the database consists of a "base tuple" that defines the minimum informational requirements of that descriptor. The database can be extended for various experiments utilizing extended tuples which can be re-used and/or modified for other experiments. In addition, the database contains an extensible framework for the definition and storage of clinical assessments and demographic data.

The intuitive web based user interface (HID GUI) can be used for the entry and management of subject’s data. A core component of this interface involves the management of behavioral and/or clinical data that uses modules which streamline the development of on-line forms (CALM) for entry and maintenance of large numbers of measures.

The HID includes a data integration engine that builds on top of the BIRN data integration environment allowing multiple sites running the HID to create a federated database so that these sites can be queried as a single database resources from the web based user interface.  There are currently 12 federated HID databases, 11 Oracle and 1 PostgreSQL versions, storing clinical information on more than 419 subject imaging visits and 3174 subject assessments within the FBIRN consortium.

The database backup (dbbackup) package aims to be a comprehensive backup scheme for the HID database instances. The package uses two different backup procedures, a hot backup performed while the database is up and running, and a cold backup performed with the database shut down.  The two methods are implemented in separate scripts which are independently scheduled through the use of cron jobs.  The cold backup is meant ot be run weekly and the hot backup daily.  There is a configuration file used to specify many of the specifics of the scripts behavior, including whether backups should be stored locally, in SRB, or both.  Included with the backup scripts are examples of configuration files, a readme, as well as instructions and scripts for restoring from backup.

Video Tutorial: http://www.fbirntutorials.org/

Schema: http://www.nbirn.net/tools/human_imaging_schema/index.shtm

GUI: http://www.nbirn.net/tools/human_imaging_gui/index.shtm