Human Imaging Database (HID) Releases

Clinical Assessment Layout Mgr 2.2

dbkeator@stage.nitrcce.org (David Keator) — Wed, 22 Sep 2010 16:58:00 GMT

Latest CALM release to go with HID release 2.2. Latest FBIRN functionality is included. See the README.html file for installation instructions.

Human Imaging Database System 2.2

dbkeator@stage.nitrcce.org (David Keator) — Wed, 22 Sep 2010 16:36:00 GMT

Version 2.2 is the latest release from the FBIRN Neuroinformatics group of the HID web application and database schema. Schemas exist for both Oracle and PostgreSQL although FBIRN has migrated solely to PostgreSQL. To install the web application see the clinical/README.html application. To install the schema, choose the platform and view the README file. For example, to install the PostgreSQL schema see schema/Postgres/db_objects/README.

Human Imaging Database System HID 1.6.3

dyounes@stage.nitrcce.org (Danny Younes) — Mon, 20 Oct 2008 22:06:00 GMT

This latest HID version release contains the complete system. The doanload contains the build installation file for the HID graphical user interface (GUI), schema, and data back-up scripts (PostgreSQL).

Please visit the BIRN web page for the latest information on the HID system, downloads, and manuals.

http://www.nbirn.net/research/function/hid.shtm

ARCHIVE: HID G. User Interface HID Graphical User Interface 1.6.2

dyounes@stage.nitrcce.org (Danny Younes) — Fri, 27 Jun 2008 21:25:00 GMT

The Human Clinical and Imaging Database has been designed so that it can be customized and extended to contain relevant information from any particular sites needs without requiring modification to the schema itself. This information consists of data concerning the research subjects used in an experiment, subject assessments and demographics, the experimental data collected, the experimental protocols used and any annotations or statistics (metadata) normally included with an experiment or study. Additionally, the database architecture uses row level fine-grain database security allowing for tight control over which individual records and fields are visible to a particular user.
The user interface architecture is based on three tier Java 2 Enterprise Edition (J2EE) architecture. It consists of a thin client tier, a servlet/JSP based middle tier and a relational database based enterprise information source (EIS) tier. The client tier consists of a web browser. The EIS tier consists of the Human Clinical and Imaging Database and a collection of stored procedures/packages for low level data access functions. The middle tier decouples presentation logic, i.e. code preparing data to be present to the user, and business logic, the code manipulating human brain imaging and/or clinical data, which allows flexibility in presentation layer selection and facilitates parallel multi-person/multi-site development. Each software layer communicates with neighbor layers via well defined interfaces, which remain stable while the actual implementation can change drastically over time facilitating software maintenance and robustness.

The complete system is used to manage and query local data at various research sites within BIRN. In addition to local operations, the system allows for mediated queries across multiple federated databases allowing researchers to discover data across all relevant sites. The current system provides an intuitive and easy to use clinical and/or derived data complex query builder, query result export for statistical analysis tools, statistical analysis of query results through the BIRN Portal, MRI image preview, conversion and download of the imaging data, as well as integration with BIRN Portal tools for data management and manipulation. Additionally, the system is being developed to provide a complete data management solution where all information regarding a subject can be maintained. A majority of the source code is generated from the database schema itself, allowing changes of the database schema to be reflected in the system easily. Development of the system continues to be a coordinated and parallel effort across multiple BIRN sites. The deployed architecture provides the extensibility, maintainability, security and parallel development features as demanded by the participating BIRN sites for building, accessing and maintaining their human brain imaging and related clinical data.

ARCHIVE: HID Schema HID Oracle & PostgreSQL Schemas

dyounes@stage.nitrcce.org (Danny Younes) — Fri, 27 Jun 2008 21:21:00 GMT

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. The Human Imaging Database at a particular site can be extended to contain relevant information concerning the research subjects used in an experiment, subject assessments, the experimental data collected, the experimental protocols used and any annotations or statistics (metadata) normally included with an experiment.

The Human Clinical and Imaging Database has been designed so that it can be customized and extended to contain relevant information from any particular sites needs without requiring modification to the schema itself. This information consists of data concerning the research subjects used in an experiment, subject assessments and demographics, the experimental data collected, the experimental protocols used and any annotations or statistics (metadata) normally included with an experiment or study. Additionally, the database architecture uses row level fine-grain database security allowing for tight control over which individual records and fields are visible to a particular user.

The major contributions from the development of the Human Imaging Database are as follows:
•The database is composed of an extendible database and structured core. The core database contains a hierarchical description of the experiment (Figure 1). It defines the structure of the experiment and how experimental protocols relate to this hierarchy. This structure allows for the storage of an experiment in a rigorous framework. Each descriptor in the database consists of a "base tuple" which defines the minimum informational requirements of that descriptor. For example, the base description of an experimental event (i.e. stimulus) contains the base information required to describe when that event occurs during an experimental protocol. However, the actual information regarding various stimuli will need to be stored in the database. Therefore, this tuple can be extended for various experiments. For example, a researcher may collect information regarding the actual properties (e.g. frequency and strength) of a tone used during an fMRI experiment. These extended tuples can be re-used and/or modified for other experiments. A comprehensive printout of the data
schema is included in the Appendix.

•An extensible framework for the definition and storage of subject assessment data. A dedicated section of the schema has been added to handle the storage of assessment data from a wide variety of assessments. Each assessment is defined through entries to parts of the schema allowing for a very flexible system that allows for the storage of virtually any assessment. Currently, some of the assessments implemented include: Anxiety Status Inventory (ASI), Beck Depression Inventory (BDI), North American Adult Reading Test (NAART), Self-rating Anxiety Scale (SAS), SCID non-patient (overview and screening module) modified by Stanford, quick mood scale, race, ethnicity, education, and occupation.

•The incorporation of information regarding the history (i.e. provenance) of how derived data was generated. All information regarding the software used to generate derived data (e.g. software name, version, hardware platform) are stored within the Human Imaging Database to allow the full reconstruction of the processing pipeline that was used to generate the data.

Clinical Assessment Layout Mgr Clinical Assessment Layout Manager (CALM) 1.6.2

dyounes@stage.nitrcce.org (Danny Younes) — Fri, 27 Jun 2008 21:03:00 GMT

The CALM tool is used to prepare on-line clinical
assessment entry forms, create the corresponding assessment meta-data in the underlying database and associate the assessment scores with the form elements on the on-line form that allows for the easy input and query of a variety of numerical and non-numerical data. In a clinical or research setting CALM can be used to streamline the development of online forms for patients’ and subjects’ data entry and for the easy maintenance and update of the ever-growing number of clinical assessments. The CALM package can generate online forms that accurately replicate any paper and pencil form, while the GAME package operates the CALM generated interface and allows for effortless quality assurance (QA) checks and clinical and research data queries. CALM provides functionality to build a new assessment from scratch or work with an already existing assessment in the HID database storing the layout and assessment association information in XML format.

The applications’ versatility is not limited to clinical forms; in fact, CALM/GAME can be used for the translation, maintenance and query of any paper and pencil form into an online form.

From a developer view point these are the highlights of the package:
•Efficiency: to speed up form designing CALM/GAME use user defined templates
•Accessibility: no Java, Javascript, or JSP coding experience is required to generate form objects
•Friendly output: the package can build forms with the similar layout as paper forms for easy data entry

From a CALM-based interface user view point these are the highlights of the package:
•A user friendly interface that permits data entry using a point and click, intuitive format.
•Built in double data entry as a cautionary step to validate the accuracy of data submitted for entry
•Build in graphical user interface allowing ability for easy data search/query/retrieval for QA queries or clinical/research questions (or in general relevant questions for any form data)

Please see the "Docs" tab for the CALM's User Manual

Clinical Assessment Layout Mgr Clinical Assessment Layout Manager (CALM) Forms Repository

dyounes@stage.nitrcce.org (Danny Younes) — Fri, 27 Jun 2008 20:59:00 GMT

The CALM Forms repository is a collection of online clinical assessment and data entry forms designed through the Clinical Assessment Layout Manager. These entry forms are frequently used for neuropsychiatric studies and have a range of clinical application.

The Online Forms are identical to their paper versions which enables the investigator to keep their data collection procedure consistent but eases the data entry into the Human Imaging Database surpassing the limitations of the paper forms.