an open source, integrated data management system ...

AN OPEN SOURCE, INTEGRATED DATA MANAGEMENT SYSTEM FOR MEDICAL REGISTRIES: A CASE STUDY USING REXDB® Charles Tirrell, Frank J. Farach, PhD, Meredith Yourd, Owen McGettrick, Oleksiy Golovko, Leon Rozenblit PhD

Prometheus Research LLC, New Haven, CT

DISCLOSURES

•I

disclose that I have a relevant financial relationship with Prometheus Research, LLC, as an employee and incentive unit holder.

PROBLEM SPACE are typically too expensive for smaller practices and organizations to develop and maintain.

• Registries

heterogeneity and complexity of source data, especially from electronic health record (EHR) systems.

• The

describe an affordable and scalable alternative: an open source solution that can integrate institutional (EHR) and primary research data, which focuses on non-technical analyst configurability.

• We

PROJECT SCOPE • We

developed an integrated registry data management system based on the Research EXchange DataBase (RexDB), an open source (AGPLv3) stack initially developed to help for the acquisition, curation, exploration and sharing of human biomedical research data.

PROJECT HISTORY •

2005 - Initial Release of RexDB for Small Research Groups at Yale

•

2007 - RexDB used for Simons Simplex Collection (Multicollection sites, significant form versioning)

•

2012 - Open Source release of RexDB 3.0 under AGLv3

•

2013 - Began adapting RexDB to support disease- and procedure-specific registries

OUR APPROACH • Analysts

can configure ETL processes that utilize HTSQL, an friendly, open source query language, which allows users to navigate, explore and manage, complex datasets with a simple query syntax.

(without help from programmers) can configure custom data structures and front-end application screens and workflows.

• Analysts

REXDB ARCHITECTURE Legacy Database

file file Legacy Files

Staff Entered Forms

RexETL

Rapidly Enter Assessments

RexAcquire

Explore, Share and Export Data

RexMart DB

RexEntry

Receive Assessments Directly from Patients

Data Explorer

Customize Solution Applications for Multi-faceted Data Management

Extract, Transform, Load Data from Multiple Sources

RexSurvey Self Reported Forms

Integrated Data Management Application

RexExplore Formbuilder

Centralized Database

Configure Electronic Data Capture Forms

Centralize, Organize and Curate All Data

RexApplication

Create Exploratory Data Marts for Data Consumers

RexMart DB

RexMart DB

RexMart

REXACQUIRE • RexAcquire

is a comprehensive Electronic Data Capture (EDC) system including an ETL mechanism.

REXAPPLICATION • RexApplication

supplies the infrastructure for the centralized database and customizable data management system.

REXMART • RexMart

enables users to create custom, shareable data sets from the central database that will allow them to explore and understand their research data.

REXDB ARCHITECTURE Legacy Database

file file Legacy Files

Staff Entered Forms

RexETL

Rapidly Enter Assessments

RexAcquire

Explore, Share and Export Data

RexMart DB

RexEntry

Receive Assessments Directly from Patients

Data Explorer

Customize Solution Applications for Multi-faceted Data Management

Extract, Transform, Load Data from Multiple Sources

RexSurvey Self Reported Forms

Integrated Data Management Application

RexExplore Formbuilder

Centralized Database

Configure Electronic Data Capture Forms

Centralize, Organize and Curate All Data

RexApplication

Create Exploratory Data Marts for Data Consumers

RexMart DB

RexMart DB

RexMart

ANALYST CONFIGURATION EXAMPLES

EXAMPLE OF ETL CONFIGURATION /source_patient

.define(

$patient_id := lower(individual),

)

{

patient_id := [$patient_id],

inddateofproc,

physicianlastname,

center,

registrytype,

patientsex,

}

:as target_patient

/:source_data

/:merge

< source_table

< transforms

! ! !

< columns to merge

! ! ! ! ! !

< target table

< source database

< action

EXAMPLE OF DATABASE SCHEMA CONFIGURATION ---

name: registry.core

---

revision: 20140301

install:

- aspect: meta:table

cmd: merge

data:

- id(): registry.demographics

facet_table:

parent_table: rex.patient

parent_column_name: patient

- aspect: meta:column

cmd: merge

data:

- id(): registry.demographics.birthdate

domain: meta.date_t

is_mandatory: 'true'

!

< Deployment Module

!

< Deployment Revision

!

< Create Tables

! !

< Create Demographics Table

!

< Foreign Key to Patient Table

! !

< Create Columns

!

< Create Birthdate Column

!

EXAMPLE OF SCREEN CONFIGURATION /patient/:

template: rex.application:/templates/two_column_layout.html

context:

menu: study_manager_navigation

title: Patients

leftcol:

filter:

type: filter

header:

text: Filter

size: 3

params:

id: address_filter

query: patient{*}

centercol:

header:

type: header

sort_order: 10

params:

< Page Path

< Template Reference

!

< Invoke a predefined menu

!

< Design Left Column of Layout

< Create Filter Object

! ! ! ! ! !

< Declare Table to query for filter

< Design Center Column of Layout

!

WHERE ARE WE NOW?

• The

level of configurability presented to analysts in RexDB is novel compared to other software platforms.

has been shown to have a short learning curve with semi-technical individuals.

• Customization

WHERE ARE WE NOW? (CON’T) • Adapting

the core RexDB study management suite to meet the needs of registry management and reporting required only a slight modification of a previously developed “research study management” model.

an open-source stack has the benefit of aligning incentives between the technology services vendor and the registry customer.

• Using

FUTURE AIMS • Refine

the configuration syntax and application building mechanism.

• Explore

the relationship between clinical registry and research data models in the future.

• Create

a Registry-specific data model, set of screen templates and data import/export modules (i.e. PQRS)

• Apply

this technology stack to additional registries for a wider perspective.

FOR MORE INFORMATION

•

For all RexDB Open source Code Repositories https://bitbucket.org/rexdb

•

rexdb.study - RexDB Study Management Application

•

Project Website - www.rexdb.org

•

Demo site of RexStudy - demo.rexdb.org