developing a suite of electronic data capture … · electronic data capture applications based on...

© 2015 Prometheus Research

Developing a Suite of Electronic Data Capture Applications Based on an Open-Source Instrument Definition StandardLeon Rozenblit, Ph.D., Founder & CEO


Contact Info & References

Leon Rozenblit, JD, Ph.D., Founder & CEO

[email protected] | @leon_rozenblit(800) 693-9057 | www.prometheusresearch.com

Documentation for today’s talk:https://doc.rexdb.org/doc/rex.instrument/https://doc.rexdb.org/doc/rex.forms/

Source code: https://bitbucket.org/rexdb

http://www.prometheusresearch.com

https://doc.rexdb.org/doc/rex.instrument/

https://doc.rexdb.org/doc/rex.forms/

https://bitbucket.org/rexdb


Disclosures✤ I disclose that I have a relevant financial relationship with

Prometheus Research, LLC, as company management and equity owner.

✤ I receive support from the NIH


Problem (acutely felt in Behavioral & Mental Health research)

✤ At this moment, multiple research groups are configuring either identical or very similar forms for use in different EDC system; Wasted time. Lack of consistency across projects.

✤ Shouldn’t they be able to download the form configuration from an open library of instrument definitions and reuse them in any common EDC application?

“Instrument” = standardized, validated form for collecting data that purports to measure some construct (e.g., a depression scale)


Grand(-ish) Vision

Develop an open-source, portable instrument definition standard that would describe the content, structure, display properties, and presentation logic for an instrument. It should:✤ Define all instrument metadata needed for transportability of data;✤ Anticipate transformation into formats supported by other platforms;✤ Allow multiple presentation property profiles and be extensible to novel

presentation systems;✤ Be human readable and editable;✤ Be available under a standard open-source license that would encourage

the evolution of a user/developer community.


Another “Standard”?

Source: http://xkcd.com/927/

http://xkcd.com/927/


Does it have to be a “STANDARD”?✤ Let’s not pretend we can get everyone to adopt a new standard.

✤ Instead, let’s build a reference implementation.

✤ Then, create open-source translators that can convert instruments between the reference implementation and existing EDCs (RedCap, Qualtrics, RexDB).

✤ Then, create an open source library of forms using that implementation.


Essential Preliminary Steps✤ Come up with an acronym: PRISMH—Portable Research

Instrument Standard for Mental Health.

✤ Get funding.*

* Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number R43MH106225. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.


Grand(-ish) Vision (cont.)

(hosting, API)Open Science Framework (OSF)

Electronic Data Capture (EDC) Tools

Portable Research Instrument Standard for

Mental Health(PRISMH)

REDCap Qualtrics RexDB Mobile EDC

Converter Modules(pluggable)

Open Library of Instrument Definitions

Source-code repository features: revision control

& forking

Sharing level settings and privacy controls

Community Features

Other EDC

This proposal

Available in OSF

Aim 1

Aim 2

Aim 3

Aim 4


Challenges✤ Instrument versioning✤ Requirement that data resulting from any presentation method

for a form can be merged together into a single data exploration source.

✤ Internationalization of instrument content.✤ Translating presentation/display properties between different

EDC platforms (question text, hints, pagination, etc).


Limitations of Common Formats✤ REDCap’s commonly-used configuration format is not open source;

presentation properties assume one app.

✤ CDISC-ODM is too complex and heavy-weight for this need.

✤ CDISC and CDASH are focused on use-cases that support FDA-regulated clinical trials (e.g. facilitating submission of data to the FDA).

✤ CDISC and CDASH do not make it obvious how to include a display characteristics layer.


Getting Started: Practical Considerations✤ We had previously developed two open source EDC applications,

each of which focuses on a specific user class.

✤ RexEntry is focused primarily on data entry by trained clinical or research staff members who require rapid and accurate data transcription.

✤ RexSurvey is focused primarily on intuitive data entry by self-reporters.

✤ The first proof of concept was to refactor these two different systems to use a common portable instrument definition: PRISMH.


Configuration Split: Instrument vs. Form✤ Instrument: Data element definition (variable name, data type);

supports transportability of data, but nothing about presentation.

✤ Form: Rapid data entry parameters (keyboard shortcuts, skip-logic).

✤ Form: Question-level display information (question titles, hints, hide/disable logic).

✤ Form: Grouping information (pagination, sections).

✤ Form: Mode-specific presentation instructions.


YAML Example: Demo Demographic FormForm PresentationInstrument

defaultLocalization: en instrument: id: "urn:demo-demographics-form" version: '1.0' pages: - id: page1 elements: - type: question options: fieldId: first_name text: en: First Name - - type: question options: fieldId: last_name text: en: Last Name - - type: question options: fieldId: gender text:

id: "urn:demo-demographics-form" version: '1.0' title: Demo Demographic Form record: - id: first_name type: text - id: last_name type: text - id: gender type: enumerations: female: {} male: {} base: enumeration - id: age type: enumerations: age18-29: {} age30-49: {} age50-64: {} age65-and-over: {}

YAML is compiled into JSON at runtime. You can configure instruments and forms directly in JSON, but it is less human-readable than YAML


RexEntry RexSurvey


Configuration (YAML)Instrument Multi-lingual Survey Form

id: "urn:demo-demographics-form" version: '1.0' title: Demo Demographic Form record: - id: first_name type: text - id: last_name type: text - id: gender type: enumerations: female: {} male: {} base: enumeration

defaultLocalization: en instrument: id: "urn:demo-demographics-form" version: '1.0' pages: - id: page1 elements: - type: header options: text: en: General Information es: Información General - type: question options: fieldId: first_name text: en: What is your first name? es: ¿Cuál es tu nombre? - type: question options: fieldId: last_name

The form is configured to display in either English or Spanish


Two Displays From One Rex.form Config. File

Electronic Data Capture => RexMart


Represented in a Study Management System

measure_type

measure_type_revision

Entity Relationship Diagram - RexStudy 4.2.0rex.study.main - acquire.yaml

acquire_channelmeasure_type_revision_channel

measure_type_revision_draft

measure_type_revision_chl_draft

Trunk Branch Cross Ternary Facet

to only one to manyto one or zero

Methods for presenting the instrument: • RexSurvey • RexEntry • RexSMS

Instruments: • Depression Scale A • IQ Test D • Demographic Form F • . . .

Instrument Versions: • Depression Scale A.2 • IQ Test D.1 • Demographic Form F.7 • . . .

Instrument Drafts: • Unpublished versions of

instruments, not available for data collection

• Once published the draft becomes available as an Instrument Version and can be used for data collection

Form Display Configuration: • One form.yaml file for

each channel that an instrument version can be presented in

Draft Form Display Configuration: • One form.yaml file for each channel

that an instrument draft can be presented in (after it is published as an instrument)


RexMartRexApp

widget

htsqlctl

convert explore

explore_ui

RexAcquire

applet

core, web, db

instrument, forms

deploy.yaml

RexSurvey RexEntry

make files urlmap.yaml

Legacy'DatabaseExternal'DBs

Legacy DatabaseRexMart

DBRexOps DB

solution_application

etl.htsql

RexPlore

RexETL RexAppBuilder

Form Builder

RexMartBuilder

Legend

Database ComponentComponent GroupConfig File

deploy

expression

End-User App

deploy.yaml

Adv. FormConfig

Analyst Config.

data flow

config. settings

mart_list.yamlform config.

instrument config.

screen_config.yaml

urlmap

etl.htsq

port

RexDB Component Architecture

RexDBRexDB Platform ArchitectureRexAcquire

fileStaff Entered Forms

fileSelf Reported

Forms

fileLegacy File

Legacy DatabaseLegacy Database

RexMart

RexPloreExplore, Share and

Export Data

RexMartBuilderCreate Exploratory Data Marts for

Data Consumers

RexMart DBRexMart DB

Analytic Read-Only System that supports ad hoc queries

by end-users

RexApp

RexAppBuilderCustomize Solution Applications

and add Applets for custom interactions

RexOps DBTransactional Read/Write System

for Operational Data

Customized AppConfigured Templates and Widgets generatecustom screens for customized interactions

with transactional and analytic data

RexMart DBRexReference DB

Read-only data for UI interaction but not for

ad hoc queries

RexFormBuilderConfigure Electronic Data Capture Forms(basic and advanced)

RexSurveyCollect

Self-Administered Forms from Participants

RexEntryRapid Form Entry for Trained Staff

RexETLExtract, Transform, Load

data from multiple sources


What Did We Learn?✤ Separating instrument content and form presentation/display definitions is

useful for supporting multiple versions, languages, and display delivery methods.

✤ There is a downside to splitting instrument definition from form definition: two files are somewhat more difficult to manage than one.

✤ Some redundancy in providing two kinds of configuration data.

✤ Will try auto-generation of a base form config file from an instrument config file.

✤ Longer-term solution: GUI Form Builder.


New FormBuilder (Beta)


Future

(hosting, API)Open Science Framework (OSF)

Electronic Data Capture (EDC) Tools

Portable Research Instrument Standard for

Mental Health(PRISMH)

REDCap Qualtrics RexDB Mobile EDC

Converter Modules(pluggable)

Open Library of Instrument Definitions

Source-code repository features: revision control

& forking

Sharing level settings and privacy controls

Community Features

Other EDC

This proposal

Available in OSF

Aim 1

Aim 2

Aim 3

Aim 4


Take Home✤ Developed an open-source portable instrument definition format.

✤ Tested it with two of our own EDC applications. It works.

✤ Now proceeding with developing translators to/from REDCap & Qualtrics.

✤ Please try it out and give us your feedback.

✤ If you want to develop translators to/from your favorite EDC app, join us!

An open-source, revision-controlled instrument-definition library, based on a portable open standard, will save resources and will enable better data sharing and interoperability across research programs and institutions.


Thank You!

✤ Prometheus Team

✤ Center for Open Science

✤ My co-authors:

✤ Charles Tirrell

✤ Jason Simeone (lead architect)

✤ Frank J. Farach


Contact Info & References

Leon Rozenblit, JD, Ph.D., Founder & CEO

[email protected] | @leon_rozenblit(800) 693-9057 | www.prometheusresearch.com

Documentation for today’s talk:https://doc.rexdb.org/doc/rex.instrument/https://doc.rexdb.org/doc/rex.forms/

Source code: https://bitbucket.org/rexdb

http://www.prometheusresearch.com

https://doc.rexdb.org/doc/rex.instrument/

https://doc.rexdb.org/doc/rex.forms/

https://bitbucket.org/rexdb

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