Making More Than the Sum of the Parts: How CTSA Hubs Can Leverage CD2H Collaborative

Informatics for Greater Translational Impact

CG Chute, MD DrPH

Acknowledgements

cd2h.org/cloud

● Melissa Haendel

● Justin Guinney

● Adam Wilcox

● Dave Eichmann

● Julie McMurry

The Center for Data to Health (CD2H) Team

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERY

The CD2H team

Expensive and insecure local and legacy

infrastructure

Legal and technical barriers to

meeting data sharing mandates and

multi-site research needs

Difficulty finding and sharing

resources and expertise

Data in different formats and shapes

makes it hard to do multi-site research

Common CTSA challenges Shared CD2H solutions

CD2H’s role is to coordinate and deliver shared informatics solutions for diverse Hub needs

Recurring

needs

across Hubs

Workforce Development

Collaboration

Integration

Methods & Processes

Informatics

Investigator

Trainee

Staff

Clinical research

Laboratory science

Population health

Basic research

Entrepreneurship

Regulatory

Co

res

Dis

cip

lin

es

Ca

ree

r st

ag

es

CONVENE DESIGN

IMPLEMENT

Increased Hub

capacity and

collaboration

CT

SA

HU

BS

Individuals

NCATS/CD2H Cloud Infrastructure

Cloud and Tool Core

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERYcd2h.org/cloud

Cloud & tool architectureExemplar Projects:● DREAM Challenges● LEAF● Competitions

Best Practices

Tool registry

Build & Test

Framework

Benchmarking

Hosted Tools

Sandboxes

Built-in Security

Get involved with the CD2H Tool and Cloud Infrastructure

Community Corecd2h.org/cloud

CTSA Cloud Hub

QA Pipeline

Hosted Resources

Benchmarking Environment

Build & Test Framework

Software Dashboard

Tool Registry

App Store

Best Practices Documentation

Analysis Sandbox

Models & Algorithms

Ontologies

Web Services

Web Applications

CTSA Tools

Cloud & tool architecture: RFC

Interactive web portal for CTSA users

Cloud-hosted web backend & service

orchestration

Distributed services for portal features

2019-09-27

cd2h.org/cloud

Journey of a software tool

CTSA Cloud HubVerified

⚪ Licence

⚪ Docs

⚪ Tests

This tool is missing several

required ingredients.

Elements needed to complete

verification of this tool:

Tool Registry

Detected Registered BenchmarkedValidatedVerified Portable

Assessing and supporting best practices for software development

Ryan completes

the registration, but now notices

that the status indicator suggests

that the software might not be

very easy to access or use. Busy

with another project, he asks his

trainee, Cynthia, to “fix it.”

PROBLEM

Cynthia looks at what’s

missing, but doesn’t really

know what to do...

Cloud Architecture

2019-09-27

cd2h.org/cloudCloud & tool architecture: RFC

DREAM Challenge Updates

● EHR Challenge in 1st Leaderboard Phase

● 241 registered participants

● Onboarding Wash U & Mt Sinai as additional

data hosts

● RA Challenge (winner of Idea Challenge) set to

launch in November

● $50k prize money donated by BMS

COMPETITIONSA platform to run NIH-style grant competitions across the CTSA

including pilot projects and research awards

USE COMPETITIONS NOW!

● Navigate to competitions.cd2h.org

● Log in using your institutional credentials

● Try it out

● Browse resources and documentation

● Sign up for demos and webinars

● Contribute feedback or feature requests to

competitions-cd2h@northwestern.edu

competitions.cd2h.org/

LEAF A lightweight, open-source, model-agnostic

web application for querying clinical data

● Flexible: Leaf can work data models:

OMOP Common Data Model, i2b2 and

SHRINE, or other proprietary or non-

standard data models.

● User Friendly: Leaf is a simple drag-

and-drop web application that queries

clinical databases, so users can focus

on accomplishing research, not

waiting for data.

● Secure: Leaf implements current best

security practices to make clinical data

both accessible and safe.

● Open: Leaf is an open-source project

by CTSAs, for CTSAs.cd2h.org/leaf

CTSA Search: Making CTSA resources more discoverable

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERY

Enabling discovery of resources and expertise within the CTSA program and beyond

Etc

Try it at labs.cd2h.org/search

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERY

CTSAsearchYour path to discovering CTSA resources

Try it at labs.cd2h.org/search

Informatics Maturity & Best PracticesAdam Wilcox, PhD University of Washington

Chunlei Wu, PhD, Scripps Boyd Knosp, MS, Iowa

Informatics maturity and best practices community core

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERYcd2h.org/maturity

Maturity Models: Research

Informatics and Open Science

Maturity (RIOSM) Model

Average Maturity Score by Domain

cd2h.org/maturitymodel

Informatics maturity and best practices community core

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERYcd2h.org/maturity

Maturity Models |

Convening of iDTF members based on break-outs

from spring meeting ● Reviewing and prioritizing additional models

Maturity of Maturity Models

What’s new We are creating a MM tool to:● Collect information on health informatics maturity at

various CTSA sites.

● Summarize that information for dissemination to the

CTSA community.

Fast Healthcare Interoperability Resources (FHIR) and the NIH Perspective

Christopher G. Chute, M.D., Dr.PH. (Johns Hopkins University) & Jerry Sheehan, M.S. (National Library of Medicine)

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERY

NIH encourages use of FHIR in research

Fast Healthcare Interoperability Resources (FHIR®)

Standard. Notice Number: NOT-OD-19-122

Release Date: July 30, 2019

“To encourage NIH researchers to

explore the use of the Fast Healthcare

Interoperability Resources (FHIR®)

standard to capture, integrate, and

exchange clinical data for research

purposes and to enhance capabilities to

share research data.”

cd2h.org/FHIR

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERY

NIH investing in FHIR tools for research

Small Business (SBIR & STTR) Applications Directed at the Adoption of the Fast

Healthcare Interoperability Resources (FHIR®) Standard

Notice Number: NOT-OD-19-127 Release Date: July 30, 2019

● Integration of patient- and population-level data from EHR systems

● Access to and management of electronic health information

● Development of clinical decision support systems

● Exchange of EHR data and health documentation

● Enhancement of privacy and security for electronic health information

● Inclusion of common data elements (CDEs) and clinical terminologies to improve interoperability of EHR

data for research and clinical care

● Support for a common structure for sharing clinical research data

● Integration of EHR and patient-originated data with clinical research data

● Design and monitoring of clinical trial protocols

● Enhancement of patient recruitment, enrollment, and consent in clinical trials

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERY

Transforming the clinical data landscape with FHIR

cd2h.org/FHIR

UNIFIED SOLUTIONCURRENT WORKAROUNDS

EXAMPLE

FHIR PAYLOADS

GITHUB.COM/DATA2HEALTH/RESOURCE-DISCOVERY

How does FHIR help?

EXAMPLE

FHIR

“shapes”

(Resources)

OBSERVATION 2

{PSA, 2.6 ng/mL}

{Serum Sodium,133 mEq/L}

OBSERVATION 1

OBSERVATION

“shape”OBSERVATION

SLOTS:

WHO, WHAT WHEN,

WHERE

TEST {coded type,

value}REFERENCE RANGE

OBSERVATION

“shape”

cd2h.org/FHIR

OMOP

PCORI

Sentinel

EHR

ACT

FHIR power for data model interoperability

CDC - Surveillance

NIH Clinical Research

FDA - Safety

National

InstituteCancerNLM

FHIR and i2b2 (applied to ACT)

Given:

● Core i2b2 is very flexible – i2b2 is more of a

meta-model than a model

● FHIR exists and is being implemented and

deployed

Would it be possible to transform FHIR data to

the i2b2 CRC cell and…

… represent the FHIR model as one i2b2 ontology

and…

… create / re-use i2b2 ontologies to provide

different views on the i2b2 FHIR data?

FHIR

Model

ACT

FHIR

HOT

Peter.Robinson@jax.org | Aaron.Zhang@jax.org GITHUB.COM/DATA2HEALTH/EHR2HPO.PRJ

Scalable tools for harvesting Human

Phenotype Ontology from the EHRCORE

ICON

● Build on success of LOINC to HPO demonstration (PMID:31119199)

● Tactical focus on demonstrating LOINC to HPO for biomarker discovery

● Opportunity to expand HPO discovery to other domains beyond labs

■ Radiology, Clinical Notes● Balance clinical vs. research application in

diagnosis and phenotyping● Recognize that only a subset of HPO can be

algorithmically discovered from the EHR● In current phase extension to radiology,

application at JHU, OHSU, new algorithms

CD2H COMMUNITY CORES:

● Join a core’s monthly call

● Signal interest in any project

● Contribute to use cases

● Explore code demos and training

● Make a feature request

● Provide feedback

● Help draft manuscripts, best practices

● Implement best practices

● Review options for technical implementation

● Contribute to data standards

● Contribute content (eg. FHIR mappings, DUAs, interviews)

● Participate in the mortality challenge

Where to start

cd2h.org/sharing

cd2h.org/discovery

cd2h.org/cloud

cd2h.org/maturity

Ways to engage

@data2health

HHS Consortium for FHIR Stack

National

InstituteCancerNLM

NCATS Biomedical Data Translator

Integrated genotype-phenotype and other biomedical

data is a resource for researchers to interrogate data

for integrative and translational science

https://ncats.nih.gov/translator

The Biolink

Model as a

foundation

Adapt from proposed NCATS Translator Methods

31

October 11, 2018

Application of

Ontology:

Crucial to

Translational

Research

Program overview / Team

introductions

Community

Development

(lead: Volchenboum;

co-lead Vasilevsky)

Data Model

harmonization

(lead: Chute)

Ontology & Terminology

Ecosystem

(lead: Solbrig)

Tools & Data Quality

(lead: Balhoff)

Program Management and operations:

(lead: Haendel, co-lead McMurry)

Programmatic oversight:

CBIIT: Sherri De Coronado, Allen Dearry

FNL: Todd Pihl

Thoughts

cd2h.org/cloud

● Coordination of effort to achieve shared goals makes sense

● CD2H, CCDH, and CDMH projects all seek to advance this

● CD2H functions as collaboration coordinators

● Participation is welcome and fostered

● The tasks are challenging

Thank You