www.1mind4research.org
THE WAY FORWARD……….
An Open-Science Framework
• Generate and Share Data:
– Use a portal system to access global coherent d...
THE CHALLENGE
DATA SHARING IS POORLY INCENTIVIZED
DATA AND TOOL SHARING IS NOT
SIMPLE ENOUGH
???
DATA SETS ARE BALKANIZED AND HARD
TO FIND
THE APOLLO PROGRAM
PORTAL ARCHITECTURE
Engagement Tools
• Facebook-like Activity Stream
• LinkedIn-like social networking
• Patient Engagemen...
CASE STUDY
tranSMART CASE STUDY: TRACK-TBI
Prepared for ONE MIND
Sirimon O’Charoen, PhD
Manager, Translational Medicine
sirimon.ochar...
Traumatic Brain Injury Numbers
• ~1.7 Million Reported TBI’s in US / Year
–
–
–
–

~52,000 Deaths ------------------------...
The Goal: Establishing the Natural History of
the TBI Spectrum
Accelerate the
understanding, both
clinically and
mechanist...
TRACK-TBI MULTICENTER INITIATIVE
• Transforming Research and Clinical
Knowledge in Traumatic Brain Injury
(TRACK-TBI) Pilo...
TRACK-TBI DATA
• Approximately 650
patients
• Mostly mild TBI

• Principle Investigators
– UCSF, San Francisco
General Hos...
TRACK-TBI DATA IN tranSMART
Goal: Curate/upload TRACK-TBI Data for data sharing and analysis at researcher’s fingertip
TRA...
tranSMART USER INTERFACE

•Data navigation: folder-structure
•Analysis: drag & drop

•Trainings were provided for all coll...
ANALYSIS EXAMPLES
• 2 Publications focus on
– Follow-up prediction
– GFAP-BDP as a diagnostic biomarker

• How do analyses...
FOLLOW-UP PREDICTION
• Outcome follow-up is challenging*
– 3-month GOS-E: 77%
– 6-month GOS-E: 69%

• Rate of successful f...
LIVE DEMO
FOLLOW-UP PREDICTION
Lost-to-follow up
(6-month)
Years of Education

History of Developmental Disorders

Success...
GFAP-BDP DIAGNOSTIC MARKER
• Glial fibrillary acidic protein (GFAP)
– Acute plasma level
– Optimal cutoff 0.68 ng/ml*

• D...
GFAP-BDP DIAGNOSTIC MARKER:
CT RESULT

Publication Figure 1

Subset1: CT negative
Subset2: CT positive
GFAP-BDP DIAGNOSTIC MARKER:
OUTCOME GOS-E

Publication Figure 5
GFAP-BDP DIAGNOSTIC MARKER:
OPTIMAL CUTOFF

Subset1: GFAP<0.68 ng/ml
Subset2: GFAP≥0.68 ng/ml
ACCOMPLISHMENTS
Pilot

Evaluation
• tranSMART
implementation
• TRACK-TBI
Pilot curation
and upload

• User trainings
(>25 ...
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tranSMART Community Meeting 5-7 Nov 13 - Session 3: tranSMART and the One Mind for Research Data Exchange Porta

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tranSMART Community Meeting 5-7 Nov 13 - Session 3: tranSMART and the One Mind for Research Data Exchange Portal
Jeff Grethe, One Mind for Research
One Mind for Research (http://1mind4research.org) is an independent, non-partisan, nonprofit
organization dedicated to curing the diseases of the brain and eliminating the stigma
and discrimination associated with mental illness and brain injuries. tranSMART will be a core
application within the One Mind Brain Data Exchange Portal, scheduled to launch publicly in
2014. Traumatic Brain Injury (TBI) affects an estimated 10 million people worldwide, and
tranSMART is one of the core applications within the portal used by researchers who are
looking to improve diagnostics and discover more effective treatments for patients suffering
from CNS- and TBI-related diseases.

Published in: Health & Medicine, Education
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  • We don’t think enough about how to give value back to the people sharing the dataCarrot versus stickCredit doesn’t get assigned to folks who share dataCulture of sharing is rarePrivacy concernsGoogle didn’t solve internet search by forcing everyone to format their web pages a certain way, facebook didn’t grow to a billion users by forcing them to share pictures, twitter didn’t become the new real-time update medium of the internet by imposing its will on end users
  • http://www.cdc.gov/traumaticbraininjury/statistics.htmlhttps://www.tbindsc.org/http://www.dddmag.com/news/2012/06/TBI-research-creates-opportunities-pharmahttp://www.cdc.gov/traumaticbraininjury/tbi_ed.html
  • tranSMART Community Meeting 5-7 Nov 13 - Session 3: tranSMART and the One Mind for Research Data Exchange Porta

    1. 1. www.1mind4research.org
    2. 2. THE WAY FORWARD………. An Open-Science Framework • Generate and Share Data: – Use a portal system to access global coherent datasets – Build an inter-operable infrastructure for collation, curation and hosting of datasets for the R&D community – Common standards and methods for the collection of the world’s largest biomarker repositories for brain disorders • Generate and Share Tools: – Collectively develop next-generation animal models, imaging tools, stem cell lines, biosensors, and more… • Generate and Share Models: – Apply advanced clinical informatics, computational biology and visualization tools to create dynamic interactive Disease Maps and inform Clinical Decisions Support and Practice Guidelines • Create Insight: – Tap Global Expertise (multi-disciplinary & global) – crowd-sourced solutions
    3. 3. THE CHALLENGE
    4. 4. DATA SHARING IS POORLY INCENTIVIZED
    5. 5. DATA AND TOOL SHARING IS NOT SIMPLE ENOUGH ???
    6. 6. DATA SETS ARE BALKANIZED AND HARD TO FIND
    7. 7. THE APOLLO PROGRAM
    8. 8. PORTAL ARCHITECTURE Engagement Tools • Facebook-like Activity Stream • LinkedIn-like social networking • Patient Engagement platforms Analytics Marketplace • Access to the world’s most advance Big Data Analytics Tools • API allows both Open-Source and Proprietary Software to Plug-In  Links Data – Experts - Analysis Data Hub • OS Infrastructure for Comprehensive Data Management • Tiered Resource Ingestion Pipeline, DataSpace, Object Models, Search, Web Services, Encyclopedias, Ontologies 8
    9. 9. CASE STUDY
    10. 10. tranSMART CASE STUDY: TRACK-TBI Prepared for ONE MIND Sirimon O’Charoen, PhD Manager, Translational Medicine sirimon.ocharoen@thomsonreuters.com
    11. 11. Traumatic Brain Injury Numbers • ~1.7 Million Reported TBI’s in US / Year – – – – ~52,000 Deaths ---------------------------------~275,000 Severe TBIs (sTBIs) ------------~1.37 M Mild TBIs (mTBIs)-----------?? M Unreported TBIs --------------- 3.4M • ~ 360,000 servicemen/veterans with war-related TBI • BUT: TBIs can happen to anyone: – ~3.8 million sports related TBIs/yr in US (3.6 M unreported) – ~300,000 vehicular TBI’s / yr in US (17% of TBIs) – 35.2% of reported TBIs from falls • TBI is a contributing factor to a third (30.5%) of all injuryrelated deaths in the United States. 11
    12. 12. The Goal: Establishing the Natural History of the TBI Spectrum Accelerate the understanding, both clinically and mechanistically, of the natural course of TBI Develop a new classification of TBI Identify predictive measures of outcomes Develop new diagnostic tools Identify new targets for therapeutic intervention In order to: Develop new treatments, preventions and cures and move the discoveries into clinical practice for improved patient outcomes 12
    13. 13. TRACK-TBI MULTICENTER INITIATIVE • Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot – Multicenter Implementation of the Common Data Elements for Traumatic Brain Injury • Aims – Test and validate Traumatic Brain Injury Common Data Elements (TBI-CDEs) – Collect neuroimaging, proteomic, and genetic biomarkers, clinical and outcome data
    14. 14. TRACK-TBI DATA • Approximately 650 patients • Mostly mild TBI • Principle Investigators – UCSF, San Francisco General Hospital • Geoffrey Manley, MD, PhD – University of Pittsburgh Medical Center • David Okonkwo, MD, PhD – University Medical Center Brackenridge • Alex Valadka, MD – Mount Sinai Rehabilitation Center • Wayne Gordon, PhD Yue JK, et al., J Neurotrauma, 2013 Jul 2.
    15. 15. TRACK-TBI DATA IN tranSMART Goal: Curate/upload TRACK-TBI Data for data sharing and analysis at researcher’s fingertip TRACK-TBI Data QuesGen Database SPSS Collaborators Curation Process CDEs Mapping Data QC ETL Delivery in tranSMART Ready for analysis -Exploratory analysis (tranSMART features) -Advanced workflow (tranSMART features) - Custom analysis (database access or R-plugin) 16
    16. 16. tranSMART USER INTERFACE •Data navigation: folder-structure •Analysis: drag & drop •Trainings were provided for all collaborators •Same curated dataset can be accessed without compressing and emailing files
    17. 17. ANALYSIS EXAMPLES • 2 Publications focus on – Follow-up prediction – GFAP-BDP as a diagnostic biomarker • How do analyses in tranSMART confirm the published results? • How quickly we can generate new hypotheses and perform exploratory analyses in tranSMART? – Data can be across domains (i.e. genotype/biomarker vs. outcome, medical history vs. follow-up)
    18. 18. FOLLOW-UP PREDICTION • Outcome follow-up is challenging* – 3-month GOS-E: 77% – 6-month GOS-E: 69% • Rate of successful follow-up significantly depends* – Years of Education – History of Developmental Disorders – Toxicology Lab Results at ED – Homelessness * Result from
    19. 19. LIVE DEMO FOLLOW-UP PREDICTION Lost-to-follow up (6-month) Years of Education History of Developmental Disorders Successful follow up (69% at 6-month)
    20. 20. GFAP-BDP DIAGNOSTIC MARKER • Glial fibrillary acidic protein (GFAP) – Acute plasma level – Optimal cutoff 0.68 ng/ml* • Discriminate* – CT intracranial lesion result – Outcomes • Other protein biomarkers may improve prediction * Result from
    21. 21. GFAP-BDP DIAGNOSTIC MARKER: CT RESULT Publication Figure 1 Subset1: CT negative Subset2: CT positive
    22. 22. GFAP-BDP DIAGNOSTIC MARKER: OUTCOME GOS-E Publication Figure 5
    23. 23. GFAP-BDP DIAGNOSTIC MARKER: OPTIMAL CUTOFF Subset1: GFAP<0.68 ng/ml Subset2: GFAP≥0.68 ng/ml
    24. 24. ACCOMPLISHMENTS Pilot Evaluation • tranSMART implementation • TRACK-TBI Pilot curation and upload • User trainings (>25 users) • Feedbacks • Validation of publication results in seconds On-going • Data access for collaborators • New data analysis • Part of One Mind Portal

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