Transcript Introduction

Shared Health Research Information Network
Current Status, Demo, and Open Source
Andrew McMurry, MS
SHRINE Architect
Harvard Medical School Center for BioMedical Informatics
Children’s Hospital Informatics Program Harvard/MIT HST
Boston University Bioinformatics PHD Student
Andrew_McMurry(@) hms.harvard.edu
History of the SHRINE world in 1 minute
Partners RPDR  i2b2 Data Repository
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Shawn Murphy et all (wont steal their thunder here)
Everyday patient encounters  huge research cohorts
SPIN  cross-hospital query model
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Extract, Transform <de-identifiy, autocode>, Load
Federated query over multiple independent hospitals
Harvard CTSA funded
Recombinant
deploying
i2b2
across
the
country
Overly
simplified:
clinical data repository + federated query = SHRINE
SHRINE Technical Architecture
Bird’s Eye View
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Leverage local i2b2 deployments
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Broadcast queries and aggregate responses across autonomous sites as
if they were “one clinical data warehouse”
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There is no central database
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Connect sites in a peer-to-peer or hub-spoke fashion
Technical Architecture
Architecture, “cell” view
Current Status : in BETA!
East Coast : Harvard Effort
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BETA system running at Harvard across BIDMC, Children’s, and
Partners representing both BWH and MGH.
Last AUG:
 Prototype 1 year of data with demographics and diagnosis
 IRB approval for demonstration only
NOW
 Patient data from 2001+
 Demographics, Diagnosis, Medications, some Labs
 Full IRB approvals
Current Status : in BETA!
Demo
use
cases,
things
to
think
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Lung cancer cases  requesting biospecimens
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Irritable Bowel Syndrome  requesting sized cohorts
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Pediatric rheumatology  Creating national registry
about…..
Current Status
West
Coast
University of Washington
UCSF
UC Davis
Nick Anderson et all
:
CICTR
Effort
Current Status
National Registry : Pediatric Rheumatology
“Grand Opportunity” Grant
60 institutions, 2 years
SHRINE has been selected as inter-institutional glue
Consented patients, prospective data collection
Shared Virtual Machine Hosting
SHRINE Open Source : brewing in the background
Fast recap of 2006 and 2009 Open Source proposals:
1. Write documentation as if we are writing code stubs
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Preconditions
Steps (Algorithm)
Post-conditions
+
+
= Use Cases or “Scenarios”
2. Test driven development
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Write the test first
Implement second
Regression test everything all the time
3. Continuous Integration
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Test everything every time you change any code
SHRINE Open Source Process
 Leveraging routine development activities
1. Public
access
2. Public
access
to
to
bug
latest
tracking
source
system
code
3. Public mailing lists
•
•
•
4. Test
Shrine-users
Shrine-developers
Shrine-announce
Driven
Development
5. Continuous integration (daily builds of the complete software)
Acknowledgements: Core SHRINE team
Zak Kohane
Griffin Weber
Shawn Murphy
Dan Nigrin
Ken Mandl
Sussane Churchill
Doug Macfadden
Matvey Palchuck
Andrew McMurry
(SHRINE Lead / HMS)
(HMS CTO / bidmc)
(I2B2 CRC / partners)
(Children’s CIO)
(Public Health Use Cases/ CHIP IHL)
(I2B2 Executive director)
(HMS CBMI IT Director)
(Ontology Lead / HMS)
(Architect / HMS)
Could give an entire talk on all the collaborators, multi-institutional
effort. Asking forgiveness from those not listed
Acknowledgements: Core SPIN team
Zak Kohane
(SPIN PI / HMS)
Frank Kuo
(PSL Program Director / BWH)
(PSL Pathologist / MGH)
(PSL Pathologist / BIDMC)
(PSL Pathologist / Children’s)
(PSL Developer / BWH )
(Biosurviellance PI/ Children’s)
(Biosurviellance Dev Lead / Children’s)
(SPIN Developer/ HMS)
(SPIN Developer / NCI at HMS)
(SPIN Developer / HMS
John Gilbertson
Mark Boguski
Antonio Perez
Mike Banos
Ken Mandl
Clint Gilbert
Greg Polumbo
Ricardo Delima
Britt Fitch
http://spin.chip.org/community.html
Acknowledgements: Core I2b2 team
https://www.i2b2.org/about/structure.html
Thank You
 http://catalyst.harvard.edu/shrine
 Andrew_McMurry
(@) hms.harvard.edu