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Shared Health Research Information Network

Shared Health Research Information Network. 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.

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Shared Health Research Information Network

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  1. Shared Health Research Information Network Andrew McMurry, MSSHRINE ArchitectHarvard Medical School Center for BioMedical Informatics Children’s Hospital Informatics Program Harvard/MIT HST Boston University Bioinformatics PHD StudentAndrew_McMurry(@) hms.harvard.edu Current Status, Demo, and Open Source

  2. History of the SHRINE world in 1 minute • Partners RPDR  i2b2 Data Repository • Shawn Murphy et all (wont steal their thunder here) • Everyday patient encounters  huge research cohorts • SPIN  cross-hospital query model • 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

  3. SHRINE Technical Architecture • Bird’s Eye View • Leverage local i2b2 deployments • Broadcast queries and aggregate responses across autonomous sites as if they were “one clinical data warehouse” • There is no central database • Connect sites in a peer-to-peer or hub-spoke fashion

  4. Technical Architecture, “cell” view Architecture

  5. Current Status : in BETA! • East Coast : Harvard Effort • 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

  6. Current Status : in BETA! • Demo use cases, things to think about….. • Lung cancer cases  requesting biospecimens • Irritable Bowel Syndrome  requesting sized cohorts • Pediatric rheumatology  Creating national registry

  7. Current Status • West Coast : CICTR Effort • University of Washington • UCSF • UC Davis • Nick Anderson et all

  8. 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

  9. SHRINE Open Source : brewing in the background Fast recap of 2006 and 2009 Open Source proposals: • Write documentation as if we are writing code stubs • Preconditions + • Steps (Algorithm) + • Post-conditions = Use Cases or “Scenarios” • Test driven development • Write the test first • Implement second • Regression test everything all the time • Continuous Integration • Test everything every time you change any code

  10. SHRINE Open Source Process  Leveraging routine development activities • Public access to bug tracking system • Public access to latest source code • Public mailing lists • Shrine-users • Shrine-developers • Shrine-announce • Test Driven Development • Continuous integration (daily builds of the complete software)

  11. Acknowledgements: Core SHRINE team • Zak Kohane (SHRINE Lead / HMS) • Griffin Weber (HMS CTO / bidmc) • Shawn Murphy (I2B2 CRC / partners) • Dan Nigrin (Children’s CIO) • Ken Mandl (Public Health Use Cases/ CHIP IHL) • Sussane Churchill (I2B2 Executive director) • Doug Macfadden (HMS CBMI IT Director) • Matvey Palchuck (Ontology Lead / HMS) • Andrew McMurry (Architect / HMS) • Could give an entire talk on all the collaborators, multi-institutional effort. Asking forgiveness from those not listed

  12. Acknowledgements: Core SPIN team • Zak Kohane (SPIN PI / HMS) • Frank Kuo (PSL Program Director / BWH) • John Gilbertson (PSL Pathologist / MGH) • Mark Boguski (PSL Pathologist / BIDMC) • Antonio Perez (PSL Pathologist / Children’s) • Mike Banos (PSL Developer / BWH ) • Ken Mandl (Biosurviellance PI/ Children’s) • Clint Gilbert (Biosurviellance Dev Lead / Children’s) • Greg Polumbo (SPIN Developer/ HMS) • Ricardo Delima (SPIN Developer / NCI at HMS) • Britt Fitch (SPIN Developer / HMS • http://spin.chip.org/community.html

  13. Acknowledgements: Core I2b2 team • https://www.i2b2.org/about/structure.html

  14. Thank You • http://catalyst.harvard.edu/shrine • Andrew_McMurry (@) hms.harvard.edu

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