biobanking informatics infrastructure to support clinical and translational research
DESCRIPTION
2013 Summit on Clinical Research InformaticsTRANSCRIPT
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
Biobanking Informatics Infrastructure to Support Clinical and Translational
Research
Bernie LaSalle Biomedical Informatics Core
Center for Clinical and Translational Research University of Utah
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
HRSA: 4 D1BRH20425-01-01 Joyce Mitchell/Bernie LaSalle
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
University of Utah - Steering Committee • Joyce Mitchell • Mary Bronner/Peter Jensen • Jeff Botkin • Jennifer Logan • Scott Narus • Ken Smith • Michael Varner • Brian Watts • Bernie LaSalle
Professional Staff Carolyn Orthner Damon Treitler Rick Bradshaw Ramkiran Gouripeddi Aldo Bernasconi Matt Whittkaer Randy Madson Mike Donnelly Ryan Butcher Cheri Hunter Dustin Schultz Vik Deshmukh Roger Mariner
Intermountain Healthcare – Steering Committee • Marc Jackson • Marc Williams • Melissa Cessna • David Neilson • Scott Narus • Nathan Hulse • Kerry Rowe • Brent Wallace • Morris Linton Professional Staff
Kira Wagner Darin Wilcox Bhanu Iyer John Holmen Jeff Ferraro Pallavi Ranade
UD0H –Barry Nangle
Supported in part by grants 1D1BRH20425 from HRSA and UL1R025764 from NCRR/NCATS.
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
Adv
isor
y
Ethics/Reg. Adv. Board Public Adv. Board Scientific Adv. Board
External
Internal
Management Committee RGE
HDROC
Mgm
t & O
ps Director & Staff
Ethics/Reg. Workgroup
Informatics Workgroup
Public Engagement Workgroup
Data Warehouses & UPDB Workgroup
Biospecimen Workgroup
Lead
ersh
ip/O
vers
ight
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
• Principles for Access to Biospecimens – Govern all biospecimens and associated meta
data as an institutional asset. – Work with Intermountain to maintain standard
data models and definitions to accommodate searching across institutions.
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
Aldo Bernasconi1 Jeffry Botkin3
Richard Bradshaw1
Melissa Cessna5
Nathan Hulse4,7 Mark Jackson4
Randy Madsen1
Roger Mariner1
Joyce Mitchell1
Carolyn Orthner1
Louisa Stark3
Dustin Schultz1
Damon Treitler1
Michael Varner2
1 Department of Biomedical Informatics, 2 Department of Obstetrics and Gynecology, 3
Department of Human Genetics, 7 Nursing Informatics University of Utah, Salt Lake City, UT 84112
4 Maternal Fetal Medicine, 5 Intermountain Biorepository, 6 Clinical Knowledge Management
Intermountain Healthcare, Salt Lake City, UT 84111
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
Empowers researchers with a linked virtual repository integrating biological sample, clinical and demographic data in real time
FURTHeR
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
• Support clinical and translational research • On-the-fly real-time federation of health information from heterogeneous data sources • Data source partners do not need to extract data and build a new database (another copy)
• Remains in its native format
• Is as up-to-date as the data source
• Join data from multiple sources for research
FURTHeR
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
Information Technology • Implementation of FQL at Intermountain
– Query translation – Data service – Transport service
• Secure query and payload transmission – Static VPN
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
Information Technology… • Federated security model
– Access Control lists – at both institutions • Secure authorization integrity
• Iterative queries Single result set – Patient demographic, clinical and
biospecimen data
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
VPN Tunnel
Web application description for FURTHeR and Intermountain Healthcare data services
Web ServicesIntermountain Data sources
Transport Service
Security
FQL Translation
Physical Query from FURTHeR
Result set from Intermountain to
FURTHeR
Requesting Query:The query from FURTHeR takes advantage of Hibernate object relational mapping idioms marshaled in xml. Use of query criteria allows close one-to-one query execution from FURTHeR to Intermountain EDW.
Result Set:The result set coming back to FURTHeR can be any structured representation of the entities. (Typically XML)
Application Logic
XML (FQL criterion)
XML
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
What we learned • Properly collected biospecimens add rich
data to cohort queries – Standard terminologies – Robust meta data
• Collection protocols • Searchable Consent forms
• Governance • Intellectual property
CENTER FOR CLINICAL AND TRANSLATIONAL SCIENCE BIOMEDICAL INFORMATICS CORE
Summary • Biospecimen data can be utilized
– Determine cohorts – Secondary data source from queries
• There is significant value in adding biospecimens to phenotype and other data
• Biobanks are under utilized1
• Opportunity within an between institutions Scuedellari M., Biobank managers bemoan underuse of collected samples Nature Medicine 19, 253 (2013) http://dx.doi.org/10.1038/nm0313-253a