Transcript Slide 1

Towards a Set of Unified NIH
Computational, Data, and Community
Infrastructures to Support Translational
Bioinformatics
Brian D. Athey, University of Michigan
Mark Ellisman, University of California, San Diego
Michael J. Becich, University of Pittsburgh Medical
Center (UPMC)
Joel Saltz, Ohio State University
March 11, 2008
1st AMIA Summit on Translational Bioinformatics
March 26, 2008
CASC
We cannot nor should not underestimate the
future relationship between bioinformatics and
the ‘omics’ and the future EHR
“Inclusion of modern genome-wide records
into the Electronic Health Record (HER)
was the number one request of HHS
Secretary Leavitt to the NIH leadership at
a small private dinner recently.”
-Donald AB Lindberg,
Director, National Library of Medicine
DoD Healthcare IT Summit
March 26, 2008
Summary of NIH Panel Members’
Informatics Efforts
• NCBCs—Basic science to translational informatics
specialty centers. Roadmap (i.e. transitional). Athey
• BIRN—Focused on community building, strong in
neurosciences. NIH Cyberinfrastructure “standard
bearer”. Ellisman/Saltz
• CTSAs—Raised level of awareness of pent-up need for
clinical and basic research informatics and IT and
requirements to interoperate with in-patient and
ambulatory IT systems. Becich/Athey
• caBIG—Focused on operationalizing network of NCIfunded Comprehensive Cancer Centers. Saltz, Becich,
Athey
Elephants in the Room
• Underspecified/non-existent research IT systems, architecture, and
integration
• Cancer Center Directors who “don’t get” caBIG or who don’t want to
• R01 investigators who aren’t primarily interested in “data sharing”
or in using somebody else’s tools
• Lack of data sharing policies for basic and clinical
• Dichotomy of proprietary systems (Hospital/Health System) and
open source (Research) solutions and the risk averse nature of
Academic Health Centers
– Think interfaces
– Some research systems proprietary (e.g. Velos, ONCOR, etc.)
• Hospital/In-patient and Ambulatory Care Information Systems
(ACIS) interoperability with research IT systems
National Infrastructure to Leverage
• Clinical and Translational Sciences Award
(CTSA) Informatics Consortium (NCRR)
– 24 Members to grow to 60 in 3 years
• NIH National Biomedical Computing Centers
(NCBCs)
• Biomedical Informatics Research Network
(BIRN; NCRR). Related NIH Cyberinfrastructure
efforts (CDI, DATANet, etc.)
• ca
BIG
Panel Goals
• Learn more about these key NIH
Informatics Infrastructure programs
• Begin a dialog, from the bottom-up, to
identify key commonalities and synergies
possible between these programs.
• Answer the question: what has to
change??
How can we build upon and sustain
these efforts?
• It’s more than standardization, ontologies, and
“harmonization”
• It is about engaging “individual investigators”
with “team science”
• How do we bridge this cultural divide?
• How do we balance an individual and individual
institution’s needs with national needs?
– E.g. pooling of genomics data to build the number of
subjects for statistical power.
• We might be preaching to the choir here.
Please spread the word back home and in DC.
NCBC Portal—Look under the buttons
www.ncbcs.org
iTools Prototype
NCBC Categorization of Scientific Ontologies
Categorization of
Scientific Ontologies
Domain
Prefix
Category
OBO Foundry
Biological process
GO
1: All NCBCs endorse
yes
Cell type
CL
3: Promising but under construction
yes
Cellular component GO
1: All NCBCs endorse
yes
Chemical entities of CHEBI
biological interest
3: Promising but under construction
yes
Current Procedural
Terminology
CPT
2: All NCBCs will use under protest
(or more often, with a wish for some
additions/corrections)
no
FlyBase
FB
1: All NCBCs endorse
no
Scope of Applications in CTSA Informatics
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Interoperability with Institutional EMR Systems
– Clinical transaction systems
– Clinical Data Repository (CDR)
– De-identification/Honest Brokering
– Tools to Facilitate Extracting/Downloading Data Software tools
CTSI Portals
Clinical Trial/Study Databases
Genomic, Proteomic, and Metabolomic High-Throughput Data
Repositories and Analysis Tools
Clinical Imaging Data Repositories and Analysis Tools
An Institutional Specimen Tracking System
A CTSA Core Lab LIMS (Laboratory Information Management System)
Population/Public Health Databases & Informatics Needs
Standards to promote Interoperation within and between CTSA sites
Informatics Teaching & Training (Interface with CTSA Education
Program)
Biomedical Informatics Research in Support of C&T Research
Faculty, Staff, and Administrative Structure for Biomedical Informatics
CTSA Consortium
CTSA National Informatics Steering Committee
CTSA Informatics Operations Committee
Interest Groups
• Collaboration Facilitation
• Education
Interest Groups Propose Projects
• Data Warehousing
• User Needs
Interest Groups Propose Projects
• Standards & Interoperability
Project Groups (tentative)
• CTSA Informatics Priorities
(Leads - Athey, Miller)
• Clinical Research Registry
(Lead - Sim, Liaison Silverstein)
• Education (Lead - Klee,
Liaison - Hersh)
• Inventory (Lead - McWeeney,
Liaison - Becich)
• IT/Informatics White Paper
(Nearing completion)
Project Incubator:
• Data Sharing (Lead - TBD, Liaison - Silverstein)
• CTSA Informatics All-Hands Meeting before AMIA (Lead - TBD; Liaison - Masys)
BIG
ca
• Must get “smaller” and scale to the user
• Must get “bigger” by scaling to the
enterprise
• Must “normalize” with NIH CTSA
Informatics, NCBCs, and BIRN.
• NCI must continue to invest in the CCC’s
personnel to adapt caBIG
• Cancer Center Directors need the “Fear of
God” relating to non-adaption.
caBIG™ Community…
Clinical Trial Management Systems
Addresses the need for consistent, open and
comprehensive tools for clinical trials management.
Integrative Cancer Research
Provides tools and systems to enable integration and
sharing of information.
Tissue Banks & Pathology Tools
In vivo Imaging
Provides for the integration, development, and
implementation of tissue and pathology tools.
Provides for the sharing and analysis of in vivo imaging data.
Responsible for evaluating, developing, and integrating systems
for vocabulary and ontology content, standards, and software
systems for content delivery.
Developing architectural standards and architecture necessary for
other workspaces.
Data Sharing and
Intellectual Capital
Vocabularies & Common
Data Elements
Architecture
sharing of data, applications and infrastructure within the
cancer community.
Training
training in the use of the caBIG™ resources including on-line
turtorials, workshops, training programs.
Strategic Planning
Assists in identifying strategic priorities for the development
and evolution of the caBIG™ effort.
Source: caBIG – Ready for Adoption/Adaption. Ken Buetow, Ph.D., June 21, 2007
caBIG November 8-9, 2007 Summit Recommendations
Summit participants, following a day and a half of deliberations in three
simultaneous subject tracks, achieved consensus on the following eight priorities
for the caBIG™ initiative:
1. Sustain its work in data standards and infrastructure.
2. Spearhead an awareness campaign.
3. Conduct a scientific demonstration project.
4. Maximize engagement with the commercial sector.
5. Establish more extensive and visible partnerships with other government
agencies.
6. Get “inside” Electronic Health Records.
7. Expand beyond cancer.
8. Expand internationally.
Source: caBIG Summit Executive Summary (January 2008)
Source: Onsemble Notes – Newsletter of the Oncore Community, Vol 3., No 1. (Spring 2008)
CTSA Institutions – Oncore / Velos
Funded CTSA Institutions
2006 Awardees
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Duke University (Velos)
Columbia University (Velos)
Mayo Clinic
Oregon Health and Science Univ (Velos)
The Rockefeller University
Univ of California, San Francisco (Velos)
Univ of California, Davis (Velos)
University of Pennsylvania
University of Pittsburgh
U Rochester Sch of Medicine and Dentistry
U Texas Health Sciences Center at Houston
Yale University
2007 Awardees
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Emory Univ (with Morehouse) (Oncore)
CWRU / Cleveland Clinic (Velos)
Weill Cornell Medical College (with Hunter)
Johns Hopkins University
Univ Of Michigan At Ann Arbor (Velos)
U Texas Southwestern Med Ctr - Dallas
Univ Of Wisconsin Madison (Oncore)
University Of Chicago (Velos)
University Of Iowa (Oncore)
University Of Washington
Vanderbilt Univ (with Meharry) (Oncore)
Washington University
http://www.ctsaweb.org
Key Challenges and Opportunities
• Sociological and Technical Complexity of the Informatics and
IT environments
– Must SIMPLIFY for users to use.
– Must continuously educate our users
• We must deploy proprietary and open source tools with the
larger integration picture in mind.
• We must build and leverage specialized and standardized IT
production resources in our AHCs.
• NIH can help us leverage these national initiatives with
attractive supplemental programs which insist on using tools
from these initiatives.
• Cancer Center leadership must make Clinical Research
Informatics a top priority (it is a “Force Multiplier”)
• A co-investment strategy with NIH and the AHCs and other
willing partners (public and private) is called for.
• Let’s sustain this discussion at AMIA, engaging our willing NIH
colleagues. Let’s start now.