Towards a Set of Unified NIH Computational, Data, and Community

Infrastructures to Support Translational Bioinformatics

Brian D. Athey, University of MichiganMark Ellisman, University of California, San DiegoMichael J. Becich, University of Pittsburgh Medical

Center (UPMC)Joel Saltz, Ohio State University

March 11, 20081st AMIA Summit on Translational Bioinformatics

March 26, 2008CASC

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 NCI-funded 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.)

• caBIG

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 biological interest

CHEBI 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• 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 National Informatics Steering Committee

Project Incubator:• Data Sharing (Lead - TBD, Liaison - Silverstein)• CTSA Informatics All-Hands Meeting before AMIA (Lead - TBD; Liaison - Masys)

CTSA Informatics Operations Committee

Interest Groups

• Collaboration Facilitation

• Education

• Data Warehousing

• User Needs

• 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)

Interest Groups Propose Projects

Interest Groups Propose Projects

CTSA Consortium

caBIG• 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…

ArchitectureDeveloping architectural standards and architecture necessary for

other workspaces.

Vocabularies & Common Data Elements

Responsible for evaluating, developing, and integrating systems for vocabulary and ontology content, standards, and software

systems for content delivery.

In vivo Imaging

Tissue Banks & Pathology ToolsProvides for the integration, development, and implementation of tissue and pathology tools.

Integrative Cancer ResearchProvides tools and systems to enable integration and sharing of information.

Clinical Trial Management SystemsAddresses the need for consistent, open and comprehensive tools for clinical trials management.

Provides for the sharing and analysis of in vivo imaging data.

Strategic Planning

Training

Data Sharing and Intellectual Capital

Assists in identifying strategic priorities for the development and evolution of the caBIG™ effort.

training in the use of the caBIG™ resources including on-line turtorials, workshops, training programs.

sharing of data, applications and infrastructure within the cancer community.

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)

Funded CTSA Institutions

CTSA Institutions – Oncore / Velos

2006 Awardees• 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• 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.