Rapid Launch of the tranSMART Foundation

Brian D. Athey, PhD University of Michigan Michael Braxenthaler, PhD Pistoia Alliance

• Created by Johnson and Johnson

• Central knowledge management

• Open source (at tranSMARTproject.org)

• Cloud computing

• Pre-competitive data sharing

tranSMART Origins (2007-2010)

Propelling Innovation in Drug Discovery: Major Problems to Address

• The pharmaceutical industry is facing the largest “patent cliff” in its history

• Venture capital to start new biotechnology firms and fund innovative drug development activities is declining

• Many companies are exiting important fields of critical need—e.g. neurodegenerative diseases, such as Alzheimer’s disease and psychiatric diseases

• As little as 15-25% of translatable research published in Nature, Science and Cell cannot be reproduced by crack teams in Pharma (Amgen, JnJ, others)

Propelling Innovation in Drug Discovery: Innovation & Pace are Required

• Depends Upon a Thriving Ecosystem and Partnership Comprised of Researchers, Industry, and Regulators

• Ecosystem Under Significant Stress with R&D Productivity in decline

• “We Stand at a Moment of Historic Progress in Biomedical Research with Extraordinary Promise for New Drug Development”

--Francis Collins

Challenge: Data Integration & Analysis

Integrating & Analyzing ‘Omics Data with the phenotype is key to translate research into patient care & accelerating cures

Need: Data Liquidity and Reciprocity How to Gain Traction?

Focus on Pre-competitive

Vignette (Academic Translation)

Accelerating Bi-directional Translation in Glomerular Disease (Matthias Kretzler, MD)

2007 – 2012: Builds International Research Network • NIH-funded across four continents • Seven pharma companies want access to data and partnership

2012: Needs ‘Omics/Participant Data Sharing & Analysis Platform • Binary cross sectional integration now, multi-scalar later • Pro-competitive space: Pharma, Academia, FDA & NIH • Is asking for tranSMART

Vignette (NFP Research Accelerator)

• Funds 600+ Researchers globally to research Huntington’s Disease

• Generates genetic, epigenetic, transcriptomic, proteomic, metabolomics and imaging data

• Needs data sharing and analysis platform that integrates experimental with clinical phenotypes

• Is asking for tranSMART

A Virtual Pharma Research NFP

Vignette (EU Pharma / Government PPP)

• More efficient Drug R&D • Enhance Europe’s competitiveness • 4 pillars: Efficacy, Safety, KM and

Education & Training

Largest Life Science PPP eTRIKS (EU Funded; IMI 5-year, €24 million )

WP1 Service Delivery

WP2 Platform Development

WP3 Standards Research / Development

WP4 Analytics Research / Content Curation

WP5 Governance

WP6 Community Engagement / Outreach

WP7 Ethics tranSMART development effort

Objectives: • Sustainable KM Platform and Service • Standardized curated TR Study Information

Members: 10 Pharma, 6 Academic/Commercial

Search and

Browse

R-based Analysis

i2b2 data to

organize studies

Molecular Data +

Data from PubMed

tranSMART: A Glimpse to the Future

Current

Future

Leveraging NIH NCBC Initiatives . . .

• i2b2 - The core of the tranSMART Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, identity management & Natural Language Processing (NLP) tools.

• NCIBI is porting a set of richly interactive tools into the search portion of tranSMART to support linking of user data with NCIBI integrated pathway, genetics, metabolomics, MeSH, and PubMed data.

• NCBO is collaborating to provide ontology services that are utilized by tranSMART.

NCATS and CTSA Synergies

CTSA Consortium 61 medical research institutions in 30 states and the District of Columbia

The NCATS mission “is to catalyze the generation of innovative methods and technologies that will enhance the development, testing and implementation of diagnostics and therapeutics across a wide range of human diseases and conditions.”

Potential to deploy tranSMART by leveraging broad i2b2 adoption across 61 CTSAs

• i2b2 is a core component of tranSMART focused on clinical phenotypes

• i2b2 is deployed globally at more than 72 AHC, HMO and company locations including 39 CTSA sites

Emerging tranSMART Vision

• An emerging global open source PPP community

• Enables “pre-competitive” data sharing, saving money & accelerating translational research to cures

• An evolving analytics and data-sharing cloud platform

• Sharable code base and reference data sets

• A global community of users, developers, and stakeholders who are the best source of innovation

tranSMART Community Ecosystem

• Pharmaceutical, Biotechnology & Information Resource Companies

• Not-for-Profit Research Organizations and Patient Advocacy Groups

• Academic Institutions (US and EU)

• Government (US and EU)

• Value-Added Service Providers

tranSMART Activities / Accomplishments

2010 Bio-IT World Best Practices and CIO 100 Awards

Jan. 2012 Released into public domain -- open source GPLv3 license

Jan. - July 2012 Janssen funds nascent community support activities (transmartproject.org)

May - Sept. 2012 Pistoia & U-M with others further develops tranSMART vision

July 2012 tranSMART 1.0GA release

Nov. 2012 Pistoia Alliance <> TM Forum - Apps in Life Science R&D - Workshop

Nov. 2012 EU IMI-funded eTRIKS Project Launch

Emerging tranSMART Foundation Public Private Partnership Vision

eTRIKS

global coordination

tranSMART Foundation

501(c)(3)

Pistoia Alliance 501(c)(6)

Pistoia Alliance (501c6)

• A global, not-for-profit, precompetitive alliance of life science companies, vendors, publishers, and academics

• Works to identify root causes of R&D inefficiencies and develops best practices, use cases, technology concepts and pilots, and business models to overcome common obstacles

• Projects are run in volunteer-led working groups, managed by an operational team of volunteers and part-time paid staff, and overseen by a Board of Directors

tranSMART Foundation

• 501(c)(3) Non-Profit (in formation) need help, funding, committed partners

• Public component of public private partnership • Academic and Not-for-Profits

• Represents all stakeholders

• Guides development / Supports community

• Accepts philanthropic donations • Provides legal structure for grants and contracts

tranSMART Foundation

Board of Directors • Gilbert S. Omenn, M.D., Ph.D. (Chair); University of Michigan • Garry Neil, M.D., Apple Tree Partners; TransCelerate BioPharma • Leroy Hood, M.D., Ph.D.; Institute for Systems Biology • Keith Elliston, Ph.D.; CHDI Foundation, Inc. • Christoph Brockel, Ph.D.; Pfizer, Pistoia Alliance • Others, TBD

Officers • Co-Chief Executive Officer, Brian Athey, Ph.D.; University of Michigan • Co-Chief Executive Officer, Michael Braxenthaler, Ph.D.; Pistoia Alliance • Executive Director, Kevin Smith, M.S.I.S.; University of Michigan • Treasurer, Ashley George, Ph.D.; GlaxoSmithKline, Pistoia Alliance

tranSMART Foundation

Working Groups Platform Development • Yike Guo, Ph.D.; Imperial College London, ID Business Solutions, Ltd. (IDBS) • Anthony Rowe, Ph.D.; Johnson & Johnson • Terry Weymouth, Ph.D.; University of Michigan, NCIBI • Mike Mendis; Harvard, i2b2 • Michael Kellen, Ph.D.; Sage Bionetworks • Dan Housman; Recombinant Data Corporation

Other Working Groups spanning US and European efforts (Need Partners) • Standards Research / Development • Analytics Research / Development • Community Engagement / Outreach

• Community Support • Data Curation and Sharing • Ethics

Funding/Sustainability Need Major Help with This

Potential funding sources . . . leading to operational sustainability

• Membership Fees: $500 for advocacy groups to $25,000 for large corporations • Consulting Fees: First stop for those with a need for data exchange to

determine potential solutions • Project Management Fees: Ensure that those with a need for data exchange

have the help of an honest broker • Not-for-profit Support: Foundations focused on national challenges including

societal need for biomedical data exchange, analysis and accelerating to cure • Government support: Compete for HHS and EU grants / contracts • Philanthropy: Ideal partner(s) to launch 501(c)(3) tranSMART Foundation

Volunteer Support in the beginning / Paid Staff as funds become available

tranSMARTproject.org

• Communications • Training • Deployments • Documentation • YouTube • Events • Fundraising

• Goal 1 Fund Not-for-Profit tranSMART Foundation to provide business and technical leadership and core teams to plan, execute and coordinate global efforts

• Goal 2 Provide community support and establish coordination of international tranSMART community

• Goal 3 Begin implementation and refine a robust business plan to provide long-term sustainable funding for the tranSMART open source community

Goals (Dec. 2012 – Nov. 2013)

Establish Non-Profit Organization

• Assess Legal Structures, Governance, and Implement (Dec. 2012 - Nov. 2013)

• Create Non-Profit Organization and establish Board of Directors (Dec. 2012 - May 2013)

• Establish Operational Teams and Working Groups (Dec. 2012 - Nov. 2013)

Timeline (Dec. 2012 – Nov. 2013)

Provide Community Support

• Transition community support (Dec. 2012 - Nov. 2013)

• Coordinate European, US and other initiatives (Dec. 2012 - Nov. 2013)

• Periodic Software Release (Dec. 2012 - Nov. 2013)

• Transition responsibility for tranSMARTproject.org to tranSMART Foundation (Dec. 2012 - Nov. 2013)

Timeline (Dec. 2012 – Nov. 2013)

Long-term Sustainable Funding

• Pistoia to develop industry business case for investment (Dec. 2012 - May 2013)

• U-M to lead development of academic/non-profit business case (Dec. 2012 - May 2013)

• Non-Profit Board of Directors to obtain supplemental near-term funds (Dec. 2012 - Nov. 2013)

• Submit proposals to Industry, NIH and VA (2013)

Timeline (Dec. 2012 – Nov. 2013)

Support tranSMART

• With Funding • tranSMART Foundation operations • Major development initiatives

• Getting Involved (In-Kind Contributions) • Define Scientific Workflows and Use Cases • Identify Reference Data and Analytical Tools to

integrate with tranSMART

• Helping us prioritize

• Joining our emerging groups

Help Us Stand Up the tranSMART Foundation!

Please get Involved . . . We need you!

Michael Braxenthaler (michael.braxenthaler@roche.com)

Brian Athey (bleu@umich.edu)

Kevin Smith (kasmith@umich.edu)