Open Science: When Theory Meets Practice
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Dorfman Lecture, University of Chicago, June 8, 2017
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Open Science: When Theory Meets Practice
- 1. Open Science: When Theory Meets Practice Philip E. Bourne PhD, FACMI Stephenson Chair of Data Science Director, Data Science Institute Professor of Biomedical Engineering peb6a@virginia.edu https://www.slideshare.net/pebourne Albert Dorfman Lecture 16/8/17
- 2. My Bias in Addressing this Question • Research in computational biology and big data • Open science zealot • AVC for Innovation UCSD • Maintained biological data resources for 15 years (PDB, IEDB) • Chief Data Officer of the NIH for 3 years (federal view) • DSI Director 1 month (state view) 2Albert Dorfman Lecture6/8/17
- 3. Open Science: One Definition • Making as much as the basic and clinical research life cycle as open as possible without compromising the wishes of all stakeholders with the view of accelerating and improving the quality of the research process. • Having as many people as possible contribute to research outcomes. 6/8/17 Albert Dorfman Lecture 3
- 4. User Case: Accelerating the Research Process … 6/8/17 Albert Dorfman Lecture 4
- 5. Diffuse Intrinsic Pontine Gliomas (DIPG) • Occur 1:100,000 individuals • Peak incidence 6-8 years of age • Median survival 9-12 months • Surgery is not an option • Chemotherapy ineffective and radiotherapy only transitive From Adam Resnick
- 6. Timeline of genomic studies in DIPG • Landmark studies identify histone mutations as recurrent driver mutations in DIPG ~2012 • Almost 3 years later, in largely the same datasets, but partially expanded, the same two groups and 2 others identify ACVR1 mutations as a secondary, co- occurring mutation From Adam Resnick
- 7. What do we need to do differently to reveal ACVR1? • ACVR1 is a targetable kinase • Inhibition of ACVR1 inhibited tumor progression in vitro • ~300 DIPG patients a year • ~60 are predicted to have ACVR1 • If large scale data sets were only integrated with TCGA and/or rare disease data in 2012, ACVR1 mutations would have been identified • 60 patients/year X 3 years = 180 children’s lives (who likely succumbed to the disease during that time) could have been impacted if only data were FAIR From Adam Resnick
- 8. Use case: Having as many people as possible contribute to research outcomes…. The Story of Meridith 6/8/17 Albert Dorfman Lecture 8
- 9. A broader example of what comes out of open science… 6/8/17 Albert Dorfman Lecture 9
- 10. Driving sharing and innovation: Open Science Prize NIH, Wellcome Trust, HHMI https://www.openscienceprize.org Accepted PLOS Biology • An international scientific challenge competition to encourage and support the prototyping and development of services, tools, or platforms that enable utilization of open content • 96 submissions received • Solvers from 45 countries, spanning 5 continents • Timeline • May 2016: Phase 1 winners announced at Health DataPalooza • Dec 1, 2016: Presentations and public voting • Feb 2017: Overall winner announced
- 11. Consider some of the history of open science from the NIH perspective … 6/8/17 Albert Dorfman Lecture 11 Some slides courtesy of Francis Collins
- 12. Laying the Foundation: Human Genome Project, Bermuda, 1996
- 14. “The HGP changed the norms around data sharing in biomedical research.”
- 15. Data Sharing: An Essential Component
- 17. A Culture of Sharing 1999 20042003 2007 20142008 Research Tools Policy NIH Data Sharing Policy Model Organism Policy Genome-wide Association (GWAS) Policy 2012 NIH Public Access Policy (Publications) Big Data to Knowledge (BD2K) Initiative Genomic Data Sharing (GDS) Policy Modernization of NIH Clinical Trials White House Initiative (2013 “Holdren Memo”)
- 18. Guiding Principle of NIH GWAS Policy The greatest public benefit will be realized if data from GWAS are made available, under terms and conditions consistent with the informed consent provided by individual participants, in a timely manner to the largest possible number of investigators. NIH expectation that data would be shared in the NIH database of Genotype and Phenotype (dbGaP)
- 19. Data Access Requests Per Year 2007–September 2015 32962 21973 0 5000 10000 15000 20000 25000 30000 35000 2007 2008 2009 2010 2011 2012 2013 2014 2015 Total Approved
- 20. A Culture of Sharing 1999 20042003 2007 20142008 Research Tools Policy NIH Data Sharing Policy Model Organism Policy Genome-wide Association (GWAS) Policy 2012 NIH Public Access Policy (Publications) Big Data to Knowledge (BD2K) Initiative Genomic Data Sharing (GDS) Policy Modernization of NIH Clinical Trials White House Initiative (2013 “Holdren Memo”)
- 21. NIH Public Access Policy for Publications • Ensures public access to published results of all research funded by NIH since 2008 • Recipients of NIH funds required to submit final peer- reviewed journal manuscripts to PubMed Central (PMC) upon acceptance for publication • Papers must be accessible to the public on PMC no later than 12 months after publication
- 22. A Culture of Sharing 1999 20042003 2007 20142008 Research Tools Policy NIH Data Sharing Policy Model Organism Policy Genome-wide Association (GWAS) Policy 2012 NIH Public Access Policy (Publications) Big Data to Knowledge (BD2K) Initiative Genomic Data Sharing (GDS) Policy Modernization of NIH Clinical Trials White House Initiative (2013 “Holdren Memo”)
- 23. Harnessing Data to Improve Health: BD2K (Big Data to Knowledge) NIH’s 6-year initiative to use data science to foster an open digital ecosystem that will accelerate efficient, cost-effective biomedical research to enhance health, lengthen life, and reduce illness and disability Programs and activities: • Advance discovery for biomedical research • Facilitate use and re-use of biomedical data • Develop analytical methods and software • Enhance biomedical data science training
- 24. Will we do this research in a different way? Will it become more like Airbnb? 6/6/17 UNC 24 Bonazzi & Bourne 2017 PLOS Biology 15(4) e2001818
- 25. I am not crazy, hear me out • Airbnb is a platform that supports a trusted relationship between consumer (renter) and supplier (host) • The platform focuses on maximizing the exchange of services between supplier and consumer and maximizing the amount of trust associated with a given stakeholder • It seems to be working: • 60 million users searching 2 million listings in 192 countries • Average of 500,000 stays per night. • Evaluation of US $25bn Bonazzi & Bourne 2017 PLOS Biology 15(4) e2001818
- 26. Is not biomedical research the same?
- 27. Paper Author Paper Reader Data Provider Data Consumer Employer Employee Reagent Provider Reagent Consumer Software Provider Software Consumer Grant Writer Grant Reviewer Supplier Consumer Platform MS Project Google Drive Coursera Researchgate Academia.edu Open Science Framework Synapse F1000 Rio Educator Student Platforms – The situation today
- 28. Commons Compliance • Treat products of research – data, methods, papers etc. as digital objects • These digital objects exist in a shared virtual space • Digital object compliance through FAIR principles: • Findable • Accessible (and usable) • Interoperable • Reusable https://commonfund.nih.gov/bd2k/commons
- 29. 1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results We Need Data and Knowledge About That Data to Interoperate 1. User clicks on content 2. Metadata and webservices to data provide an interactive view that can be annotated 3. Selecting features provides a data/knowledge mashup 4. Analysis leads to new content I can share 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle PLoS Comp. Biol. 2005 1(3) e34
- 30. Incentives • Airbnb • Monetize unutilized space • Ease of use • New vacation experience • Commons • Need to improve rigor and reproducibility • Productivity • Sustainability • Education and training • Opportunity to undertake elastic compute on large complex data https://commonfund.nih.gov/bd2k/commons
- 31. A Culture of Sharing 1999 20042003 2007 20142008 Research Tools Policy NIH Data Sharing Policy Model Organism Policy Genome-wide Association (GWAS) Policy 2012 NIH Public Access Policy (Publications) Big Data to Knowledge (BD2K) Initiative Genomic Data Sharing (GDS) Policy Modernization of NIH Clinical Trials White House Initiative (2013 “Holdren Memo”)
- 32. NIH Genomic Data Sharing (GDS) Policy • Purpose • Sets forth expectations, responsibilities that ensure broad, responsible sharing of genomic research data in a timely manner • Scope • All NIH-funded research generating large-scale human or non- human genomic data – and their use for subsequent research • Data to be submitted to NIH-designated data repositories (e.g., dbGaP, GEO, GenBank, WormBase, FlyBase, Rat Genome Database) • Applies to all funding mechanisms (grants, contracts, intramural support) with no minimum threshold for cost • Released August 2014; effective January 25, 2015 gds.nih.gov
- 33. Data Sharing Goes Global: GA4GH Global Alliance for Genomics and Health • Accelerating the potential of genomic medicine to advance human health, by: • Establishing common framework of approaches to enable effective, responsible sharing of genomic and clinical data • Catalyzing data sharing projects that drive and demonstrate value of data sharing • Alliance*: >350 leading institutions (healthcare, research, advocacy, life science, IT) representing 35 countries • Working groups (Clinical, Data, Security, Regulatory & Ethics) assess, prioritize needs • Form task teams to produce tools, solutions, demonstration projects *Statistics as of October 5, 2015
- 34. A Culture of Sharing 1999 20042003 2007 20142008 Research Tools Policy NIH Data Sharing Policy Model Organism Policy Genome-wide Association (GWAS) Policy 2012 NIH Public Access Policy (Publications) Big Data to Knowledge (BD2K) Initiative Genomic Data Sharing (GDS) Policy Modernization of NIH Clinical Trials White House Initiative (2013 “Holdren Memo”)
- 35. Modernizing NIH Clinical Trials Activities: The Need • NIH-Funded trials published within 100 months of completion Less than 50% published within 30 months of completion BMJ 2012;344:d7292
- 36. Modernizing NIH Clinical Trials Activities: Call to Action
- 37. Progress has Been Made 6/8/17 Albert Dorfman Lecture 37
- 38. Improvements to the Common Rule 6/8/17 Albert Dorfman Lecture 38
- 39. Acknowledgements 6/6/17 UNC 39 The BD2K Team at NIH My New Colleagues at UVA The 150 folks who have passed through my laboratory https://docs.google.com/spreadsheets/d/1QZ48UaKcwDl_iFCvBmJsT03FK-bMchdfuIHe9Oxc-rw/edit#gid=0
Notas do Editor
- One example: BrainBox, an Open Neuroimaging Laboratory that will enable collaboration around annotation, discovery and analysis of publicly available brain imaging data. OpenAQ: A Global Community Building the First Open, Real-Time Air Quality Data Hub for the World Real-Time Evolutionary Tracking for Pathogen Surveillance and Epidemiological Investigation Open Neuroimaging Laboratory OpenTrialsFDA Fruit Fly Brain Observatory MyGene2: Accelerating Gene Discovery with Radically Open Data Sharing
- “As biology’s first large-scale project, the HGP paved the way for numerous consortium-based research ventures. The NHGRI alone has been involved in launching more than 25 such projects since 2000. These have presented new challenges to biomedical research — demanding, for instance, that diverse groups from different countries and disciplines come together to share and analyse vast data sets.” “The HGP changed the norms around data sharing in biomedical research.”
- Added (10/1/15): TCGA, dbGaP, GTR
- Fig. a. Polymorphic variants within sampled populations. The area of each pie is proportional to the number of polymorphisms within a population. Pies are divided into four slices, representing variants private to a population (darker colour unique to population), private to a continental area (lighter colour shared across continental group), shared across continental areas (light grey), and shared across all continents (dark grey). Dashed lines indicate populations sampled outside of their ancestral continental region.
- 2013 White House Initiative: “Increasing Access to the Results of Federally Funded Scientific Research”
- Updated to include numbers through September 2015. From Dina Paltoo [10/6/15]: “The data in the first slide is for all of dbGaP 2007-2014. The information came from a version of what is on the GDS website (https://gds.nih.gov/19dataaccesscommitteereview_dbGaP.html) and in a Nature Genetics paper (http://www.nature.com/ng/journal/v46/n9/full/ng.3062.html), but results from information that we receive from NCBI.”
- 2013 White House Initiative: “Increasing Access to the Results of Federally Funded Scientific Research”
- The NIH Public Access Policy implements Division F Section 217 of PL 111-8 (Omnibus Appropriations Act, 2009). http://publicaccess.nih.gov/policy.htm OSP’s summary: The NIH Public Access Policy for publications has been in a requirement for all recipients of NIH funds since 2008. It implements Division G, Title II, Section 218 of PL 110-161 (Consolidated Appropriations Act, 2008). The NIH Public Access Policy ensures that the public has access to the published results of NIH-funded research. It requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to the digital archive PubMed Central (PMC) upon acceptance for publication. Scientists can also deposit papers through partnerships NIH has established with publishers. To help advance science and improve human health, the Policy requires that NIH supported papers are accessible to the public on PMC no later than 12 months after publication.
- 2013 White House Initiative: “Increasing Access to the Results of Federally Funded Scientific Research”
- Updated by ADDS group 8/25/15
- 29
- 2013 White House Initiative: “Increasing Access to the Results of Federally Funded Scientific Research”
- 2013 White House Initiative: “Increasing Access to the Results of Federally Funded Scientific Research”
- Figure 2. Cumulative percentage of studies published in a peer reviewed biomedical journal indexed by Medline during 100 months after trial completion among all NIH funded clinical trials registered within ClinicalTrials.gov Public benefits to clinical trials data-sharing (OSP): Inform future research and research funding decisions Mitigate bias (e.g., non publication of results, especially negative results) Prevent duplication of unsafe trials Meet ethical obligation to human subjects (i.e., that results inform science) Increase access to data about marketed products All contribute to public trust in clinical research Source: Ross JS, Tse T, Zarin DA, Xu H, Zhou L, Krumholz HM. Publication of NIH funded trials registered in ClinicalTrials.gov: cross-sectional analysis. BMJ 2012;344:d7292.