The document discusses the vision for data science at the National Institutes of Health (NIH). It outlines the goals of fostering an open ecosystem to enable biomedical research as a digital enterprise. Examples are provided of how precision medicine could benefit patients in the near future through large national research cohorts, improved understanding of diseases like diabetes through genomics, and new technologies. The document also discusses several key elements needed for the digital research enterprise, including communities, policies, infrastructure, and workforce training through initiatives like the Big Data to Knowledge program.
One Funder’s View for Advancing Open SciencePhilip Bourne
Robert Wood Johnson Foundation & SPARC Workshop on October 19, 2015 intended to catalyze a dialogue about opportunities for philanthropy and other funders in open access.
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
One Funder’s View for Advancing Open SciencePhilip Bourne
Robert Wood Johnson Foundation & SPARC Workshop on October 19, 2015 intended to catalyze a dialogue about opportunities for philanthropy and other funders in open access.
Big Data in Biomedicine – An NIH PerspectivePhilip Bourne
Keynote at the IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, November 10, 2015.
https://cci.drexel.edu/ieeebibm/bibm2015/
SCUP 2016 Mid-Atlantic Symposium: Big Data: Academy Research, Facilities, and Infrastructure Implications and Opportunities. John Hopkins, May 13, 2016
NITRD Big Data Interagency Working Group Workshop: Pioneering the Future of Federally Supported Data Repositories Jan 13, 2021 - Opening comments on where we are and one suggestion of where we might go with an International Data Science Institute (IDSI) - A blue sky view.
From Research to Practice - New Models for Data-sharing and Collaboration to ...Health Data Consortium
Watch the webinar here: http://encore.meetingbridge.com/MB005418/140528/
Webinar transcript: http://hdc.membershipsoftware.org/Files/webinars/HDC-PwC%20NIH%20&%20PCORI%20Webinar%20Transcript%205_28_14.pdf
Patient-Centered Outcomes Research Institute (PCORI) Executive Director Joe Selby, MD, MPH; National Institutes of Health (NIH) Director and PCORI Board of Governors member Francis Collins, MD, PhD; and NIH Associate Director for Data Science Philip Bourne, PhD discussed new and emerging trends in big data for health, including:
- How researchers, patients, clinicians, and others are forging new models for data-sharing.
- Leveraging the quantity, variety, and analytic potential of health-related data for research and practice.
- Addressing patients’ perspectives, needs, and concerns in creating new opportunities for innovation and translational science.
- Exciting initiatives such as PCORnet, the National Patient-Centered Clinical Research Network initiative that PCORI is now helping to develop, and related open data and technology efforts such - as the NIH Health Systems Collaboratory and Big Data to Knowledge (BD2K) initiative.
Discover more health data resources on our website at http://www.healthdataconsortium.org/
Research in the time of Covid: Surveying impacts on Early Career ResearchersRebecca Grant
Based on a survey of over 4,500 researchers published in the white paper The State of Open Data 2020, this session will explore the impacts of the pandemic on early career reearchers (ECRs), their research practice, and how they interact with open data. We will discuss the specific challenges reported by ECRs, as well as the gaps in training and support that they have identified that would encourage their sharing and reuse of research data.
Presentation at the E-ARMA conference 2021.
Do Open data badges influence author behaviour? A case study at Springer NatureRebecca Grant
Digital badges have previously been shown to incentivise journal authors to share their data openly. In this paper we introduce an Open data badging project at the Springer Nature journal BMC Microbiology. The development of the Open data badge is described, as well as the challenges of developing standard badging criteria and ensuring authors’ awareness of the badges. Next steps for the badging project are outlined, which are based on the experiences of the team assessing the badges, the number of badges awarded at the journal to date, and the results of an author survey.
Digital transformation to enable a FAIR approach for health data scienceVarsha Khodiyar
Invited talk for ConTech Pharma on 1st March 2022
Abstract
Health Data Research UK is the UK’s national institute for health data science, with a mission to unite the UK’s health data to enable discoveries that improve people’s lives. In this talk, Dr Varsha Khodiyar will outline how HDR UK is bringing together disparate health data from all four countries of the United Kingdom, creating the infrastructure to enable discovery of and access to health data, and the convening standards making bodies to improve data linkage and data reuse. Varsha will also discuss how HDR UK is moving beyond the traditional confines of FAIR data to also ensure that data sharing and data use is transparent and ‘fair’ for the patients and lay public who are the subjects of these datasets.
Why is the NIH investing $100M at the intersection of data science and health research? The NIH seeks to invest in ways to help researchers easily find, access, analyze, and curate research data. Researchers want visual analytics, and to build the database into a “social network” – being able to “friend” or “like” the data.
Data Harmonization for a Molecularly Driven Health SystemWarren Kibbe
Maximizing the value of data, computing, data science in an academic medical center, or 'towards a molecularly informed Learning Health System. Given in October at the University of Florida in Gainesville
The slide presentation that preceded of the annual Health Datapalooza in Washington DC, PCORI was pleased to participate in the latest installment in the Health Data Consortium and PricewaterhouseCoopers (PwC) Innovators in Health Data Series, a webinar featuring PCORI Executive Director Joe Selby, MD, MPH; NIH Director and PCORI Board of Governors member Francis Collins, MD, PhD; and Philip Bourne, PhD, NIH’s Associate Director for Data Science.
SCUP 2016 Mid-Atlantic Symposium: Big Data: Academy Research, Facilities, and Infrastructure Implications and Opportunities. John Hopkins, May 13, 2016
NITRD Big Data Interagency Working Group Workshop: Pioneering the Future of Federally Supported Data Repositories Jan 13, 2021 - Opening comments on where we are and one suggestion of where we might go with an International Data Science Institute (IDSI) - A blue sky view.
From Research to Practice - New Models for Data-sharing and Collaboration to ...Health Data Consortium
Watch the webinar here: http://encore.meetingbridge.com/MB005418/140528/
Webinar transcript: http://hdc.membershipsoftware.org/Files/webinars/HDC-PwC%20NIH%20&%20PCORI%20Webinar%20Transcript%205_28_14.pdf
Patient-Centered Outcomes Research Institute (PCORI) Executive Director Joe Selby, MD, MPH; National Institutes of Health (NIH) Director and PCORI Board of Governors member Francis Collins, MD, PhD; and NIH Associate Director for Data Science Philip Bourne, PhD discussed new and emerging trends in big data for health, including:
- How researchers, patients, clinicians, and others are forging new models for data-sharing.
- Leveraging the quantity, variety, and analytic potential of health-related data for research and practice.
- Addressing patients’ perspectives, needs, and concerns in creating new opportunities for innovation and translational science.
- Exciting initiatives such as PCORnet, the National Patient-Centered Clinical Research Network initiative that PCORI is now helping to develop, and related open data and technology efforts such - as the NIH Health Systems Collaboratory and Big Data to Knowledge (BD2K) initiative.
Discover more health data resources on our website at http://www.healthdataconsortium.org/
Research in the time of Covid: Surveying impacts on Early Career ResearchersRebecca Grant
Based on a survey of over 4,500 researchers published in the white paper The State of Open Data 2020, this session will explore the impacts of the pandemic on early career reearchers (ECRs), their research practice, and how they interact with open data. We will discuss the specific challenges reported by ECRs, as well as the gaps in training and support that they have identified that would encourage their sharing and reuse of research data.
Presentation at the E-ARMA conference 2021.
Do Open data badges influence author behaviour? A case study at Springer NatureRebecca Grant
Digital badges have previously been shown to incentivise journal authors to share their data openly. In this paper we introduce an Open data badging project at the Springer Nature journal BMC Microbiology. The development of the Open data badge is described, as well as the challenges of developing standard badging criteria and ensuring authors’ awareness of the badges. Next steps for the badging project are outlined, which are based on the experiences of the team assessing the badges, the number of badges awarded at the journal to date, and the results of an author survey.
Digital transformation to enable a FAIR approach for health data scienceVarsha Khodiyar
Invited talk for ConTech Pharma on 1st March 2022
Abstract
Health Data Research UK is the UK’s national institute for health data science, with a mission to unite the UK’s health data to enable discoveries that improve people’s lives. In this talk, Dr Varsha Khodiyar will outline how HDR UK is bringing together disparate health data from all four countries of the United Kingdom, creating the infrastructure to enable discovery of and access to health data, and the convening standards making bodies to improve data linkage and data reuse. Varsha will also discuss how HDR UK is moving beyond the traditional confines of FAIR data to also ensure that data sharing and data use is transparent and ‘fair’ for the patients and lay public who are the subjects of these datasets.
Why is the NIH investing $100M at the intersection of data science and health research? The NIH seeks to invest in ways to help researchers easily find, access, analyze, and curate research data. Researchers want visual analytics, and to build the database into a “social network” – being able to “friend” or “like” the data.
Data Harmonization for a Molecularly Driven Health SystemWarren Kibbe
Maximizing the value of data, computing, data science in an academic medical center, or 'towards a molecularly informed Learning Health System. Given in October at the University of Florida in Gainesville
The slide presentation that preceded of the annual Health Datapalooza in Washington DC, PCORI was pleased to participate in the latest installment in the Health Data Consortium and PricewaterhouseCoopers (PwC) Innovators in Health Data Series, a webinar featuring PCORI Executive Director Joe Selby, MD, MPH; NIH Director and PCORI Board of Governors member Francis Collins, MD, PhD; and Philip Bourne, PhD, NIH’s Associate Director for Data Science.
Improving health care outcomes with responsible data scienceWessel Kraaij
Keynote presentation by Wessel Kraaij at the Dutch pattern recognition and impage processing society (NVPBV) 29/5/2018, Eindhoven.
This talk discusses
1. trends in health care and respondible data science and their intersection
2. Secure federated analytics on distributed data repositories
3. Generating clinically relevant hypotheses from patient forum discussions.
Precision and Participatory Medicine - Medinfo 2015 Panel on big data. Includes the proposal to use the term Expotype to characterise the Exposome of an individual. Electronic expo typing would refer to the automatic construction of individual expo types from electronic clinical records and other sources of environmental risk factor and exposure data.
From personal health data to a personalized adviceWessel Kraaij
Invited talk at the health track of ICT.OPEN 2018, 20-3-2018
1. Related Data science challenges to Digital Health trends
2. Designing an infrastructure to support secure learning from distributed health data repositories, for personalized health advice
3. Supporting patients with rare diseases with patient driven research and the generation of new hypotheses based on patient experiences.
Presented online as part of the NASM series in Advancing Drug Discovery see https://www.nationalacademies.org/event/40883_09-2023_advancing-drug-discovery-data-science-meets-drug-discovery
For a panel discussion at the Associate Research Libraries Spring meeting April 27, 2022, Montreal https://www.arl.org/schedule-for-spring-2022-association-meeting/
Frontiers of Computing at the Cellular and Molecular ScalesPhilip Bourne
3 basic points when establishing a new biomedical initiative. Presented at Frontiers of Computing in Health and Society, George Mason University, September 21, 2021.
We all have good and bad thoughts from time to time and situation to situation. We are bombarded daily with spiraling thoughts(both negative and positive) creating all-consuming feel , making us difficult to manage with associated suffering. Good thoughts are like our Mob Signal (Positive thought) amidst noise(negative thought) in the atmosphere. Negative thoughts like noise outweigh positive thoughts. These thoughts often create unwanted confusion, trouble, stress and frustration in our mind as well as chaos in our physical world. Negative thoughts are also known as “distorted thinking”.
How to Create Map Views in the Odoo 17 ERPCeline George
The map views are useful for providing a geographical representation of data. They allow users to visualize and analyze the data in a more intuitive manner.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
How to Split Bills in the Odoo 17 POS ModuleCeline George
Bills have a main role in point of sale procedure. It will help to track sales, handling payments and giving receipts to customers. Bill splitting also has an important role in POS. For example, If some friends come together for dinner and if they want to divide the bill then it is possible by POS bill splitting. This slide will show how to split bills in odoo 17 POS.
This is a presentation by Dada Robert in a Your Skill Boost masterclass organised by the Excellence Foundation for South Sudan (EFSS) on Saturday, the 25th and Sunday, the 26th of May 2024.
He discussed the concept of quality improvement, emphasizing its applicability to various aspects of life, including personal, project, and program improvements. He defined quality as doing the right thing at the right time in the right way to achieve the best possible results and discussed the concept of the "gap" between what we know and what we do, and how this gap represents the areas we need to improve. He explained the scientific approach to quality improvement, which involves systematic performance analysis, testing and learning, and implementing change ideas. He also highlighted the importance of client focus and a team approach to quality improvement.
The Indian economy is classified into different sectors to simplify the analysis and understanding of economic activities. For Class 10, it's essential to grasp the sectors of the Indian economy, understand their characteristics, and recognize their importance. This guide will provide detailed notes on the Sectors of the Indian Economy Class 10, using specific long-tail keywords to enhance comprehension.
For more information, visit-www.vavaclasses.com
Sectors of the Indian Economy - Class 10 Study Notes pdf
The Vision for Data @ the NIH
1. The Vision for Data @ the NIH
Philip E. Bourne, PhD, FACMI
Associate Director for Data Science
National Institutes of Health
Bio-IT World, Boston
April 21, 2015
2. Office of Biomedical
Data Science
Mission Statement
To foster an open ecosystem that
enables biomedical research to be
conducted as a digital enterprise that
enhances health, lengthens life and
reduces illness and disability & to
train the next generation of data
scientists
Goals expanded from recommendations in the June 2012 DIWG and
BRWWG reports.
4. 1. We are at a Point of Deception …
Evidence:
– Google car
– 3D printers
– Waze
– Robotics
– Sensors
From: The Second Machine Age: Work, Progress,
and Prosperity in a Time of Brilliant Technologies
by Erik Brynjolfsson & Andrew McAfee
5. 1. We Are At a Point of Deception
The 6D Exponential Framework
Digitization of Basic &
Clinical Research & EHR’s
Deception
We Are Here
Disruption
Demonetization
Dematerialization
Democratization
Open science
Patient centered health care
6. 2. Democratization Will Follow
The Story of Meredith
http://fora.tv/2012/04/20/Congress_Unplugged_
Phil_Bourne
Stephen Friend
9. “And that’s why we’re here today. Because something
called precision medicine … gives us one of the greatest
opportunities for new medical breakthroughs that we
have ever seen.”
President Barack Obama
January 30, 2015
10. Precision Medicine Initiative
Vision: Build a broad research program to encourage
creative approaches to precision medicine, test them
rigorously, and, ultimately, use them to build the
evidence base needed to guide clinical practice.
Near Term: apply the tenets of precision medicine to a
major health threat – cancer
Longer Term: generate the knowledge base necessary
to move precision medicine into virtually all areas of
health and disease
11. Precision Medicine Initiative
National Research Cohort
– >1 million U.S. volunteers
– Numerous existing cohorts (many funded by NIH)
– New volunteers
Participants will be centrally involved in design and
implementation of the cohort
They will be able to share genomic data, lifestyle
information, biological samples – all linked to their
electronic health records
12. National Research Cohort:
What Early Success Might Look Like
A real test of pharmacogenomics—right drug at the right
dose for the right patient
New therapeutic targets by identifying loss-of-function
mutations protective against common diseases
– PCSK9 for cardiovascular disease
– SLC30A8 for type 2 diabetes
Resilience – finding individuals who should be ill but aren’t
New ways to evaluate mHealth technologies for
prevention/management of chronic diseases
13. Precision Medicine:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits her
doctor
Now
– Though woman’s glucose control has been suboptimal,
doctor renews her prescription for drug often used for type 2
diabetes
– Continues to monitor blood glucose with fingersticks and
glucometer, despite dissatisfaction with these methods
14. Precision Medicine:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits her
doctor
Future: + 2 years
– Volunteers for new national research network
• Sample of her DNA, along with her health information,
sent to researchers for sequencing/analysis
• Can view her health/research data via smartphone
– Agrees to researchers’ request to track her glucose levels
via tiny implantable chip that sends wireless signals to her
watch, researchers’ computers
• Using these data, she changes diet,
medicine dose schedule
15. Other Diseases:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits her
doctor
Future: + 5 years
– Receives word from her doctor about a new drug based
upon improved molecular understanding of type 2 diabetes
– When she enters drug’s name into her smartphone’s Rx
app, her genomic data show she’ll metabolize the drug
slowly
• Her doctor alters the dose accordingly
16. Other Diseases:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits her
doctor
Future: + 10 years
– Celebrates her 60th birthday and reflects with her family
about how proud she is to be part of cohort study
– Her glucose levels remain well controlled; she’s suffered no
diabetes-related complications
– Her children decide to volunteer for cohort study
18. The BD2K Program is Central
to the Mission
Planned – Black; Available- Green
19. Elements of The Digital Enterprise
Communities Policies
Infrastructure
• Intersection:
• Sustainability
• Efficiency
• Collaboration
• Training
20. Elements of The Digital Enterprise
Communities Policies
Infrastructure
• Intersection:
• Sustainability
• Efficiency
• Collaboration
• Training
Virtuous
Research
Cycle
22. Big Data: The study involved
MRI images & GWAS data
from over 30,000 people
Collaboration: Data came
from many different sights
affiliated with the ENIGMA
consortium
Methods: To homogenize
data from different sites, the
group designed standardized
protocols for image analysis,
quality assessment, genetic
imputation, and association
Found five novel genetic
variants
Results provided insight into
the variability of brain
development, and may be
applied to study of
neuropsychiatric dysfunction
23. Community – Enigma, BD2K
Policy
– Improved consent methods
– Cloud accessibility for human subjects data
– Trusted partners
– Data sharing
Infrastructure
– Standards, compute resources, software
24. Communities: Thus Far
Visioning workshop convened 9/3/14
Launched BD2K ($32M)
– 12 Centers of data excellence
– Data Discovery Index Coordination Consortium
(DDICC)
– Training awards
First successful consortia meeting 11/3-4
Workshops to inform future funding
– Software indexing and discoverability
– Gaming
25. Communities: 2015 Activities
New FOAs with outreach to new
communities – math, stats, comp science etc.
Work with e.g GA4GH, RDA, FORCE11,
NDS ….
IDEAS lab with NSF
Competition with international funders
Software carpentry, hackathons, Pi Day
26. Communities: Questions?
Societies of the modern age?
How to enable these groups?
How to marry the funding of individuals with
the funding of communities?
27. Policies: Now & Forthcoming
Data Sharing
– Genomic data sharing announced
– Data sharing plans on all research awards
– Data sharing plan enforcement
• Machine readable plan
• Repository requirements to include grant numbers
http://www.nih.gov/news/health/aug2014/od-27.htm
28. Policies - Forthcoming
Data Citation
– Goal: legitimize data as a form of scholarship
– Process:
• Machine readable standard for data citation (done)
• Endorsement of data citation for inclusion in NIH bib
sketch, grants, reports, etc.
• Example formats for human readable data citations
• Slowly work into NLM/NCBI workflow
dbGaP in the cloud (done!)
31. The Commons: Compute Platforms
The Commons
Conceptual Framework
Public Cloud
Platforms
Super Computing
(HPC) Platforms
Other
Platforms ?
Google, AWS (Amazon)
Microsoft (Azure), IBM,
other?
In house compute
solutions
Private clouds, HPC
– Pharma
– The Broad
– Bionimbus
Traditionally low access
by NIH
33. Infrastructure: Standards
2013 Workshop on Frameworks for Community-
Based Standards
August 2014 Input on Information Resources for
Data-Related Standards Widely Used in Biomedical
Science – 30 responses
Feb 2015 Workshop Community-based Data and
Metadata Standards
Internal CDE Registry project
34. Elements of The Digital Enterprise
Communities Policies
Infrastructure
• Intersection:
• Sustainability
• Efficiency
• Collaboration
• Training
35. Elements of The Digital Enterprise
Communities Policies
Infrastructure
• Intersection:
• Sustainability
• Efficiency
• Collaboration
• Training
37. Problem: Lack of
Biomedical Data Science Specialists
BD2K T32/T15
BD2K K01
Career path workshops – eg AAU
Challenge
model of
funding
38. Problem: Limited Access to
Data Science Training
BD2K R25
Metadata
for training
materials
Community-sourced
cataloging and indexing
of training opportunities
Measure utility
NIH Workforce Development Center
RFA-ES-15-004
39. I not only use all the brains
I have, but all I can borrow.
– Woodrow Wilson
40. Associate Director for Data Science
Commons BD2K Efficiency
Sustainability Education Innovation Process
• Cloud – Data &
Compute
• Search
• Security
• Reproducibility
Standards
• App Store
• Coordinate
• Hands-on
• Syllabus
• MOOCs
• Community
• Centers
• Training Grants
• Catalogs
• Standards
• Analysis
• Data
Resource
Support
• Metrics
• Best
Practices
• Evaluation
• Portfolio
Analysis
The Biomedical Research Digital Enterprise
Partnerships
Collaboration
rogrammatic Theme
Deliverable
Example Features • IC’s
• Researchers
• Federal
Agencies
• International
Partners
• Computer
Scientists
Scientific Data Council External Advisory Board
Training
Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med 2(8): e124. doi:10.1371/journal.pmed.0020124
http://www.reuters.com/article/2012/03/28/us-science-cancer-idUSBRE82R12P20120328
Photos: FC tweet; RK screen grab
Draft vision statement taken from Collins/Varmus NEJM article, pg 1, colum2, last sentence
Images that reflect both cancer and cohort study
Images of people from Infographic (NOTE: Image is just a placeholder—Jill will tweak)
Detailed Notes:
National Research Cohort <<OR name of study>>
>1 million U.S. volunteers committed to participating in research
Will combine a number of existing cohorts
Will include Dept of Veterans Affairs Million Veteran Program—note Veteran is singular per http://www.research.va.gov/MVP/
Images--pharmacogenomics—helix on pill, bottle, prescription pad, Drug targets—DNA helix, whatever we might have used for PCSK9, unidentifiable pills/capsules; smart phone, the “fall prevention” watch from gerontology meeting, other mobile health images
Molecular structure structure of PCSK9 from NIBIB database.
Images: Overweight woman, someone testing blood sugar, pills for metformin or other diabetes drug?
Images: DNA sequencing, readouts, pills, maybe the DNA on pill bottle that we’ve used for pharmacogenomics.