NIH Strategic Plan For Data Science
NIH Strategic Plan For Data Science
NIH Strategic Plan For Data Science
Introduction
As articulated in the National Institutes of Health (NIH)-Wide Strategic Plan 1, our nation and the world
stand at a unique moment of opportunity in biomedical research, and data science is an integral
contributor. Understanding basic biological mechanisms through NIH-funded research depends upon
vast amounts of data and has propelled biomedicine into the sphere of “Big Data” along with other
sectors of the national and global economies. Reflecting today’s highly integrated biomedical research
landscape, NIH defines data science as “the interdisciplinary field of inquiry in which quantitative and
analytical approaches, processes, and systems are developed and used to extract knowledge and
insights from increasingly large and/or complex sets of data.”
NIH supports the generation and analysis of substantial quantities of biomedical research data (see, for
example, text box “Big Data from the Resolution Revolution 2”), including numerous data sets emanating
from fundamental research using model organisms (such as mice, fruit flies, and zebrafish), clinical
studies (including medical images), and
Big Data from the Resolution Revolution observational and epidemiological studies
One of the revolutionary advances in microscope, (including data from electronic medical records).
detectors, and algorithms, cryogenic electron By 2025, the total amount of genomics data alone
microscopy (cryoEM) has become one of the areas of
is expected to equal or exceed totals from the
science (along with astronomy, collider data, and
three other major producers of large amounts of
genomics) that have entered the Big Data arena,
data: astronomy, YouTube, and Twitter. 3 Indeed,
pushing hardware and software requirements to
unprecedented levels. Current cryoEM detector next-generation sequencing data, stored at the
systems are fast enough to collect movies instead of National Institutes of Health (NIH’s) National
single integrated images, and users now typically Center for Biotechnology Information (NCBI), has
acquire up to 2,000 movies in a single day. As is the been growing exponentially for many years and
case with astronomy, collider physics, and genomics, shows no signs of slowing (see Fig. 1, below).
scientists using cryoEM generate several terabytes of
data per day. The generation of most biomedical data is highly
distributed and is accomplished mainly by
individual scientists or relatively small groups of researchers. Moreover, data also exist in a wide variety
of formats, which complicates the ability of researchers to find and use biomedical research data
generated by others and creates the need for extensive data “cleaning.” According to a 2016 survey, data
1
NIH-Wide Strategic Plan Fiscal Years 2016-2020: Available at: https://www.nih.gov/sites/default/files/about-
nih/strategic-plan-fy2016-2020-508.pdf
2
Baldwin PR, Tan YZ, Eng ET, Rice WJ, et al. Big data in cryoEM: automated collection, processing and accessibility
of EM data. Curr Open Microbiology 2018;43:1–8.
3
Stephens, et al., Big Data: Astronomical or Genomical? PLOS Biology 2015 (July 7, 2015) Available at:
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002195
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scientists across a wide array of fields said they spend most of their work time (about 80 percent) doing
what they least like to do: collecting existing data sets and organizing data. 4 That leaves less than 20
percent of their time for creative tasks like mining data for patterns that lead to new research discoveries.
Advances in storage, communications, and processing have led to new research methods and tools that
were simply not possible just a decade ago. Machine learning, deep learning, artificial intelligence, and
virtual-reality technologies are examples of data-related innovations that may yield transformative
changes for biomedical research over the coming decade. The ability to experiment with new ways to
optimize technology-intensive research will inform decisions regarding
future policies, approaches, and business practices, and will allow NIH to Note: Please see Glossary
adopt more cost-effective ways to capture, access, sustain, and for definitions of terms
reuse high-value biomedical data resources in the future. To this end, NIH related to data science.
must weave its existing data-science efforts into the larger data ecosystem
and fully intends to take advantage of current and emerging data-management and technological
expertise, computational platforms, and tools available from the commercial sector through a variety of
innovative public-private partnerships.
4
CrowdFlower 2016 Data Science Report. Available at: http://visit.crowdflower.com/rs/416-ZBE-
142/images/CrowdFlower_DataScienceReport_2016.pdf
2
The fastest supercomputers in the world today perform a quadrillion (1015) calculations each second:
known as the petascale level. The next frontier is exascale computing (which is 1,000 times faster than
petascale, or a quintillion (1018) calculations each second). Reaching exascale-level computing is a
technical milestone that is expected to have profound impacts on everyday life. At the exascale level of
computing speed, supercomputers will be able to more realistically mimic the speed of life operating
inside the human body, enabling promising new avenues of pursuit for biomedical research that involves
clinical data. These data-intensive programs may well be among the earliest adopters and drivers of
exascale computing: They include the All of Us Research Program and the Cancer MoonshotSM
components of the Precision Medicine Initiative, the Human Connectome project, the Brain Research
through Advancing Innovative Neurotechnologies (BRAIN) initiative, and many others.
Throughout the research enterprise, NIH must continue to balance the need for maximizing
opportunities to advance biomedical research with responsible strategies for sustaining public trust,
participant safety, and data security. Proper handling of the vast domain of clinical data that is being
continually generated from a range of data producers is a challenge for NIH and the biomedical research
community, including the private sector. Patient-related data can arise from a wide array of sources,
including specialized research projects and trials; epidemiology; genomic analyses; clinical-care
processes; imaging assessments; environmental-exposure records; and a host of social indicators now
linked to health such as educational records, employment history, and genealogical records. NIH must
develop, promote, and practice robust and proactive information-security approaches to ensure
appropriate stewardship of patient data and to enable scientific advances stemming from authentic,
trusted data sources.
Data quality and integrity must be maintained at all stages of the research life cycle—from collection
through curation, use, dissemination, and retirement. It is essential that NIH implement comprehensive
security controls consistent with the risk of harm if data are breached or corrupted. NIH must also
continually revisit its approaches to keep pace with ever-increasing information security threats that
arise in the global information technology environment. This work must be done in close partnership
with private, public, and academic entities that have expertise in information security and related areas.
As an initial step to strengthen the NIH approach to data science, in 2014, the NIH Director created a
unique position, the Associate Director for Data Science, to lead NIH in advancing data science across
the Agency, and established the Big Data to Knowledge (BD2K) program. NIH’s past investment in the
BD2K software-development initiative launched in 2014 produced a number of tools and methods that
can now be refined and made available to help tackle a variety of challenges. These include data-
compression formats, suites of algorithms, web-based software, application-programming interfaces
(APIs), public databases, computational approaches, among others.
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In subsequent years, NIH's needs have evolved, and as such the agency has established a new position
to advance NIH data science across the extramural and intramural research communities. The inaugural
NIH Chief Data Strategist, in close collaboration with the NIH Scientific Data Council and NIH Data
Science Policy Council, will guide the development and implementation of NIH’s data-science activities
and provide leadership within the broader biomedical research data ecosystem. This new leadership
position will also forge partnerships outside NIH’s boundaries, including with other federal and
international funding agencies and with the private sector to ensure synergy and efficiency, and prevent
unnecessary duplication of efforts.
As a result of the rapid pace of change in biomedical research and information technology, several
pressing issues related to the data-resource ecosystem confront NIH and other components of the
biomedical research community, including:
• The growing costs of managing data could diminish NIH’s ability to enable scientists to generate
data for understanding biology and improving health.
• The current data-resource ecosystem tends to be “siloed” and is not optimally integrated or
interconnected.
• Important datasets exist in many different formats and are often not easily shared, findable, or
interoperable.
• Historically, NIH has often supported data resources using funding approaches designed for research
projects, which has led to a misalignment of objectives and review expectations.
• Funding for tool development and data resources has become entangled, making it difficult to
assess the utility of each independently and to optimize value and efficiency.
• There is currently no general system to transform, or harden, innovative algorithms and tools
created by academic scientists into enterprise-ready resources that meet industry standards of ease
of use and efficiency of operation.
As a public steward of taxpayer funds, NIH must think and plan carefully to ensure that its resources are
spent efficiently toward extracting the most benefit from its investments. Because of these issues, NIH
has adopted a unified vision, and a corporate strategy for attaining that vision, that will best serve the
biomedical research enterprise in the coming decades.
This document, the NIH Strategic Plan for Data Science describes NIH’s Overarching Goals, Strategic
Objectives, and Implementation Tactics for modernizing the NIH-funded biomedical data-resource
ecosystem. In establishing this plan, NIH addresses storing data efficiently and securely; making data
usable to as many people as possible (including researchers, institutions, and the public); developing a
research workforce poised to capitalize on advances in data science and information technology; and
setting policies for productive, efficient, secure, and ethical data use. As articulated herein, this strategic
plan commits to ensuring that all data-science activities and products supported by the agency adhere
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to the FAIR principles, meaning that data be Findable, Accessible, Interoperable, and Reusable (see text
box “What is FAIR?”). 5
As outlined in the five Overarching Goals and correspondent Strategic Objectives (Fig. 2), NIH’s strategic
approach will move toward a common architecture, infrastructure, and set of tools upon which
individual Institutes and Centers (ICs) and scientific communities will build and tailor for specific needs.
A Software as a Service (SaaS) framework, in which software licensing and delivery are provided and
hosted by centralized resources, will greatly facilitate access to, analysis and curation of, and sharing of
all NIH-funded data. Adhering to NIH’s data-science vision outlined herein, and compatible with the NIH
mission, the NIH Chief Data Strategist, in conjunction with the NIH Scientific Data Council and NIH Data
Science Policy Council, will serve as leads for implementing this strategic plan. Evaluation is a critical
component of stewardship of federal resources, and over the course of 2018, NIH will develop
performance measures and specific milestones that will be used to gauge the progress of this strategic
5
Wilkinson MD et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data.
2016;3:160018.
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plan and guide any necessary course corrections. Example metrics and milestones appear at the end of
each Goal section. These will be established in concert with the NIH Chief Data Strategist and NIH IC
leadership.
Cross-Cutting Themes
The Overarching Goals, Strategic Objectives, and Implementation Tactics outlined in this plan are highly
integrated. The central aim is to modernize the data-resource ecosystem to increase its utility for
researchers and other stakeholders, as well as to optimize its operational efficiency. The many
connections between infrastructure, resources, tools, workforce, and policies call us to articulate a
number of cross-cutting themes, presented below, that layer across the intentions and actions outlined
in this document.
• Support common infrastructure and architecture on which more specialized platforms can be built
and interconnected.
• Leverage commercial tools, technologies, services, and expertise; and adopt and adapt tools and
technologies from other fields for use in biomedical research.
• Enhance the nation’s biomedical data science research workforce through improved training
programs and novel partnerships.
• Enhance data sharing, access, and interoperability such that NIH-supported data resources are FAIR.
• Ensure information security of patient and participant data.
• Improve the ability to capture, curate, store, and analyze clinical data for biomedical research.
• Coordinate and collaborate with other federal, private and international funding agencies and
organizations to promote economies of scale and synergies and prevent unnecessary duplication.
Data science holds significant potential for accelerating the pace of biomedical research. To this end,
NIH will continue to leverage its roles as an influential convener and major funding agency to encourage
rapid, open sharing of data and greater harmonization of scientific efforts. Through implementing this
strategic plan, NIH will enhance the scientific community’s ability to address new challenges in
accessing, managing, analyzing, integrating, and making reusable the huge amounts of data being
generated by the biomedical research ecosystem.
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Overarching Goals, Strategic Objectives, and Implementation Tactics
Ensuring that the biomedical research data-resource ecosystem is FAIR (see text box) is a laudable but
complex goal to achieve on a large scale, especially given the international expanse of biomedical
research data resources and their use. NIH as the world’s largest funder of biomedical research can play
a leadership role by developing practical and effective policies and principles related to the storage, use,
and security of biomedical data. In this strategic plan, NIH articulates specific priorities that address
developing reliable, accessible, and appropriately secured modes of storage; transforming a fragmented
set of individual components into a coordinated, efficient, and optimally useful ecosystem; reducing
unnecessary redundancies and increasing synergies and economies of scale; and strengthening
coordination and interactions—both within NIH and between NIH and its stakeholder communities.
Paramount is the need to establish organizing principles and policies for an efficient yet nimble funding
model for data science infrastructure that serves the needs of NIH and its stakeholders.
GOAL 1
Support a Highly Efficient and Effective Biomedical Research Data Infrastructure
NIH ICs routinely support intramural and extramural research projects that generate tremendous
amounts of biomedical data. Regardless of format, all types of data require hardware, architecture, and
platforms to capture, organize, store, allow access to, and perform computations with it. As projects
mature, data have traditionally been stored and made available to the broader community via public
repositories or at data generators’ or data aggregators’ local institutions. This model has become
strained as the number of data-intensive projects—and the amount of data generated for each
project—continues to grow rapidly.
Large-scale cloud-computing platforms are shared environments for data storage, access, and
computing. They rely on using distributed data-storage resources for accessibility and economy of
scale—similar conceptually to storage and distribution of utilities like electricity and water. Cloud
environments thus have the potential to streamline NIH data use by allowing rapid and seamless access,
as well as to improve efficiencies by minimizing infrastructure and maintenance costs. NIH will leverage
what is available in the private sector, either through strategic partnerships or procurement, to create a
workable Platform as a Service (PaaS) environment. NIH will partner with cloud service providers for
cloud storage, computational, and related infrastructure services needed to facilitate the deposit,
storage, and access to large, high-value NIH data sets (see text box “Science in the Cloud: The NIH Data
Commons”). These negotiations may result in partnership agreements with top infrastructure providers
from U.S.-based companies whose focus includes support for research. Suitable cloud environments will
house diverse data types and high-value data sets created with public funds and ensure that they are
stable and secure, to protect against data compromise or loss and available for research use and reuse.
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NIH’s cloud marketplace initiative will be the first step in a phased operational framework that
establishes a SaaS paradigm for NIH and its stakeholders.
Implementation Tactics:
• Leverage existing federal, academic, and commercial computer systems for data storage and
analysis.
• Adopt and adapt emerging and specialized technologies (see text box “Graphical Processing Units”).
• Support technical and infrastructure needs for data security,
authorization of use, and unique identifiers to index and Graphical Processing Units
locate data. The workhorses of most computers are
central-processing units, or CPUs, which
perform computing functions as specified by
Objective 1-2 | Connect NIH Data Systems computer programs. Specialized versions of
these, called graphical processing units, or
More than 3,000 different groups and individuals submit data via GPUs, are dedicated exclusively to imagery, or
NCBI systems daily. Among these are genome sequences from graphics. These elements have driven the
humans and research organisms; gene-expression data; motion-picture and video-game industries,
chemical structures and properties, including safety and toxicity and, more recently, have been adapted for
data; information about clinical trials and their results; data on use in biomedical research with very large and
genotype-phenotype correlations; and others. Beyond NIH- complex data sets such as molecular, cellular,
funded scientists and research centers, many other individuals radiological, or clinical images.
and groups contribute data to the biomedical research data
ecosystem, including other federal agencies, publishers, state public-health laboratories, genetic-testing
laboratories, and biotech and pharmaceutical companies. NIH will develop strategies to link high-value
NIH data systems, building a framework to ensure they can be used together rather than existing as
isolated data silos (see text box, below, “Biomedical Data Translator”). A key goal is to promote
expanded data sharing to benefit not only biomedical researchers but also policymakers, funding
agencies, professional organizations, and the public.
Implementation Tactics:
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• Link the NIH Data Commons (see text box, above) and existing, widely-used NIH databases/data
repositories using NCBI as a coordinating hub.
• Ensure that new NIH data resources are connected to other NIH systems upon implementation.
• When appropriate, develop connections to non-NIH data resources.
Goal 1: Evaluation
For this Goal, “Support a Highly Efficient and Effective Biomedical Research Data Infrastructure,”
potential measures of progress include: quantity of cloud storage and computing used by NIH and by
NIH-funded researchers; unit costs for cloud storage and computing; number of technologies adapted
for use by NIH-funded resources; quantity of NIH data resources incorporated into the NIH Data
Commons; and quantity of NIH data resources linked together.
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GOAL 2
Promote Modernization of the Data-Resources Ecosystem
To promote modernization of the data-repository ecosystem, NIH will refocus its funding priorities on
the utility, user service, accessibility, and efficiency of operation of repositories (see Current Data
Science Challenges for NIH). Wherever possible, data repositories should be integrated and contain
harmonized data for all related organisms, systems, or conditions, allowing for seamless comparison. To
improve evaluation of data-repository utility, and allow those who run them to focus on the particular
goals they need to achieve to best support the research community and operate as efficiently as
possible, NIH will distinguish between databases and knowledgebases (see text box “Databases and
Knowledgebases: What’s the Difference?”) and will support each separately from one another as well as
from the development and dissemination of tools used to analyze data (see Goal 3 for NIH’s proposed
new strategies for tool development). Although a grey area does exist between databases and
knowledgebases, and some data types currently appropriate for a knowledgebase may eventually
harden and become core data more appropriate for a database, this distinction will allow improved
focus and coherence in the support and operation of modern data resources. Funding approaches used
for databases and knowledgebases will be appropriate for resources and focus on user service, utility,
Knowledgebases accumulate, organize, and link growing bodies of information related to core datasets. A
knowledgebase may contain information about expression patterns, splicing variants, localization, and protein-
protein interaction and pathway networks related to an organism or set of organisms. Knowledgebases typically
require significant curation beyond the quality assurance/quality control and annotation needed for databases.
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and operational efficiency rather than on research project goals. As such, NIH will establish procedures
and metrics to monitor data usage and impact—including usage patterns within individual datasets.
Implementation Tactics:
• Separate the support of databases and knowledgebases (see text box, above).
• Use appropriate and separate funding strategies, review criteria, and management for each
repository type.
• Dynamically measure data use, utility, and modification.
• Ensure privacy and security.
• Create unified, efficient, and secure authorization of access to sensitive data.
• Employ explicit evaluation, lifecycle, sustainability, and sunsetting expectations for data resources.
Currently, most data generated by biomedical researchers are small-scale datasets produced by
individual laboratories. In contrast, large, organized consortia, including various programs specific to NIH
ICs and the NIH Common Fund, generate large, high-value datasets that are relatively small in numbers
but used by thousands of researchers. Whereas these large datasets generally reside in dedicated data
resources, a current dilemma for NIH is determining how to store and make accessible all of the smaller
datasets from individual laboratories. NIH will create an environment in which individual laboratories
can link datasets to publications in the NCBI’s PubMed Central publication database. Part of that effort
includes development of the NIH Data Commons Pilot, the first trans-NIH effort to create a shared,
cloud-based environment for data storage, access and computation.
Implementation Tactics:
Objective 2-3 | Leverage Ongoing Initiatives to Better Integrate Clinical and Observational Data
into Biomedical Data Science
NIH has several large-scale, ongoing efforts that are building high-value resources that include clinical
and observational data from individual volunteers and patients (for one example, see text box, below,
“TB Portals”). These efforts also include the All of Us Research Program and Cancer MoonshotSM, the
National Heart, Lung and Blood Institute’s Trans-Omics for Precision Medicine (TOPMed) program, the
Environmental Influences on Child Health Outcomes (ECHO) program, and various datasets generated by
scientists conducting research in the NIH Clinical Center (see text box, below, “Big Data for Health”). NIH
will leverage these and other related initiatives to integrate the patient health data they contain into the
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biomedical data-science ecosystem in ways that maintain security and confidentiality and are consistent
with informed consent, applicable laws, and high standards for ethical conduct of research (see Clinical
Data and Information Security).
TB Portals
The National Institute of Allergy and Infectious Diseases Tuberculosis (TB) Portals Program is a multi-national
collaboration for data sharing and analysis to advance TB research. A consortium of clinicians and scientists from
countries with a heavy burden of TB, especially drug-resistant TB, work together with data scientists and information
technology professionals to collect multi-domain TB data and make it available to the clinical and research communities.
The Office of the National Coordinator for Health Information Technology (ONC), within the Department
of Health and Human Services, leads national health information technology efforts. ONC coordinates
nationwide efforts to implement and use the most advanced health information technology and the
electronic exchange of health information, enhancing the ability to extract and share data between
federal health agencies such as the Food and Drug Administration, the Centers for Disease Control, and
the Centers for Medicare and Medicaid Services. ONC’s interoperability initiatives are those that make
electronic medical records more accessible for research, and NIH continues to adopt these practices
such as standardizing terminology, or
vocabularies, for clinical care. The NIH Clinical Big Data for Health
Two signature NIH projects that aim to garner health insights from
Center has in place the Biomedical
human data are the All of Us Research Program and the Cancer
Translational Research Information System
Moonshot. The All of Us Research Program aims to gather data over
(BTRIS), which is a resource available to the
time from 1 million or more people living in the United States, with
NIH intramural community that brings the ultimate goal of accelerating research and improving health.
together clinical research data from the Scientists plan to use All of Us Research Program data to learn more
Clinical Center and other NIH ICs. BTRIS about how individual differences in lifestyle, environment, and
provides clinical investigators with access to biological makeup can influence health and disease. Participants in
identifiable data for subjects on their own the All of Us Research Program may be invited to use wearable
active protocols, while providing all NIH sensors that will provide real-time measurements of their health and
investigators with access to data without environmental exposures, significantly expanding this type of
personal identifiers across all research. The Cancer Moonshot aims to accelerate cancer research
to make more therapies available to more patients, while also
protocols. Additionally, NIH encourages
improving our ability to prevent cancer and detect it at an early
researchers to use common data elements, or
stage. Data-intensive strategies include mining past patient data to
CDEs, which helps improve accuracy, predict responses to standard treatments and future patient
consistency, and interoperability among data outcomes, developing a three-dimensional cancer atlas to view how
sets within various areas of health and human tumors change over time, and a Cancer Research Data
disease research. Commons.
Implementation Tactics:
• Create efficient linkages among NIH data resources that contain clinical and observational
information.
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• Develop and implement universal credentialing protocols and user authorization systems that work
across NIH data resources and platforms.
• Promote use of the NIH Common Data Elements Repository.
Goal 2: Evaluation
For this Goal, “Promote Modernization of the Data-Resources Ecosystem,” potential measures of
progress include: data resource use metrics (overall and individual datasets); quantity of databases and
knowledgebases supported using resource-based funding mechanisms; cost-efficiency improvements
over baseline (e.g., cost per unit of use by researchers, cost per amount of data stored, average cost per
resource) of NIH-supported data resources; quantity of datasets deposited (over baseline) and linked to
publications in PubMed Central; linkages between NIH clinical and observational data resources; and
usage of the NIH Common Data Elements Repository.
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GOAL 3
Support the Development and Dissemination of Advanced Data Management, Analytics, and
Visualization Tools
Extracting understanding from large-scale or complex biomedical research data requires algorithms,
software, models, statistics, visualization tools, and other advanced approaches such as machine
learning, deep learning, and artificial intelligence (see text box “Thinking Machines 6”). Accomplishing
NIH’s goal of optimizing the biomedical data-science
Thinking Machines ecosystem requires prioritizing development and
Artificial intelligence, machine learning, and deep dissemination of accessible and efficient methods for
learning are computer algorithms that change as advanced data management, analysis, and
they are exposed to more data. Many are adept at visualization. To make the best tools available to the
recognizing objects in images, thus enabling
research community, NIH will leverage existing
machines to find patterns in data in ways that are
vibrant tool-sharing systems to help establish a more
not only cost-effective but also potentially beyond
human abilities. “Centaur radiologists,” hybrids of
competitive “marketplace” for tool developers and
human and computer expertise, will likely offer the providers than currently exists. By separating the
opportunity to interpret data from a range of evaluation and funding for tool development and
sources, including electronic medical records. Such dissemination from support for databases and
hybrid person-machine interpretations will likely knowledgebases, innovative new tools and methods
have a formative role in customizing care to should rapidly overtake and supplant older, obsolete
individual patients. ones. The goal of creating a more competitive
marketplace, in which open-source programs,
workflows, and other applications can be provided directly to users, could also allow direct linkages to
key data resources for real-time data analysis.
Objective 3-1 | Support Useful, Generalizable, and Accessible Tools and Workflows
Historically, because data resources have generally been funded through NIH research grants, applicants
have emphasized development of new tools in order to meet innovation expectations associated with
conducting research. This strategy can shift the focus of data resources away from their core function of
providing reliable and efficient access to high-quality data. In addition, coupling review and funding of
data resources to tool development can inhibit the type of open competition among developers that
allows support of the most innovative and useful tools (see Current Data Science Challenges for NIH). To
address these concerns, NIH will evaluate and fund tool development separately from support of
databases and knowledgebases. NIH will also promote the establishment of environments in which high-
quality, open-source data management, analytics, and visualization tools can be obtained and used
directly with data in the NIH Data Commons and/or other cloud environments. A key step will be
leveraging through partnerships or procurement expertise in systems integration/engineering to refine
and harden tools from academia to improve software design, usability, performance, and efficiency.
6
Dreyer KJ, Geis JR. When Machines Think: Radiology's Next Frontier. Radiology. 2017 Dec;285(3):713-718. doi:
10.1148/radiol.2017171183.
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Implementation Tactics:
• Separate support for tools development from support for databases and knowledgebases.
• Use appropriate funding mechanism, scientific review, and management for tool development.
• Establish partnerships to allow systems integrators/engineers from the private sector to refine and
optimize prototype tools developed in academia to make them efficient, cost-effective, and widely
useful for biomedical research.
• Employ a range of incentives to promote data-science and tool innovation including “hackathons,”
prizes, public-private partnerships, and other approaches.
An important opportunity and challenge is to adopt for use in biomedical research tools that have been
developed by fields outside of the biomedical sciences. For example, the same software used by NASA
scientists to determine the depths of lakes from space is being tested for use in medical-image analysis
for mammography, X Rays, computerized tomography (CT) and magnetic resonance imaging (MRI)
scans, as well as for ultrasound measurements. 7 Specialized tools developed for one subfield of
biomedical research might also be adopted for different purposes by researchers in other areas.
It will also be important to develop and adopt better tools for collecting and efficiently assimilating data
from disparate and dynamic sources that combine to inform us about the health of individuals and
populations. Novel data-science algorithms will likely create new knowledge and innovative solutions
relevant to health disparities and disease prevention. New approaches and tools have the potential to
transform data combined from various structured and unstructured sources into actionable information
that can be used to identify needs, provide services, and predict and prevent poor outcomes in
vulnerable populations. Toward identifying and stratifying risk, employing standardized data formats
and vocabularies should advance our understanding of relationships between demographic information,
social determinants of health, and health outcomes. One especially ripe opportunity for use in
community-based research is broader use of rapidly evolving mobile-device technologies and
information-sharing platforms. These resources, such as wearable devices, can capture a wide variety of
health and lifestyle-related data from individual volunteers that could help transform our understanding
of both normal human biology and disease states.
7
NASA Technology Transfer Program: Hierarchical Image Segmentation: Available at
https://technology.nasa.gov//t2media/tops/pdf/GSC-TOPS-14.pdf
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Finally, there is a critical need for better methods to mine the wealth of data available in electronic
medical records (see text box “Linking Genomic Data to Health: eMERGE”). These records present great
opportunities for advancing medical research and improving human health—particularly in the area of
precision medicine—but they also pose tremendous challenges (see “Clinical Data and Information
Security”). For example, patient confidentiality must be assured, and the level of access granted by each
individual to researchers has to be obtained,
Linking Genomic Data to Health: eMERGE
eMERGE is an NIH-funded national network organized and
recorded, and obeyed. Equally challenging is the
funded by the National Human Genome Research Institute that fact that electronic medical records are
combines DNA biorepositories with electronic medical record controlled by thousands of different hospitals
systems for large scale, high-throughput genetic research in and other organizations using dozens of
support of implementing genomic medicine. Begun in 2007, the different commercial computer platforms that
project merges genetic data from patients with their electronic do not currently share a uniform language or
medical records and facilitates sharing of the data for data standards. Because of these challenges,
biomedical research. eMERGE currently involves 14 sites across NIH will support additional research to find
the country that collect, store, and share patient data for
better ways to allow clinical data to be used
biomedical discovery aiming to improve patient care.
securely, ethically, and legally, to advance
medicine. NIH will also work with other federal
and state agencies, private healthcare and insurance providers, and patient advocacy groups to find
more efficient paths to realize the promise of electronic medical records and other clinical data for
medical research.
Implementation Tactics:
• Adopt and adapt emerging and specialized methods, tools, software, and workflows.
• Promote development and adoption of better mobile-device and data-interface tools.
• Support research to develop improved methods for using electronic medical records and other
clinical data securely and ethically for medical research.
Data that is not easily located is likely to be underused and of little value to the broader research
community. NIH has invested in developing resources, such as the Data Discovery Index that is part of
the NIH Data Commons pilot, to enable data reuse. Such a resource will exceed a mere cataloging
function and will also contain platforms and tools by which biomedical researchers can find and reuse
data and that will support data-citation metrics. NIH will continue to invest in development of improved
approaches for making data findable and accessible. For example, the NIH Data Commons pilot is
creating search and analysis workspaces that support a broad range of authenticated users, and where
users with all levels of expertise can access and interact with data and tools. Collaboration will be
integral to this approach, which, in addition to continued research and development, must involve a
community-driven process for identifying and implementing optimal standards to improve indexing,
understandability, reuse, and citation of datasets.
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Implementation Tactics:
• Promote community development and adoption of uniform standards for data indexing, citation,
and modification-tracking (provenance).
Goal 3: Evaluation
For this Goal, “Support the Development and Dissemination of Advanced Data Management, Analytics,
and Visualization Tools,” potential measures of progress include: quantity of new software tools
developed; citations of tool use; downloads of tools from tool repositories; and quantity of tools
adapted from other fields for use in biomedical research.
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GOAL 4
Enhance Workforce Development for Biomedical Data Science
Innovative contributions to biology from computer science, mathematics, statistics, and other
quantitative fields have facilitated the shift in biomedicine described throughout this document. NIH
recognizes that data scientists perform far more than a support function, as data science has evolved to
be an investigative domain in its own right. While NIH has supported quantitative training at various
levels along the biomedical career path, more needs to be done to facilitate familiarity and expertise
with data-science approaches and effective and secure use of various types of biomedical research data.
There is also a need to grow and diversify the pipeline of researchers developing new tools and analytic
methods for broad use by the biomedical research community. Finally, data-science approaches will be
essential for NIH to achieve the stewardship goals outlined in the NIH-wide strategic plan and are likely
to facilitate the agency’s ability to monitor demographic trends among its workforce and thus address
diversity gaps (see text box, below, “Data Science and Diversity”).
Given the importance of data science for biomedical research, NIH needs an internal workforce that is
increasingly skilled in this area. This includes ensuring that NIH program and review staff who administer
and manage grants and coordinate the evaluation
of applications have sufficient experience with and Data Science and Diversity
knowledge of data science. To begin to address this Data-driven approaches offer opportunities to address gaps in
scientific workforce diversity, by observing and influencing
need, NIH will develop training programs for its
system-wide patterns. NIH has applied this strategy to
staff to improve their knowledge and skills in areas
understand factors driving recruitment and retention of
related to data science. In addition, NIH will recruit undergraduate students from underrepresented groups as well
a cohort of data scientists and others with as to study various approaches to mentoring. Additional
expertise in areas such as project management, systems-based approaches to workforce modeling, including at
systems engineering, and computer science from the faculty level at NIH-funded institutions, offer promise for
the private sector and academia for short-term (1- understanding effects on diversity in various contexts.
to 3-year) national service sabbaticals. These “NIH
Data Fellows” will be embedded within a range of high-profile, transformative NIH projects such as All of
Us, the Cancer MoonshotSM and the BRAIN initiative and will serve to provide innovation and expertise
not readily available within the federal government.
Implementation Tactics:
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Modern biomedical research is becoming increasingly quantitative and it is essential that the next
generation of researchers be equipped with the skills needed to take advantage of the growing promise
of data science for advancing human health. NIH will work to ensure that NIH-funded training and
fellowship programs emphasize teaching of quantitative and computational skills and integrate training
in data-science approaches throughout their curricula and during mentored research. In addition, NIH
will partner with institutions to engage librarians and information specialists in finding new paths in
areas such as library science that have the potential to enrich the data-science ecosystem for biomedical
research.
Implementation Tactics:
• Enhance quantitative and computational training for graduate students and postdoctoral fellows.
• Build on diversity-enhancing efforts in data science, such as the NIH BD2K Diversity Initiative. 8
• Engage librarians and information specialists in developing data-science solutions and programs.
• Employ data-driven methods to monitor workforce diversity.
As a field, data science crosses boundaries between research and practice, as well as between science
and policy. NIH will promote knowledge exchange and development of best practices for the collection,
organization, preservation, and dissemination of information resources across communities. Part of this
effort is nurturing cultural change, emphasizing the role of data science in discovery and health, and
enabling citizen scientists access to data without compromising its privacy or security. NIH recognizes its
role in the larger data-science ecosystem and that NIH-generated biomedical data are used often by the
private sector, clinicians, and other public groups. As part of the BD2K effort, NIH encouraged
development of new or significantly adapted interactive digital media that engages the public, experts
or non-experts, in performing some aspect of biomedical research via crowdsourcing. NIH will work to
find additional ways to engage the public and healthcare providers in making use of biomedical data and
data-science tools. Doing so will help to expand the biomedical “sandbox” to researchers without access
to large-scale computational resources, such as non-research academic organizations, community
colleges, and citizen scientists.
Implementation Tactics:
• Give citizen scientists access to appropriate data, tools, and educational resources (see text box
“Citizen Science”).
• Develop materials to train healthcare providers in data science-related clinical applications.
8
Canner JE, McEligot AJ, Pérez ME, Qian L, Zhang X. Enhancing Diversity in Biomedical Data Science. Ethn Dis.
2017;27(2):107-116.
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Citizen Science
Citizen science aims to bring science and science policy processes to the public, to ensure that science is responsive to
public concerns and needs and to harness an additional resource to capture data and innovation in a wide variety of
fields. One example is EyeWire, an online resource launched in 2012 that challenges players to map the three-
dimensional structure of neurons in the retina of a mouse using real electron-microscopy images. About 70,000 players
from more than 130 countries play this scientific “game,” which is helping researchers discover how neurons connect
to process visual information.
Goal 4: Evaluation
For this Goal, “Enhance Workforce Development for Biomedical Data Science,” potential measures of
progress include: quantity of new data science-related training programs for NIH staff and participation
in these programs; number of NIH Data Fellows recruited; number of NIH-funded training programs that
increase requirements for quantitative and computational skills development; and demographic,
geographic, and disciplinary diversity of NIH-funded quantitative scientists.
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GOAL 5
Enact Appropriate Policies to Promote Stewardship and Sustainability
Creating and maintaining an efficient and effective biomedical data-science ecosystem requires policies
and practices appropriate for optimal governance, financial management, evaluation, and sustainable
stewardship of resources. Because cultural issues are central to implementing policies, appropriate
reward, review, and expectation systems are central to making data FAIR and for incentivizing
researchers to share their data and analysis tools widely for reuse by others. To ensure researchers
collecting data understand and comply with data-security and confidentiality standards, it will be
important for NIH to collaborate with the research community on strategies to guide general practice in
data security and privacy matters and to collaborate with industry leaders who set standards in the
information-security arena.
Currently, most biomedical data do not adhere to FAIR principles and thus are difficult to find and
access. Moreover, complex or integrated analysis requires that data are interoperable and reusable
across multiple domains with high fidelity. Thus, through appropriate policies and practices and as a
core data-management activity, NIH will strive to ensure that all data in NIH-supported data resources
are FAIR. The NIH Data Commons Pilot will be a starting point toward accomplishing this objective.
While freely sharing high-value data is a critical goal for advancing research, NIH must ensure that its
policies are achievable and sustainable and do not impose unnecessary burdens or untenable
expectations on grantee institutions. Therefore, policies must reflect the data use and evaluation
metrics and methods that will be established in Objective 2-1 to guide what data need to be made
accessible and when they should be moved to less-accessible but less-expensive archive storage or
retired altogether. NIH will also promote community-guided development of model open data-use
licenses that will facilitate data sharing while simultaneously allowing protection of confidentiality and
intellectual property. In addition, the NIH Data Commons pilot is establishing ways to use controlled-
access data through appropriate authentication and protocols.
Implementation Tactics:
The rapidly growing amount of data generated by the biomedical research enterprise creates an urgent
need for developing clear guidelines for what data must be stored and shared, where and in what form
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it must be stored, as well as practical solutions for sustaining valuable data resources and determining
priorities for data-resource funding. In addition, to produce the most scientific value for taxpayers’
investments and to provide researchers with the best access to data resources possible, NIH must work
with the community to improve the efficiency of operation of these resources and, wherever possible,
create synergies and economies of scale. Toward achieving these goals, NIH will collaborate with its
stakeholders—including academia, other U.S. and international funding agencies, journals, and the
private sector—to establish a wide range of metrics to dynamically measure data use, utility, and
modification, as well as measures of the operational efficiency of the resources themselves. Creating
incentives and expectations for depositing FAIR-compliant data in NIH-funded repositories, data
commons, or other NIH data systems, will enhance data sharing and reuse and allow NIH to accurately
assess data usage and lifecycles. This information will be essential for making informed decisions about
priorities for data-resource support. In addition, NIH will engage the broader data-science community in
testing the utility of the NIH Data Commons as it is developed. As it refines these systems, NIH will seek
input from entities with expertise in research ethics, privacy regulations and statutes, and data security
to ensure NIH-supported data resources maintain research-participant confidentiality.
Implementation Tactics:
• Develop standard use, utility, and efficiency metrics and review expectations for data resources and
tools.
• Establish sustainability models for data resources.
• Develop a reward and expectation system for investigators to make data FAIR and for ensuring
open-source data-analysis tools are available.
Goal 5: Evaluation
For this Goal, “Enact Appropriate Policies to Promote Stewardship and Sustainability,” potential
measures of progress include: establishment and use of open-data licenses; development and
performance of metrics to assess data resource use, utility and efficiency of operation; and usage of
data-security protection guidelines by NIH-funded researchers using clinical data.
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Conclusion
Accessible, well-organized, secure, and efficiently operated data resources are critical enablers of
modern scientific inquiry. With publication of the NIH Strategic Plan for Data Science, NIH aims to
maximize the value of data generated through NIH-funded efforts to enable biomedical discovery and
innovation. Doing so is critical for keeping the United States at the forefront of biomedical research,
ensuring continued advances toward improving the nation’s health.
This strategic plan is highly interconnected but rests upon five pillars, its Overarching Goals:
As articulated in this plan, NIH considers essential the need to coordinate and collaborate with other
federal, private and international agencies and organizations in the data-resource ecosystem to
promote economies of scale and synergies and prevent unnecessary duplication. NIH's goal is to
maximize the utility of the data resource ecosystem for researchers and to ensure optimal scientific
return on investment for taxpayers. A central facet of the plan is engagement of industry partners who
have expertise in key areas related to information technology, complementing the research strengths of
NIH and the academic community, and helping ensure that we achieve the plan’s Goals and Objectives
in an efficient manner. As outlined above, NIH's vision is to move toward a common framework upon
which individual ICs and scientific fields will build and adapt. The inaugural NIH Chief Data Strategist, in
conjunction with the NIH Scientific Data Council and NIH Data Science Policy Council, will lead efforts to
manage this new system and will take the lead on implementing this strategic plan, in close
collaboration with NIH IC leadership and staff.
NIH recognizes fully that technological advancement and unprecedented growth in biomedical data
have created great opportunities, but they have also introduced great challenges for protecting the
privacy and security of patient and other research data. NIH must work with its stakeholders and experts
in the private sector and other federal agencies to promote and practice robust and proactive
information-security procedures to ensure appropriate stewardship of patient and research-participant
data while at the same time enabling scientific and medical advances. Because the data-science
ecosystem is evolving rapidly, this strategic plan is intended to be nimble enough to make necessary
course corrections through an ongoing process of performance evaluation, needs assessment, and
research and technology landscape surveys. NIH’s corporate strategy for positioning itself within a highly
dynamic biomedical data-science enterprise will poise the agency to maximize the utility of data science
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for discovery while minimizing duplication of effort and ensuring that its research investments are cost-
effective for American taxpayers.
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Glossary
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Hardening—process of optimizing a tool or algorithm to industry standards to ensure efficiency, ease of
use, security, and utility.
Hardware—collection of physical parts of a computer system
Indexing—methods to allow data finding and retrieving
Interoperability—in computer systems, the ability to exchange and make use of information from
various sources and of different types
Intramural—research or other activities conducted by, or in support of, NIH employees on its Bethesda,
Maryland, campus or at one of the other NIH satellite campuses across the country.
Knowledgebase—virtual resource that accumulates, organizes, and links growing bodies of information
related to core datasets
Machine learning—a field of computer science that gives computers the ability to learn without being
explicitly programmed by humans
Metadata—data that describe other data. Examples include title, abstract, author, and keywords
(publications); organization and relationships of digital materials; and file types or modification dates.
NIH IC—NIH Institute or Center
'Omics —collective characterization and measurement of pools of biological molecules that translate
into the structure, function, and dynamics of an organism or organisms. Examples include genomics,
proteomics, metabolomics, and others.
Petascale computing—a computer system capable performing one quadrillion (1015) calculations per
second. It is currently used in weather and climate simulation, nuclear simulations, cosmology, quantum
chemistry, lower-level organism brain simulation, and fusion science.
Phenotype—the set of observable characteristics of an individual resulting from the interaction of its
genotype with the environment
Platform—group of technologies (software and hardware) upon which other applications, processes, or
technologies are developed
Platform as a Service (PaaS)—a type of cloud computing that allows users to develop, run, and manage
applications without the complexity of building and maintaining an overarching infrastructure
Provenance—timeline of ownership, location, and modification
Retirement (of data)—the practice of shutting down redundant or obsolete business applications while
retaining access to the historical data
Software—programs and other operating information used by a computer
Software as a Service (SaaS)—software licensing and delivery model in which software is licensed on a
subscription basis and is centrally hosted
System integrator/system engineer—individual who refines and hardens tools from academia to
improve user design, authentication and testing, and optimize productivity, efficiency, and
outcomes/performance
Unique identifiers—an alphanumeric string (such as 1a2b3c) used to uniquely identify an object or
entity on the internet
Universal—for biomedical data, usable in research studies regardless of the specific disease or condition
of interest (compare to domain-specific)
Wearables—devices that can be worn by a consumer that collect data to track health
Workflow—defined series of tasks for processing data
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