Data Management (RCR-Basic)

Content Author

• Julie Goldman, MLIS

Harvard Medical School, Countway Library

Introduction
The scientific method relies on hypothesis-driven experiments. Researchers collect, analyze, and
interpret data and communicate the results to others who can assess the quality of their work.
They build enough hypotheses consistent with the data that lead to support for a theory.

However, the real-world research process is rarely this clean and linear. Researchers need to
ensure that others can use their data through the complex journey of study design and data
collection, analysis, and visualization. One way to achieve this is to describe studies in enough
detail so that others may assess and replicate them.

Replicability refers to a researcher’s ability “to duplicate the results of a

prior study if the same procedures are followed but new data are
collected. That is, a failure to replicate a scientific finding is commonly
thought to occur when one study documents relations between two or
more variables and a subsequent attempt to implement the same
operations fails to yield the same relations with the new data” (Bollen et
al. 2015).

Research must be rigorous, innovative, ethical, organized, and reproducible. Organized practices,
workflows, and tools can help maximize insights and knowledge. Research data management
(RDM) is the process of providing the appropriate labeling, storage, and access to data.

Reproducibility refers to a researcher’s ability “to duplicate the results

of a prior study using the same materials and procedures as were used by
the original investigator. So, in an attempt to reproduce a published
statistical analysis, a second researcher might use the same raw data to
build the same analysis files and implement the same statistical analysis
to determine whether they yield the same results” (Bollen et al. 2015).

Each step of the research process should involve managing the research project data. This
module introduces relevant RDM concepts and provides relatable examples and case studies.
Learning Objectives

By the end of this module, you should be able to:

• Identify the steps, concepts, and importance of data management throughout a

research study.
• Describe institutional support services that can help manage your research data.
• Evaluate methodological, technological, and regulatory considerations that affect
data management practices.
• Explain the documentation needed to facilitate accessibility and reproducibility of
research findings.
• Recognize ethical and compliance issues relating to data ownership, sharing, and
protection.

The Data Lifecycle

It is crucial to think of research data as a scholarly resource. Data refer to entities used as
evidence of phenomena for research or scholarship (Borgman 2015). Data take many different
forms, and encoding occurs in many formats. Data are not raw or pure. The social, cultural, and
research context helps give meaning to data.

Scientific data are “the recorded factual material commonly accepted in

the scientific community as necessary to validate and replicate research
findings, regardless of whether the data are used to support scholarly
publications. Scientific data do not include laboratory notebooks,
preliminary analyses, completed case report forms, drafts of scientific
papers, plans for future research, peer reviews, communications with
colleagues, or physical objects, such as laboratory specimens” (NIH
2020).

The following table provides examples of data by discipline (Boyd 2019):

Sciences and Social Sciences Humanities

Engineering

• Observations • Observations • Primary

Evidence • Measurements • Measurements sources
• Trace
information
 • Instruments • Survey and • Art and
Source • Field interview artefacts
observations responses • Documents
• Field and
observations manuscripts

• Binary data • Audio or • Audio or

Format • Images video video
• Elements of recordings recordings
laboratory • Diaries • Books and
notebooks • Images papers
• Samples and • Spreadsheets • Images
specimens • Transcripts • Maps and
• Statistics geographic
• Tabular data information
systems
• Text files
• Three-
dimensional
models
Data are often presented in a tabular form, such as a spreadsheet. However, not all data are
numerical, and not all data are digital. From the examples in the previous table, research domains
will work with various types of data, including quantitative, qualitative, and physical.

Data are never neutral. Data are the product of decisions made throughout the processes of
collecting, processing, and analyzing phenomena; how information is visualized; and where and
how information can be accessed. These decisions result in datasets that reflect the perspectives
and biases of the people who produce and manage data (D’Ignazio and Klein 2020). As a
researcher, you must be aware of your biases to ensure research quality.

Data Management and Sharing

As research becomes more intensive and the amount of data produced grows, managing data is
more important than ever. Data management is “the process of validating, organizing, protecting,
maintaining, and processing scientific data to ensure the accessibility, reliability, and quality of
the scientific data” (NIH 2020). Carefully storing and documenting data allows more people to
use the data consistently and accurately in the future.

A discipline-specific set of knowledge, practices, and skills influences how researchers collect,
create, manipulate, analyze, and share data. Recently, there has been noticeable progress in open
data practices. A 2020 study found that 86.7 percent of researchers across disciplines were
willing to share data across a broad group of researchers (Tenopir et al. 2020). In the same study,
48.6 percent of researchers reported that their primary funding agency required a data
management plan (DMP). Therefore, policy implementation is one way for funders, publishers,
and organizations to encourage and require data sharing. For example, per the National Institutes
of Health (NIH) Data Management and Sharing (DMS) Policy, researchers must prospectively
plan how scientific data will be preserved and shared by submitting a data management and
sharing plan (DMSP) (NIH 2020). Many additional research funders have or are developing data
sharing policies (SPARC n.d.).

Data Lifecycle
While policies influence data practices, early and attentive management at each step of the data
lifecycle ensures the discoverability and longevity of the research. The data lifecycle represents
the stages that occur in the research process.

The data lifecycle provides “a high level overview of the stages involved
in successful management and preservation of data for use and reuse”
(DataONE n.d.). Multiple versions of a data lifecycle exist, with
differences attributable to variations in practices across domains or
communities.

The data lifecycle is also a tool to explore institutional landscapes for data policies and services.
Many experts across an institution can help with data management. For instance, you may need
to consult experts from administration, information technology, the library, and other offices to
help implement data management strategies.

The following visual shows the core stages of the data lifecycle. The expanded view on the right
includes a middle layer for processes and concepts integral to each stage and an outer layer for
potential data service providers at an academic institution. These varied stakeholders are
individuals and groups invested in specific lifecycle component activities.
Source: Biomedical Data Lifecycle by LMA Research Data Management Working Group is
licensed under CC BY-NC 4.0 and used with permission (Harvard n.d.a).

Research Planning
RDM is essential for responsible research, and planning should begin early. As mentioned
previously, policies are one way funders, publishers, and organizations encourage and require
data sharing.

The Health Insurance Portability and Accountability Act (HIPAA) sets standards for the privacy
and security of patient data. In 2003, the NIH instituted a data sharing plan for some proposals,
and in 2011, the National Science Foundation (NSF) was the first agency to require a DMP with
all grant submissions.

In 2013, the Executive Office of the President’s Office of Science and Technology Policy
(OSTP) issued a memo, which was a significant directive for the whole research enterprise. It
drove funding agencies and journals, such as journals published by the Public Library of Science
(PLOS), to require that data underlying published results be made publicly available. The NIH is
the latest agency to enact a more encompassing policy for research it funds.

The following graphic provides a timeline of recent developments related to data sharing:
Data Management Plan (DMP)
A goal without a plan is just a wish.”Antoine de Saint-Exupéry
A formal DMP is typically a two-page document that outlines how the research team will
manage data throughout a project. While a DMP may be required for a funding application, it
should accompany any research project as a living document that describes the entire project.
Researchers should frequently refer to and update their DMP.

A DMP “is a formal document that outlines what you will do with your
data during and after a research project. Most researchers collect data
with some form of plan in mind, but [it is] often inadequately
documented and incompletely thought out. Many data management
issues can be handled easily or avoided entirely by planning ahead. With
the right process and framework, it [does not] take too long and can pay
off enormously in the long run” (DMPTool n.d.).

DMPs come in many forms. However, they generally ask for the same information, are
appropriate for the data generated, and reflect the accepted practices and standards in the
proposed research area. The following table outlines the elements of an NIH and NSF data
management plan (NIH n.d.; NSF 2020):

1. Data Type: Provide types and amount of

NIH DMSP scientific data you expect to generate; data
Template that you will preserve and share; and
metadata, other relevant data, and associated
documentation.
2. Related Tools, Software, and/or Code: State
whether specialized tools, software, and/or
code are necessary to access or manipulate
shared data.
3. Standards: State what common data
standards you will apply to the data and
associated metadata.
4. Data Preservation, Access, and Associated
Timelines: State the repository where you
will archive data and metadata, how you will
make the data findable and identifiable, and
when and how long the data will be available.
 5. Access, Distribution, or Reuse
Considerations: Describe factors affecting
access, distribution, or reuse of data; whether
you will control access to scientific data; and
protections for privacy, rights, and
confidentiality.
6. Oversight of Data Management and
Sharing: Describe how you will manage and
monitor compliance.

1. Data and Materials Produced: Describe the

NSF Biological types of data, physical samples or collections,
Sciences DMP software, curriculum materials, and other
Template materials you expect to produce during the
project.
2. Standards, Formats, and
Metadata: Describe the standards you will
use for all anticipated data types, including
data or file format and metadata.
3. Roles and Responsibilities: Describe the
roles and responsibilities of all parties with
respect to data management.
4. Dissemination Methods: Describe the
dissemination methods that you will use to
make data and metadata available to others
during the award period.
5. Policies for Data Sharing and Public
Access: Describe the principal investigator’s
(PI) policies for data sharing, public access,
and reuse.
6. Archiving, Storage, and
Preservation: Where relevant, describe plans
for archiving data, samples, software, and
other research products.

Many services and resources are available to help write a DMP. Examples of important
stakeholders include:
The DMPTool (n.d.b) is a free web-based tool that provides basic templates to help researchers
construct DMPs for specific funding agencies. It also provides funder mandates, institutional
requirements, instructional materials to help build a DMP, and other resources to fulfill data
management requirements.

Case Study

Using Third-Party Data Sources

Active Research Phase

The active research phase involves working with data during the “collect and create” and
“analyze and collaborate” stages of the data lifecycle. Research projects generate, collect, or
acquire various types of data (DMPTool n.d.a). Although data come from many different
sources, they make up four main categories. The category or categories data come from will
affect a researcher’s data management choices throughout a project. The following table
provides a definition and examples for each category (DMPTool n.d.a):

Observatio Experiment Simulati Derived/

nal al on Compiled

Definiti Captured in Typically Machine- Generated

on real time, generated in generated from
typically the from test existing
outside the laboratory models. datasets.
laboratory. or under Likely to Reproduci
Usually controlled be ble but
irreplaceabl conditions. reproduci can be
e, and Often ble if the expensive
therefore, reproducible model and time
the most but can be and consumin
important expensive inputs are g.
to and time preserved
safeguard. consuming. .
 Examp Sensor Gene Climate Text and
les readings, sequences, and data
telemetry, chromatogra economic mining,
survey ms, and models. compiled
results, and magnetic database,
images. field and three-
readings. dimension
al models.

Data analysis is a process of inspecting, cleaning, transforming, and modeling data to discover
useful information, inform conclusions, and support decision-making (HHS ORI n.d.). A
researcher's choices while analyzing data can also contribute to effectively managing the data.

For example, multiple statistical packages are used in clinical research, including Stata, SPSS,
SAS, and R for statistical analysis of quantitative data; NVivo for qualitative data analysis;
OMERO for biological microscope images; and ArcGIS for analyzing geospatial data.
Researchers should consider data privacy, the location of data storage, licensing fees, common
uses, and availability when choosing the right tool. Many academic institutions offer licenses to
use these tools and direct support.

Data Organization
Data organization refers to the classification and organization of datasets to make them more
useful. Systematic file naming can contribute to project documentation, workflow organization,
and sharing.

Additionally, file versioning prevents file overwriting and loss. It is helpful to use versioning
software or append file names with version numbers to keep track of all the changes made during
data cleaning and analysis. Researchers should always keep a copy of the raw data in the event
they must reanalyze the data or satisfy regulatory requirements (Briney et al. 2020).

Case Study

File Organization
 Data Documentation
Documentation refers to information needed to use data. Researchers should consider any
documentation to be part of their data. Documentation is often called metadata or “data about
data” (DMPTool n.d.a).

“Metadata, the information we create, store, and share to describe things,

allows us to interact with these things to obtain the knowledge we need.
The classic definition is literal, based on the etymology of the word
itself—metadata is ‘data about data’” (Riley 2017).

Metadata enable researchers to understand, use, and share data in the present and future; help
other researchers discover, access, use, repurpose, and cite data; and facilitate long-term archival
and preservation of data (Harvard n.d.b). Many fields within the biomedical science community
are developing standards for what metadata to collect across different data types. However, it is a
best practice to consult community standards before collecting research data (Harvard n.d.b).
FAIRSharing.org provides more information on data standards, databases, and data policies
(Sansone et al. 2019).

Researchers can maintain documentation in various forms (Harvard n.d.b):

Additionally, there are many free tools to help researchers document data, including project and
citation management tools, electronic laboratory notebooks (ELNs), and protocol creation tools.

Although researchers often use paper laboratory notebooks to take notes, there are many benefits
to aligning digital research practices with digital documentation. The following table outlines the
potential benefits and challenges of using ELNs (Harvard n.d.c):

Benefits Challenges

• Support the findable, • Researchers need dedicated

accessible, interoperable, and tablets while in the
reusable (FAIR) principles, laboratory
which are recognized by the • Use of voice input or optical
research community character recognition plug-
• Enable oversight by PIs ins
• Support sharing of data and • Use of time-saving features
documentation with like linking experiments to
collaborators raw data files and results and
• Eliminate issues with poor automatic date and time
handwriting and damaged stamping to prove
paper notebooks provenance
• Can prevent data from being • Integration with other
lost when researchers leave research software to capture
• Generally provide excellent data and information
security and auditing features • Time and effort to set up
• Can allow for integration with
other applications, making the
research process and
publishing easier
Researchers should learn the data analysis standards in their field and common approaches for
maintaining research integrity. For example, when working with images, it is “crucial to always
use a copy of the original image” and export the data to standard formats (Cromey 2012).
Overwriting the original image when editing in a proprietary image editing software (for
example, Adobe Photoshop®) can change embedded metadata. This information may be needed
to perform re-analysis or ensure any manipulations performed were appropriate.

Data Storage
Each stage of the data lifecycle revolves around data storage. Proper storage throughout the data
lifecycle is imperative to ensure that data remain secure and adhere to recommended safety
protocols. Data safety protects the security of research participants and ensures the integrity of
research data. Regulated data that fall under HIPAA, the Family Educational Rights and Privacy
Act (FERPA), and other state and federal laws may have more stringent and defined institutional
compliance practices.

HIPAA “is a federal law that required the creation of national standards
to protect sensitive patient health information from being disclosed
without the patient’s consent or knowledge” (CDC 2022). FERPA is a
federal law that protects the privacy of student educational records (ED
2021).

Additionally, research collaboration may involve the sharing of research materials. Researchers
may be subject to the U.S. export control regulations and trade sanctions set forth by the U.S.
Department of Commerce, U.S. Department of State, and U.S. Department of the Treasury.

Different approaches may be necessary to uphold data confidentiality, integrity, and availability
depending on the data type and the technologies used to record the data. Research teams must
adhere to regulatory, organizational, and discipline-specific professional requirements. Training
is critical when complex data acquisition or storage instruments and methodologies are used. In
addition to training, it will be necessary to specify procedures for periodic testing of data
collection and storage devices and confirming data backups.
 Confidentiality Integrity Availability

Confidentiality Integrity refers to Availability

refers to preventing the responsibility refers to ensuring
inappropriate users to record, store, that all
or uses of data. and preserve data appropriate users
This is usually appropriately have access to
discussed within during the study’s data whenever
the context of entire lifecycle. It necessary. As
protecting the is essential to with integrity,
privacy of research perform data availability
subjects, which is a quality assurance concerns can
regulatory and checks to extend past the
ethical requirement maintain data formal end of the
if those subjects are fidelity, study to ensure
human beings. particularly access by others
Confidentiality also during data who wish to
involves protecting collection. replicate the
intellectual Identifying work.
property (IP) discrepancies in
related to the recorded data,
research. There missing data, or
may be regulations sources of error
prohibiting the improves the
unauthorized accuracy of data
handling or analysis and the
disclosure of validity of
classified findings.
information or
materials.

Dissemination and Preservation

Although dissemination, sharing, and preservation of research results typically happen after
project completion, researchers should have a plan for when and how these activities will occur.
Data sharing is about making the underlying research results available to others for evaluation
and reuse.
 Data Sharing Requirements for Sensitive Research Data
Researchers must consider IP and national security when sharing sensitive research data. Grant
funding awards, especially from U.S. federal agencies, go to the organization, not the individual
researcher. As a result, agencies consider the data that a researcher creates using funding to be
“owned” by the organization where the researcher works.

Researchers should adhere to any laws and regulations regarding data security for specific data
types. For instance, state and federal laws protect personally identifiable data such as names and
social security numbers. It is important to de-identify sensitive data for public sharing to avoid a
breach of confidentiality.

Protected health information is health information that identifies the

individual or for which there is a reasonable basis to believe it can be
used to identify the individual. This includes “information, including
demographic data, which relates to: the individual’s past, present, or
future physical or mental health or condition; the provision of health care
to the individual; and the past, present, or future payment for the
provision of health care to the individual” (HHS 2022).

Researchers must also comply with Institutional Review Board and participant consent
stipulations. Informed consent is the consent that a participant, parent, or legal guardian gives to
participate in a study only after understanding the relevant facts and risks involved. For example,
researchers must secure consent from research participants if they want to provide data to a
journal or contribute data to a repository.

It is vital to consider data sharing on a spectrum when working with sensitive data (Goldman et
al. 2019):

Open Access Mediated Closed

Metadata are A description of Metadata are not

entirely the dataset is publicly available
discoverable published

Data are accessible Mediated access Data are not

and immediately to data via a data discoverable or
downloadable custodian available to third
parties

Preferred option Good option for Safest option for

for non-sensitive sensitive or highly sensitive
data from confidential data data
completed projects

It is essential to evaluate datasets for identifiable information prior to sharing. In addition,

researchers should de-identify sensitive data that are shared publicly. Another aspect that may
dictate the data-sharing level is the data use agreement.
 There are no restrictions on using de-identified health information
because it neither identifies nor provides a reasonable basis to identify an
individual (HHS 2022). However, de-identification processes are labor
and time intensive. Two methods for de-identification include (HHS
2022):

• “Expert determination” on statistically de-identified datasets: A

formal determination by a qualified statistician.
• “Safe harbor” anonymization level: The removal of specified
identifiers of the individual and the individual’s connections.

A data use agreement is a binding contract between organizations that

governs the transfer and use of data, promising specified safeguards for
the protected health information within the dataset (HHS 2018).

Data Access and Reuse

Data curation is a specific data management task that helps ensure the robust and appropriate
sharing of datasets. It involves processes such as adding metadata; depositing data into a
repository; validating file checksums and file fixity checks; and other tasks to organize, clean,
describe, enhance, store, and preserve data. All these activities enable data discovery, ensure
quality, add value, and allow for reuse over time.

Researchers can make data available under an appropriate license to promote sharing and
unlimited use of their data. Raw data are generally considered facts and cannot be copyrighted.
However, researchers can copyright or license data they gather uniquely and originally (such as
data in a database). Open Data Commons and Creative Commons offer various licenses that
represent the range of rights for the creator and licensee of the data (Harvard n.d.d):
A data repository is the most suitable venue to provide and maintain access to shared data. A
research data repository “can be described as a subtype of a sustainable information
infrastructure which provides long term storage and access to research data” (Kindling et al.
2017). The three major types of digital data repositories are institutional, disciplinary, and
generalist.

Ideally, scientific data should be shared and preserved through repositories rather than kept only
by the researcher or organization and provided on request. However, this is not always practical.
For example, American Indian and Alaska Native communities may wish to manage, preserve,
and share their data on their terms (NIH 2020). The use of a quality data repository generally
improves the FAIRness of the data (Wilkinson et al. 2016):

Many organizations have policies on whether to send research records to an archive or how to
destroy them when they are no longer required. Retention policies help researchers understand
how long they must keep their data to comply with the terms of their grant. These policies also
serve to support organizations or archives in identifying the data and records that they might
maintain permanently as part of the historical record of a discipline or organization or as IP.
Records to retain include the raw data integral to substantiating published research.

Case Study
 Sharing Data Internationally

Putting It Together and Wrap-Up

RDM is crucial for project success even after a research grant ends. A team member’s departure
from a project or an organization can negatively impact segments of the data lifecycle and hinder
data accessibility and findability. When employees leave, they take their skills and project
knowledge with them. Therefore, recording essential project-related information and datasets is
important to ensure future users’ success.

You can follow this ten-step process to ensure proper research data offboarding:

1 Create a descriptive knowledge transfer file with relevant

metadata about all data worked on and published

2 Determine the data retention requirements

3 Review and organize data in collaborative folders with

documentation so that colleagues can easily access and
understand them

4 Transfer file folders and webpage or website ownership, as

appropriate

5 Identify data for migration to long-term storage

6 Delete duplicate or dispensable data to help reduce laboratory

or departmental storage usage, as appropriate
 7 Review policies of confidentiality, data security, and IP

8 Identify publisher, funder, and/or institutional requirements

for data sharing

9 Identify the dataset(s) you should deposit and share in public

or non-public repositories

10 Ensure that you securely store sensitive data if transferring

data to another organization prior to your departure

Along the road to discovery, researchers must develop systematic data management plans and
processes to ensure the quality of the research. Research does not always proceed in a neat and
orderly fashion. Therefore, DMPs are always subject to change. A well-designed and maintained
DMP is a foundational element of a research project. It will help lead to successful conclusions
and allow additional researchers to continue building on the findings with available, well-
documented data and replicable procedures.

Some final tips to get started with data management include:

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