The end of April will mark four months—and ten application due dates—since the NIH’s Data Management and Sharing Policy (2023) went into effect. Judging by the application drafts that HSLS librarians have read, Pitt health sciences researchers are rising to the challenge and writing data management and sharing plans that demonstrate careful thought about how their research data will be organized, shared, and preserved.
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data-management
NIH Releases Public Access Plan for Public Comment
The National Institutes of Health (NIH) announced that the NIH Plan to Enhance Public Access to the Results of NIH-Supported Research (NIH’s Public Access Plan) is now available for public review and comment. NIH prepared this plan to accelerate access to the results of NIH-funded research and address the guidance issued last August by the White House Office of Science and Technology Policy (OSTP) on equitable public access to federally funded research results.
Celebrating Love Data Week 2023
February 13-17, 2023, is Love Data Week (LDW), an international event designed to raise awareness about research data management, sharing, preservation, and—most importantly—how we at the libraries can help you! To celebrate, a variety of workshops, presentations, and drop-in help sessions have been planned throughout February.
To tie in with the Pitt 2023 Year of Emotional Well-Being, many of the LDW presentations emphasize healthy learning and professional development. These sessions will help you learn to avoid getting hung up on producing the perfect code or plot, instead focusing on starting where you are and working with the tools available to you.
Featured Workshop: NIH DMS Catalog vs. Repository for Restricted Datasets
Join us for this online workshop:
Monday, February 13, 2023, 11 a.m.-noon
Love Data Week 2023 features this online workshop to help researchers who are preparing for the NIH’s Policy for Data Management and Sharing (DMS Policy).
New HSLS Guide for NIH Data Management and Sharing Policy
The National Institutes of Health’s new Policy for Data Management and Sharing (DMS Policy), which goes into effect January 25, 2023, will require NIH-funded researchers to submit a plan outlining how scientific data from their research will be managed and shared within their funding application. The policy includes an expectation that researchers will maximize their data sharing within ethical, legal, or technical constraints, and it explicitly encourages researchers to incorporate data sharing, via deposit into a public repository, into their standard research process.
To help University of Pittsburgh researchers comply with the new policy, HSLS Data Services has put together a new guide, with each topic of the guide organized into three sections:
- Learning content
- Videos (forthcoming) and slides
- Related resources, including official notices and guidance from the NIH
International Open Access Week, October 24-30: Think Globally, Learn Locally
Open access to scientific research made headlines this summer when the White House Office of Science and Technology Policy (OSTP) issued a new memo on August 25, 2022, with updated requirements for federally funded research, to make publications and results freely and immediately available. Learn more about open access for scientific publications, data, and software with classes at the Health Sciences Library System during International Open Access Week, a week of global advocacy for open access to research, happening from October 24 through 30.
Whether you’re new to open access or have specific questions, drop-in sessions are a great place to talk with HSLS specialists. Join Stephen Gabrielson, the library’s Scholarly Communication Librarian, for “Open Access Drop-In Session: How Does Open Access Publishing Work?” on Monday, October 24, from 11 a.m. to noon. Bring your questions about how to publish open-access articles, sources of funding for article processing fees (APCs), how to find reputable no-APC journals, and how to self-archive your manuscript in an open-access repository. HSLS also has a guide to scholarly communication and publishing, including open-access publishing, available all the time: Scholarly Communication and Publishing Guide.
HSLS Data Services
The success of a research project hinges on the quality of its data, and keeping clearly organized, well-documented data and analyses helps to ensure high data quality. The HSLS Data Services team can help you find, manage, publish, and share your data for any type of research project. We offer consultations, classes, and customized trainings in the following areas:
Research data management
Organizing files, writing documentation, and safely storing datasets are essential skills for managing data throughout the research lifecycle. We are available for personal consultations on research data management topics at any time, and offer workshops throughout the semester. In particular, we offer:
- One-hour Introduction to Research Data Management classes that are suitable for everyone, but may be especially helpful for new graduate students and project staff
- In-depth workshops on file-naming best practices, writing a data management plan for grant applications, and responsibly reusing data (or making your data available for reuse)
- One-on-one meetings on writing and implementing a data management and sharing plan (DMSP) for the NIH’s new data management and sharing policy that goes into effect in January 2023
Whole Genome Sequences from a Diverse Human Population Now Available Through the All of Us Research Hub
In March 2022, the All of Us Research Program announced the release of its initial genomic dataset: nearly 100,000 whole genome sequences and 165,000 genotyping arrays, with nearly 50% coming from people who self-identify with a racial or ethnic minority group.
In an announcement about the release of the genomic data, Kelsey Mayo, Ph.D., scientific portfolio and product manager at the Vanderbilt University Medical Center Data and Research Center, states:
“What’s going to grab researchers’ attention is the diversity of the cohort. Half of our cohort is non-European. More than 90% of participants in genome-wide association studies have been of European descent. There’s just a real absence of genetic data from African, Asian, and Latino people. All of Us participants are providing this important data that’s been missing in health research. So we are going to have that new genetic information that’s been missing.”
Plans for forthcoming releases include data from participants who self-identify as American Indian or Alaska Native, with resources to provide important context for researchers.
New NIH Website for Scientific Data Sharing
After a long development process, the NIH’s new Data Management and Sharing (DMS) Policy will go into effect on January 25, 2023. The key feature of the new policy is that all researchers applying to the NIH for funding will be required to submit a Data Management and Sharing Plan (or DMSP) with their funding proposal; previously, many centers and funding opportunities had required a similar data management plan, but the requirement was not universal. The new policy does not require that researchers share their data (either with other researchers or with the public) but does convey “an expectation that researchers will maximize appropriate data sharing when developing plans.”
With January 2023 fast approaching, many have asked for more specific guidance from the NIH. The NIH has recently launched the Scientific Data Sharing website with helpful notices that expand the DMS Policy, such as:
- Supplemental Information to the NIH Policy for Data Management and Sharing: Elements of an NIH Data Management and Sharing Plan
- Supplemental Information to the NIH Policy for Data Management and Sharing: Allowable Costs for Data Management and Sharing
- Supplemental Information to the NIH Policy for Data Management and Sharing: Selecting a Repository for Data Resulting from NIH-Supported Research
Pitt Resources for Bioinformatics Data Analysis: The Four ‘C’s
Does your research involve identifying correlations between gene sequences and diseases, predicting protein structures from amino acid sequences, transcriptomics, metabolomics, or any of the many other ‘omics? If so, then you have a lot of data that requires analysis: a process of inspecting, cleaning, transforming, and modeling data with the goal of discovering useful information, suggesting conclusions, and supporting decision making.
The “four ‘C’s” is shorthand to describe broad categories of options for analyzing bioinformatics data, including paying someone else to do it (Core labs), working with another researcher (Collaboration), and doing it yourself either by learning to program (Coding) or using out-of-the-box software (Commercially-licensed tools). The University of Pittsburgh provides numerous options in these four categories to help you with your data analysis needs.
Featured Workshops: Love Data Week
Love Data Week, February 14-18, 2022, is an international event designed to raise awareness about research data management, sharing, and preservation. To celebrate, HSLS will be hosting a variety of featured workshops*:
- Preparing for the New NIH Data Management & Sharing Plan: Session 1 — Elements, Costs, & Tools, Monday, February 14, 2022, noon-1 p.m.
- Publicly Available Social Justice Data, Tuesday, February 15, 2022, 8:30-10 a.m.
- Data Organization in Spreadsheets, Thursday, February 17, 2022, noon-1:30 p.m.
PubMed Central Article Datasets are Now Available in the Cloud
The National Library of Medicine (NLM) recently announced that two PubMed Central article datasets are openly available in the cloud. This news is especially of interest for those conducting research utilizing text mining methodology or other types of secondary analysis.
PubMed Central (PMC) is a free full-text archive of biomedical and life sciences journal literature from the U.S. National Institutes of Health’s National Library of Medicine (NIH/NLM). For nearly two decades NLM has supported the retrieval and download of machine-readable open access journal articles through the PMC Open Archives Initiative (PMC-OAI) and FTP (file transfer protocol). To enhance access, these datasets are now also available on the Amazon Web Services (AWS) Registry of Open Data as part of AWS’s Open Data Sponsorship Program (ODP). Benefits to working with the datasets in the cloud include access to uncompressed individual full-text article files in XML and plain text as well as faster download and transfer speeds.
In summary, PMC Article Datasets housed on AWS include:
- The PMC Open Access (OA) Subset: includes all articles and preprints in PMC with a machine-readable Creative Commons license that allows reuse (to date more than 3.4 million).
- The Author Manuscript Dataset: includes accepted author manuscripts collected under a funder policy in PMC and made available in machine-readable formats for text mining (to date more than 700,000).
Two New LabArchives Products for Pitt Researchers
The University of Pittsburgh has licensed a cloud-based Electronic Research Notebook, LabArchives, since 2016. LabArchives research notebooks assist with the organization and management of laboratory data, safely and conveniently across multiple platforms and devices. Whether managing a research lab as a principal investigator or reviewing students’ lab work as an instructor, LabArchives supports effective research data management plans and helps improve student learning. Pitt researchers seeking to make the transition from paper-based to electronic lab notebooks can watch YouTube videos, read our guide, or attend one of our training sessions.
LabArchives has expanded beyond electronic research notebooks for Research and Education to include two products that we are excited to announce are now available to researchers with a Pitt email address: Inventory and Scheduler.
LabArchives Inventory streamlines the organization, tracking, and ordering of lab inventory. Whether you need to order inventory from a vendor or manage your in-lab created materials, LabArchives Inventory provides a simple and customizable solution for your physical inventory management needs. Use Inventory to customize your inventory types and storage locations, add and manage lab inventory items, and then use the ordering options to request and receive materials. Continue reading
Take Your Data Practices from Good to Best with HSLS Data Services
The HSLS Data Services team is thrilled that Pitt has declared 2021-22 to be the Year of Data and Society, because for us, every day is a day for data. Whether you are embarking on your first research project or have dozens of completed studies under your belt, we are here to help you improve the efficiency and reliability of your data-handling workflows at every step in the research process. We offer consultations, classes, and customized trainings in the following areas:
Research data management
Organizing files, writing documentation, and safely storing datasets are key practices for working with data effectively. They are also required discussion items for data management plans, which will be mandated in all NIH grant applications after January 2023. (Read the official NIH notice.) We recommend our Introduction to Research Data Management workshops especially for new graduate students to set themselves up with good habits from the start, but in-depth consultations are available for any lab, research group, or individual. Continue reading