Informing Success from the Outside In: Introducing the NLM Board of Regents CGR Working Group

Guest post by Valerie Schneider, PhD, staff scientist at the National Library of Medicine (NLM) National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), and Kristi Holmes, PhD, Director of Galter Health Sciences Library & Learning Center and Professor of Preventive Medicine at Northwestern University Feinberg School of Medicine.

Last year, we described how NLM is developing the NIH Comparative Genomics Resource (CGR)—a project that offers content, tools, and interfaces for genomic data resources associated with eukaryotic research organisms—in two blog posts:

Eukaryote refers to any single-celled or multicellular organisms whose cell contains a distinct and membrane-bound nucleus. Since eukaryotes all likely evolved from the same common ancestry, studying them can grant us insight into how other eukaryotes—including those in humans—work and makes CGR and its resources that much more important to eukaryotic research.

CGR aims to:

  • Promote high-quality eukaryotic genomic data submission.
  • Enrich NLM’s genomic-related content with community-sourced content.
  • Facilitate comparative biological analyses.
  • Support the development of the next generation of scientists.

Since our last two posts, the team at NCBI has been hard at work making important technical and content updates to and socializing CGR’s suite of tools. For instance, they published new webpages that organize genome-related data by taxonomy, making it available for browsing and immediate download. They also created the ClusteredNR Database, a new database for the Basic Local Alignment Search Tool (BLAST), to provide results with greater taxonomic context for sequence searches, and incorporated new gene information from the Alliance of Genome Resources, an organization that unites data and information for model organisms’ unique aspects, into Gene. NCBI is also engaging with genomics communities to understand their needs and requirements for comparative genomics through the NLM Board of Regents Comparative Genomics Working Group.

The working group is lending their perspective and extensive expertise to the project, activities that are essential to CGR’s success and development. We have charged working group members with guiding the development of a new approach to scientific discovery that relies on genomic-related data from research organisms, helping project teams keep pace with changes in the field, and understanding the scientific community’s needs and expectations for key functionalities. To do this, working group members help NLM set development priorities such as exploring CGR’s integration with existing infrastructures and related workforce development opportunities.

Projects like CGR highlight how critical interdisciplinary collaboration is to modern research and how success requires community perspectives and involvement. Working group members will be sharing more information about this project at upcoming conferences and in biomedical literature, and our team at NCBI will also share events and resources through our NIH Comparative Genomics Resource website.

If you are a member of a model organism community, are working on emerging eukaryotic research models, or support eukaryotic genomic data—whether you are a researcher, educator, student, scholarly society member, librarian, data scientist, database resource manager, developer, epidemiologist, or other stakeholder in our progress—we encourage you to reach out and get involved. Here are a few suggestions:

  • Invite us to join you at a conference, teach a workshop, partner on a webinar, or discuss other ideas you may have to foster information sharing and feedback.
  • Use and share CGR’s suite of tools and share your feedback.
  • Be on the lookout for project updates and events on the CGR website or follow @NCBI on Twitter.

We’re always excited to get feedback through CGR listening sessions and user testing for tool and resource updates. Email cgr@nlm.nih.gov to learn all the ways you can participate.

Thank you to the members of the NLM Board of Regents CGR Working Group!

Alejandro Sanchez Alvarado, PhD

Executive Director and Chief Scientific Officer
Priscilla Wood Neaves Chair in the Biomedical Sciences
Stowers Institute for Medical for Medical Research

Hannah Carey, PhD
Professor, Department of Comparative Biosciences, School of Veterinary Medicine
University of Wisconsin-Madison

Wayne Frankel, PhD
Professor, Department of Genetics & Development
Director of Preclinical Models, Institute of Genomic Medicine
Columbia University Medical Center

Kristi L. Holmes, PhD (Chair)
Director, Galter Health Services Library & Learning Center
Professor of Preventive Medicine (Health & Biomedical Informatics)
Northwestern University Feinberg School of Medicine

Ani W. Manichaikul, PhD
Associate Professor, Center for Public Health Genomics
University of Virginia School of Medicine

Len Pennacchio, PhD
Senior Scientist
Lawrence Berkeley National Laboratory

Valerie Schneider, PhD (Executive Secretary)
Program Head, Sequence Enhancements, Tools and Delivery (SeqPlus)
HHS/NIH/NLM/NCBI

Kenneth Stuart, PhD
Professor, Center of Global Infectious Disease Research
Seattle Children’s Research Institute

Tandy Warnow, PhD
Grainger Distinguished Chair in Engineering
Associate Head of Computer Science
University of Illinois, Champaign-Urbana

Rick Woychik, PhD (NIH CGR Steering Committee Liaison)
Director, National Institute of Environmental Health Sciences (NIEHS) and the National Toxicology Program (NTP)

Cathy Wu, PhD
Unidel Edward G. Jefferson Chair in Engineering and Computer Science
Director, Center for Bioinformatics & Computational Biology
Director, Data Science Institute
University of Delaware

Dr. Schneider is the deputy director of Sequence Offerings and the head of the Sequence Plus program. In these roles, she coordinates efforts associated with the curation, enhancement, and organization of sequence data, as well as oversees tools and resources that enable the public to access, analyze, and visualize biomedical data. She also manages NCBI’s involvement in the Genome Reference Consortium, which is the international collaboration tasked with maintaining the value of the human reference genome assembly.

Dr. Holmes is dedicated to empowering discovery and equitable access to knowledge through the development of computational and social architectures to support these goals. She also serves on the leadership team of the Northwestern University Clinical and Translational Sciences Institute.

Bridging the Resource Divide for Artificial Intelligence Research

This blog post is by Lynne Parker, Director, National AI Initiative Office and was originally posted on the White House Office of Science and Technology Policy blog. The Office of Science and Technology Policy and the National Science Foundation are seeking comments on the initial findings and recommendations contained in the interim report of the National Artificial Intelligence Research Resource (NAIRR) Task Force (“Task Force”) and particularly on potential approaches to implement those recommendations. We encourage you to read the RFI and submit comments on Implementing Initial Findings and Recommendations of the National Artificial Intelligence Research Resource Task Force by June 30, 2022.

Artificial Intelligence (AI) is transforming our world. The field is an engine of innovation that is already driving scientific discovery, economic growth, and new jobs. AI is an integral component of solutions ranging from those that tackle routine daily tasks to societal-level challenges, while also giving rise to new challenges necessitating further study and action. Most Americans already interact with AI-based systems on a daily basis, such as those that help us find the best routes to work and school, select the items we buy, and ask our phones to remind us of upcoming appointments.

Once studied by few, AI courses are now among the most popular across America’s universities. AI-based companies are being founded and scaled at a rapid rate. Worldwide AI-related research publications and patent applications continue to climb. 

However, this growth in the importance of AI to our future and the size of the AI community obscures the reality that the pathways to participate in AI research and development (R&D) often remain limited to those with access to certain essential resources. Progress at the current frontiers of AI is often tied to the use of large volumes of advanced computational power and data, and access to those resources today is too often limited to large technology companies and well-resourced universities. Consequently, the breadth of ideas and perspectives incorporated into AI innovations can be limited and lead to the creation of systems that perpetuate biases and other systemic inequalities.

This growing resource divide has the potential to adversely skew our AI research ecosystem, and in the process, threaten our Nation’s ability to cultivate an AI research community and workforce that reflects America’s rich diversity – and harness AI in a manner that serves all Americans. To prevent unintended consequences or disparate impacts from the use of AI, it matters who is doing the AI research and development.

Established in June 2021 pursuant to the National AI Initiative Act of 2020, the National AI Research Resource (NAIRR) Task Force has been seeking to address this resource divide. As a Congressionally-chartered Federal advisory committee, the NAIRR Task Force has been developing a plan for the establishment of a National AI Research Resource that would democratize access to AI R&D for America’s researchers and students. The NAIRR is envisioned as a broadly available and federated collection of resources, including computational infrastructure, public- and private-sector data, and testbeds. These resources would be made easily accessible in a manner that protects privacy, with accompanying educational tools and user support to facilitate their use. An important element of the NAIRR will be the expertise to design, deploy, federate, and operate these resources.

Since its establishment, the Task Force has held 7 public meetings, engaged with 39 experts on a wide range of aspects related to the design of the NAIRR, and considered 84 responses from the public to a request for information (RFI). Materials from all public meetings and responses to the RFI can be found at www.AI.gov/nairrtf.

Today, as co-chair of the Task Force and as part of OSTP’s broader work to advance the responsible research, development, and use of AI, I am proud to announce the submission of the interim report of the NAIRR Task Force to the President and Congress. This report lays out a vision for how this national cyberinfrastructure could be structured, designed, operated, and governed to meet the needs of America’s research community. In the report, the Task Force presents an approach to establishing the NAIRR that builds on existing and future Federal investments; designs in protections for privacy, civil rights, and civil liberties; and promotes diversity and equitable access. It details how the NAIRR should support the full spectrum of AI research – from foundational to use-inspired to translational – by providing opportunities for students and researchers to access resources that would otherwise be out of their reach. The vision laid out in this interim report is the first step towards a more equitable future for AI R&D in America – a future where innovation can flourish and the promise of AI can be realized in a way that works for all Americans.

Going forward, the Task Force will develop a roadmap for achieving the vision defined in the interim report. This implementation roadmap is planned for release as the final report of the Task Force at the end of this year. To inform this work, we are asking for feedback from the public on the findings and recommendations presented in the interim report as well as how those recommendations could be effectively implemented. Public responses to this request for information will be accepted through June 30, 2022. In addition, OSTP and the National Science Foundation will host a public listening session on June 23 to provide additional means for public input. Please see here for more information on how to participate.

If successful, the NAIRR would transform the U.S. national AI research ecosystem by strengthening and democratizing foundational, use-inspired, and translational AI R&D in the United States. The interim report of the NAIRR Task Force being released today represents a first step towards this future, putting forward a vision for the NAIRR for public comment and feedback.

We Can’t Go It Alone!

In February, I received the Miles Conrad Award from the National Information Standards Organization (NISO). NISO espouses a wonderful vision: “. . . a world where all can benefit from the unfettered exchange of information.” As the Director of the National Library of Medicine (NLM), this is music to my ears.

Standards are essential to NLM’s mission! Standards bring structure to information, assure common understanding, and make the products of scientific efforts—including literature and data—easier to discover. NLM’s efforts are devoted to the creation, dissemination, and use of terminology and messaging standards. These efforts include attaching indexing terms to citations in PubMed, our biomedical literature database housing over 34 million citations; using reference models to describe genome sequences; and serving as the HHS repository for the clinical terminologies needed to support health care delivery. NLM improves health and accelerates biomedical discovery by advancing the availability and use of standards. Standards are dynamic tools that must capture the context of biomedicine and health care at a given moment yet reflect the scientific development and changes in community vernacular.

By their very nature, standards create consensus across two or more parties on how to properly name, structure, or label phenomena. No single entity can create a standard all by itself! Standards are effective because they shape the conversation between and among entities, achieving a common goal by drawing on a common representation.

NLM alone cannot create, promulgate, or enforce standards. We work in partnership with professional societies, standards development organizations, and other federal entities, including the Office of the National Coordinator for Health Information Technology, to foster interoperability of clinical data. We support the development and distribution of SNOMED CT (the Systematized Nomenclature of Medicine – Clinical Terms) and the specific extension of SNOMED in the United States. We developed the MeSH (Medical Subject Headings) thesaurus, a controlled vocabulary used to index articles in PubMed. We also support the development and distribution of LOINC (the Logical Observation Identifiers Names and Codes), a common language—that is, a set of identifiers names and codes—used to identify health measurements, observations, and documents. Finally, we maintain RxNorm, a normalized naming system for generic and branded drugs and their uses, to support message exchanges across pharmacy management and drug interaction software.

Partnerships help us create and deploy standard ways to make scientific literature discoverable and accessible. To this end, we were instrumental in the adoption of NISO’s JATS (Journal Article Tag Suite), an XML format for describing the content of published articles, which we encourage journals to use when submitting citations to PubMed so users can efficiently search the literature and articles as they are described. MeSH RDF (Resource Description Framework) is a linked data representation of the MeSH vocabulary on the web, and the BIBFRAME (Bibliographic Framework) Initiative—a data exchange format initiated by the Library of Congress—adds MeSH RDF URIs (Uniform Resource Identifiers) to link data that will support complete bibliographic descriptions and foster resource sharing across the web and through the networked world.

Standards provide the resources necessary to understand complex phenomena and share scientific insights. Leveraging partnerships in order to develop and deploy these standards both allows efficiencies and produces a more connected, interoperable, understandable world of knowledge. Given the speed at which biomedical knowledge is growing, leveraging these partnerships assures that the institutions charged with acquiring and disseminating all the knowledge relevant to biomedicine and health can successfully and effectively meet their missions.

Gearing Up for 2023 Part II: Implementing the NIH Data Management and Sharing Policy

This blog post is by Lyric Jorgenson, PhD, the Acting Director of the NIH Office of Science Policy. It was originally posted on May 12 on the NIH Office of Science Policy Under the Poliscope blog. We encourage you to read it and submit comments and feedback on the draft supplemental information to the NIH Policy for Data Management and Sharing: Protecting Privacy When Sharing Human Research Participant Data by June 27.

Sequels are all the rage these days.  I figure if Marvel can make endless “Avengers” movies, I could start making blog sequels.  Back in the beginning of the year, I wrote Part I of this blog series about how NIH is working to implement the new NIH Data Management and Sharing Policy (DMS Policy).  I mentioned at that time that additional resources were forthcoming.

I should note that when we started to receive comments on what was to become the NIH DMS Policy, one thing in particular stood out to us.  Many commentors told us it would be helpful to have clear information on how to protect the privacy and respect the autonomy of participants when sharing data.  Now, we all know that cliffhangers build anticipation, so without further delay, I want to share with you some of the tools NIH has been working on to answer that call.

First, if you have seen the Avengers movies, you likely will have noticed that they tend to introduce a new villain that the team needs to battle with either new tools (think of OSP with Thor’s Stormbreaker axe) or the help of new superheroes like Captain Marvel. While not exactly a new villain, the lack of consistent consent language to facilitate secondary research with data and biospecimens is certainly a challenge many of our stakeholders have raised and one that we thought we could help address.

NIH has a long history of developing consent language and, as such, our team worked across the agency – and with you! – to develop a new resource that shares best practices for developing informed consents to facilitate data/biospecimen storage and sharing for future use.  It also provides modifiable sample language that investigators and IRBs can use to assist in the clear communication of potential risks and benefits associated with data/biospecimen storage and sharing.  In developing this resource, we engaged with key federal partners, as well as scientific societies and associations.  Importantly, we also considered the 102 comments from stakeholders in response to a RFI that we issued in 2021.

As for our second resource, we are requesting public comment on protecting the privacy of research participants when data is shared. I think I need to be upfront and acknowledge that we have issued many of these types of requests over the last several months and NIH understands the effort that folks take to thoughtfully respond.  With that said, we think the research community will greatly benefit from this resource and we want to hear your thoughts on whether it hits the mark or needs adjustment.

When reviewing the document, please bear in mind that the main purpose is to provide researchers with information on:

  • Operational Principles for Protecting Participant Privacy when Sharing Scientific Data
  • Best Practices for Protecting Participant Privacy when Sharing Scientific Data
  • Points to Consider for Designating Scientific Data for Controlled Access

Comments on the draft will be accepted until June 27, 2022, and full information and how to submit a comment can be found here.

Finally, every sequel needs a twist ending! In November 2021, NIH published a request for comments on the future directions of the NIH Genomic Data Sharing Policy.  We are still reviewing the many points and perspectives that were raised, but while we consider next steps, the comments we received are now available on the OSP website.  Okay, so maybe that twist wasn’t as big as, say, Darth Vader revealing he is (spoiler alert) Luke’s father in The Empire Strikes Back, but it’s still pretty good for the science policy world.

With a little more than half a year left until the implementation date of the NIH DMS Policy, we will continue to provide updates and resources over the next several months.

Midnight in the Library

Right now, I am reading The Midnight Library by Matt Haig. It’s a fanciful story of a woman in limbo between life and death who finds herself in a magical library, and each book represents one of the lives she could have lived had she made even one tiny different decision. She then finds herself in many of these lives, experiencing what could have been.

This book got me thinking about how NLM helps people experience lives that could be. I see this on two levels:

The first is the scientific pathway: What if . . . ? What if we knew more about the interactions between evolutionary forces and molecular constraints (like the work of Aravind Iyer, PhD), or fully appreciated the potential of proteins for genome engineering (like the discoveries made by Eugene Koonin, PhD), or could envision how and why proteins fold or switch their folds (as explored by Lauren Porter, PhD), or had the power to enable machines to understand human thought (like the research from Dina Demner-Fushman, MD, PhD). In addition to the discoveries by our NLM intramural researchers, our vast literature and data repositories hold answers that could change lives: why some genetic structures lead to human characteristics, or why a certain biochemical compound helps prevent infection. We help scientists discover these pathways and connections by providing them with the tools to uncover what could be.

The second is how NLM helps people see their what if using the amazing richness of the resources that we make available through our collections. Our resources—which encompass clinical insights, medical information, care guidelines, and self-management—help clinicians determine how to care for people with complex diseases or diagnose an illness in a timely manner. Our repository of clinical information available through PubMed ensures that those in need can access well-reasoned, recognized guiding principles for their care, and our MedlinePlus web resource provides patients and their families and friends with reliable, up-to-date health information to support and encourage healthy behavioral changes.

As in The Midnight Library, books alone do not inspire discovery, guide clinical care, or inform self-management. In Haig’s novel, a fictional librarian who knows the collection shows the main character how to select books by carefully listening to her goals and needs. It is the main character’s engagement with the books that helps her explore the lives she could have lived. At NLM, we too have librarians—located in Bethesda, Maryland, and around the country through NLM’s Network of the National Library of Medicine—who organize the library’s collections and guide patrons toward the best choice of resources. Our resources must be findable, accessible, interoperable, reusable, and actionable! And then, the person—scientist, clinician, patient—must actively engage with the material.

As we approach the future of data-powered health, guided by the NLM Strategic Plan (2017-2027), we will fulfill our mission to collect biomedical literature, organize it, preserve it, and make it accessible to the world. As the knowledge of health and biomedicine continues to grow faster than we can process, we will turn our attention to applying emerging tools, including machine learning and artificial intelligence, to make it easier to find our materials and more efficient to examine them. Through our Extramural Programs, we will continue to stimulate new ways of presenting information to scientists, clinicians, patients, and the public so they can explore possible lives to be lived and test out their promise of better health for society. What lives can we help you explore?

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