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.

A New Frontier: The Impact of a 1959 Board Meeting

Guest blog by Ken Koyle, MA, Deputy Chief of the History of Medicine Division (HMD) at the NIH National Library of Medicine. This post celebrates the important work performed by our archival professionals and the archival collections held by the library, from which the source material was drawn, as NLM celebrates International Archives Week #IAW2022.

In November 1959, when construction of NLM’s current building at NIH was still underway and digital computing was in its infancy, the NLM Board of Regents convened on the third floor of the Old Red Brick building for a demonstration of the indexing process. When Board Chairman Michael E. DeBakey, MD, asked if computer technology could be used in indexing, NLM Director Col. Frank B. Rogers, MD, was ready with an answer. Dr. Rogers, clearly interested in the emerging technology of automated data processing (ADP), described an article by Robert S. Ledley, DDS, in that month’s issue of Science and noted that Dr. Ledley was already contracted with NLM to report on using computers in indexing.

Black-and-white photo of Dr. Rogers leaning on a stack of books with bookshelves in background.
Dr. Frank Rogers at NLM, 1962.

Dr. Rogers was instrumental in NLM’s first explorations of automated processes and had a clear vision of the potential of electronic computing, including how it could improve efficiency at NLM, but his optimism was tempered by prescient realism. Dr. Rogers recognized—and conveyed to the Board—that the potential benefits of ADP would require a commensurate investment of staff time and labor. “We should not forget that ‘automatically’ means ‘because we told it to do so beforehand,’ and this in itself may turn out to be quite a trick.” Dr. Rogers made it clear that the computer age would bring a change in work, but not necessarily a reduction in work. “Remarkable as the capacity of the computer may be for sustaining a long sequence of operations, it is nevertheless ultimately only the end-phase of that still longer sequence which must include as a first phase the human labor of input.”

Acknowledging the upfront labor investment in ADP was only part of Dr. Rogers’ insight. He also explained that the human work was not only substantial and necessary, but also incredibly complex: “The instructions [for a computer] are a thousand times more detailed, for the simplest task, than those required to be given to the . . . clerk.” Unleashing computers’ potential would require staff to think in new ways, conceive new methods of organizing data, and embark on a new journey of continuous learning and professional development.

Black-and-white photo of members of the NLM Board of Regents posing for a photo. Four members sit behind a table stacked with papers. 13 members stand in the background. Dr. Rogers is featured on the far right.
Dr. Frank Rogers (far right) with the NLM Board of Regents meeting in the “Old Red Brick,” 1957.

Along with the challenges of training staff to work with ADP equipment came the interminable problem of cost. Much as today’s public institutions are grappling with the costs of cloud computing, digitization, and increasing storage requirements, Dr. Rogers had to balance the potential benefits with the considerable costs of computer equipment. The type of computer necessary to realize Dr. Rogers’ vision would cost about $1.5 million in 1960—98% of NLM’s total budget of $1,566,000.

Undeterred, Dr. Rogers found an answer to the funding problem by collaborating with another agency that would benefit from the increased processing speed of scientific literature that the envisioned system could provide: the National Heart Institute. They provided the initial funding, NLM did the legwork, and in 1963, the new MEDLARS computer went into service. Dr. Rogers had realized his vision of bringing automated indexing to NLM. As Surgeon General Luther Terry said at the Board meeting in April 1961, “If any institution ever stood on the borderland of a new frontier it is the National Library of Medicine.”

Computer operators working with the Honeywell 800 mainframe computer, originally acquired by NLM in the 1960s.

Dr. Rogers was very clear about the issues of cost, labor, and expectations in his 1960 presentation to the Board, including his overarching concern about balancing NLM’s core mission with these potential new directions:

[The] purpose of the Library is not to operate a particular machine system, however great an acrobatic achievement that might be in itself. It is not to publish and distribute a particular index in a particular way, however ingenious and successful that operation may be deemed to be. It is not even just to be a good library, however great and distinguished that library may be. It is rather, by virtue of being a library, to use every available bibliothecal means to promote awareness of and access to the subject content of recorded medical knowledge, to the end that the science of medicine will advance and prosper.

More than 60 years later, NLM still holds fast to that purpose. As stated in our statutory mission and reiterated in our current strategic plan, we are here “to assist the advancement of medical and related sciences and to aid in the dissemination and exchange of scientific and other information important to the progress of medicine and to the public health.” Our continued pioneering work in data science is just one way we accomplish that mission.

Mr. Koyle joined HMD in the NLM Division of Library Operations in 2012. Before joining NLM, Ken served as a medical evacuation helicopter pilot and a historian in the U.S. Army. He is the co-editor with Jeffrey Reznick of Images of America: U.S. National Library of Medicine, a collaborative work with HMD staff.

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