Do You Play Word Games?

There is an astoundingly popular word game in which the player gets six tries to guess the word of the day, which has been pre-drawn from a list of five-letter words. The only skills one needs are the ability to recognize the alphabet and basic English-language spelling ability. My sisters and I play every day and compare how many tries it takes each of us to come up with the answer. It’s fun, challenging, and easy at the same time, and it gives us a quick way to share time together.

Today’s answer got me thinking (no spoiler alerts here!), what words describe NLM, its mission, and its impact? Let me share a few with you:

HEALTH

Health, that state of optimal well-being for all, is the North Star of all we do here at the National Institutes of Health. NIH’s motto is “Turning Discovery Into Health,” and NLM’s job is to turn information into discovery. The literature collected by NLM provides rich descriptions that help scientists and clinicians understand health and illness, discover new therapies, and relay patients’ experience. In fact, NLM has played an important role in almost every biomedical and clinical discovery of the past 50 years, each of which fosters the world’s understanding of health.

TRUST

The cornerstone of our great national library is the provision of high-quality, trusted resources to the scientific community and general public. We imbue trust in our resources by following important principles of libraries, including collecting widely from literature resources recognized for meeting standards of scientific communication. We provide documentation and publicly available standard practices and policies. Our work is overseen by an NLM Board of Regents as well as by NIH leadership. These checks and balances help us accommodate a body of scientific resources that are congruent with the scientific and clinical knowledge at the time they are collected and reflective of diverse viewpoints and knowledge maturation.

SERVE

NLM serves science and society by collecting, curating, and connecting all types of scientific communication artifacts and making these accessible to the public. Our biomedical literature resources are open to the world, presenting almost 35 million citations, close to 8.5 million machine- and human-readable full-text articles, and over 1,000 consumer-level health information topics. We provide specialized genomic data resources that help scientists discover the origins of life for many species. By linking the genomic data with the literature, NLM can help clinicians make decisions about how to treat complex illnesses that arise from genetic anomalies.

ALIGN

Biologists use laboratory procedures to distill the genetic material out of samples collected from humans, animals, and other types of matter like wastewater and then compare the sampled genetic material to other known records of genetic materials. Using this process, scientists align and compare one set of proteins gleaned from their experiments to others stored in our genomic repositories to detect genetic anomalies or determine if a discovered sequence is actually a new organism or a variant of a known species. Researchers “align” this newly acquired genetic structure with known structures. But we have millions of records of genetic samples, so this process can be time consuming. However, NLM has built the tool to blast through this alignment challenge!

BLAST

The Basic Local Alignment Search Tool (BLAST) is an algorithm and program developed by NLM staff at our National Center for Biotechnology Information that finds regions of similarities between genetic sequences. The program compares nucleotide or protein sequences to reference sequence databases and calculates the statistical significance of any matches. BLAST helps scientists understand functional and evolutionary relationships between sequences, and it can also be used to identify members of gene families.

It actually takes more than a few five-letter words to describe what NLM does and what it means to science and society. Nonetheless, it was quite fun to wordplay NLM!

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.

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