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:
- A Journey to Spur Innovation and Discovery
- Using Comparative Genomics to Advance Scientific Discoveries
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 firstname.lastname@example.org 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
Lawrence Berkeley National Laboratory
Valerie Schneider, PhD (Executive Secretary)
Program Head, Sequence Enhancements, Tools and Delivery (SeqPlus)
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.
Professor, Preventive Medicine, Northwestern University Feinberg School of Medicine
Dr. Holmes is the director of the Galter Health Sciences Library & Learning Center and Professor of Preventive Medicine (Health & Biomedical Informatics) and Medical Education at Northwestern University Feinberg School of Medicine. Her work 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.