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The newsletter of NNLM Pacific Southwest Region
Updated: 2 hours 15 min ago

NLM Establishes a Five-Year Development Plan for MEDLINE!

Tue, 2018-07-24 14:38

In December 2016, the National Library of Medicine established the MeSH (Medical Subject Heading) Indexing Assessment Project to evaluate the impact on users of assigning MeSH terms to MEDLINE citations. The project findings confirmed the value of MEDLINE indexing and the value of applying selected non-subject metadata to MEDLINE citations. In response to the findings and as part of its Strategic Plan, NLM created the five-year development plan, MEDLINE 2022. A Working Group, comprised of members from across all NLM departments, was charged with the plan’s implementation.

MEDLINE 2022 has eight specific goals describing challenges that must be addressed to maintain the usefulness of MEDLINE as a tool for discovering and analyzing the biomedical research literature:

  1. Investigate the use of authoritative vocabularies in MEDLINE indexing in addition to, or as a partial replacement for MeSH, for some topics or types of metadata, for example, chemical names.
  2. Implement a range of indexing methods to ensure the timely assignment of MeSH or terms from other approved vocabularies to MEDLINE citations.
  3. Support the discoverability of content.
  4. Support the pharmacology and toxicology research communities by sustaining and improving the discoverability of chemical information in MEDLINE/PubMed citations.
  5. Support NIH and other funding organizations by ensuring the discoverability of funding information in MEDLINE/PubMed.
  6. Support the genetics research community by adding relevant gene information to MEDLINE/PubMed citations.
  7. Support the NLM pivot to data science as described in the new NLM Strategic Plan.
  8. Update MEDLINE journal requirements to support these goals and strategies.

The goals of MEDLINE 2022 align with the goals of the NLM Strategic Plan, most importantly Goal 1: Accelerate discovery and advance health by providing the tools for data-driven research. MEDLINE has provided access to the biomedical literature for more than 45 years, evolving as publishing and information retrieval have evolved. The MEDLINE 2022 project aims to ensure that MEDLINE continues to evolve to meet the needs of users in an age of data-driven discovery. NLM will keep its many stakeholders informed of progress with the implementation of MEDLINE 2022 by publishing future NLM Technical Bulletin articles with details about different aspects of this project.

Categories: Data Science

All of Us: Imagining the Future; Pondering the Past – Health Information for Public Librarians Symposium, Atlanta 2018

Mon, 2018-07-23 16:24

by Peg Eby-Jager, A.M.L.S.
Librarian | Consumer Health Information Specialist

“All is flux; nothing is stationary.”
Heraclitus (c.535 – c.475 BC)

“Just when I discovered the meaning of life, they changed it.”
George Carlin (1937 – 2008)

CHIS Quest
When I found out about the Public Librarians Symposium, late and serendipitously, I’d been scouting for continuing education credits in light of a fast approaching deadline for renewing my Consumer Health Information Specialization (CHIS) certificate; I was a surprised to learn that travel awards were available to public librarians as well. Great news! My thoughts then quickly shifted back to the sobering present with the realization that I’d need to be in Atlanta in about three weeks. Quick work, collegiality, and good fortune were needed, and thankfully everything fell into place. I registered for the meeting, booked travel and accommodations, and leveraged a change in my work schedule. Being awarded a travel grant was, as they say, just gravy, and I was looking forward to attending the Symposium, earning CHIS credits, connecting with colleagues, and learning about the All of Us Research Program – a precision medicine initiative that I knew next to nothing about.

The Symposium

“This year’s conference also offers something special: a symposium dedicated to health information for public librarians…designed to help public librarians develop skills in providing consumer health information to enhance health and well-being and to encourage and expand health literacy throughout the communities.”

From NLM Director’s blog, Musings from the Mezzanine

All of Us

“The All of Us Research Program, is a historic effort to gather data from one million or more people living in the United States to accelerate research and improve health. By taking into account individual differences in lifestyle, environment, and biology, researchers will uncover paths toward delivering precision medicine.”


I was in the go-mode for Atlanta. But first, gentle reader, a brief detour through patient data history.

Interest in Consumer Health
The one constant among my professional interests since earning a library degree in 1985 is my abiding interest in consumer health information. And during those thirty-plus years, there have been seismic changes in virtually every aspect of health care – patient records included. My first job as a freshly minted librarian was with the Commission on Professional and Hospital Activities (CPHA), a think tank, whose primary data asset comprised anonymous, patient-level records supplied by over 25% of North American acute care facilities. That was a huge data set, to be sure. However, the limitations of those records compared to what I would be hearing about at the Symposium makes all the difference between planting a single seed and the bounty reaped from a worldwide harvest.

Among CPHA’s many study reports and products was an annual series of books that listed average length of hospital stay, organized by diagnoses and stratified by a few additional criteria. It would never make the NY Times best-seller list, but it was CPHA’s hot product, bringing in significant income that fueled research. And CPHA was pushing the envelope, as their public health researchers worked to develop new analytical models yielding a more precise picture of how precious medical resources were being utilized.

Finding ways to accurately measure utilization of medical resources was The Holy Grail. But in the 1980s, CPHA’s anonymous hospital discharge records offered only a static slice of patient data and were not linked to any longitudinal cohort. Further, patient medical records were typically handwritten by physicians and stored in paper files in their offices. The necessary technology and infrastructure did not yet exist.

book titled Length of Stay showing the front cover and the book opened to pages with lots of data

In 1985, the availability of patient data from longitudinal studies was greatly limited. “Length of Stay” data were derived from anonymous hospital discharge records and were not linked to patient medical records. (Photo credit: Peg Eby-Jager)

To be clear: back in the day, CPHA’s published studies and data products were a big deal. It wasn’t unusual for a client to refer to us as “the only game in town.” But the All of Us Program, as I would soon learn at the Symposium, intends to change the game entirely. Building and sustaining the largest, most diverse, markedly innovative, longitudinal patient data set is the goal. “Change” hardly describes what is in store; a better term would be “reinvention.”

And what better place than Atlanta, a city that has reinvented itself time after time, to begin learning about All of Us?

MLA & M.J.T.
Day One of the Symposium began with a beautiful buffet breakfast offering a range of choices from bacon-and-eggs to copious fresh fruits and yogurt. My body clock was still set on PDT, but a second cup of coffee fueled a speedy circumnavigation of the Hyatt’s Regency Ballroom. Tables were quickly filling, the Symposium would soon kick off, and I didn’t see a single familiar face.

Mary-Kate Finnegan presenting a poster at a symposium

Mary-Kate Finnegan from University of the Pacific in Stockton presenting a poster at the symposium

Pretty quickly, I was invited to join a table near the podium. A friendly person called me over, and introduced herself as “M.J. Tooey,” whose name that I recognized as a past president of MLA. After a warm welcome, introductions, and a little get-acquainted chat with everyone at the table, M.J. clued me in on what to expect at the kickoff.

I had closely followed MLA’s pre-conference planning instructions, and I’d studied the presentations and posters that would be available to Symposium attendees. I knew which presentations I’d attend and which posters I wanted to see. I’d familiarized myself with the Hyatt map, and I knew where to be and when to be there. I definitely had a plan. But M.J. Tooey made sure that I knew that Patti Brennan, the current director of the National Library of Medicine, would soon be joining our table prior to giving her keynote speech. And that was just so very thoughtful and considerate of her. Moments like this leave lasting impressions.

Data-Driven Discovery
Patti Brennan’s keynote focused on “data-powered health” and the critical role of the All of Us Research Program’s one million-plus cohort to the future of precision medicine. Beginning with a quick overview of NLM’s strategic plan, she invited us to consider that every research article begets its own data set, and then to imagine the biomedical discovery implications of harnessing vast quantities of data that are made widely available. She talked about the need to find new ways to get information into the hands of laypeople and how those data could be used by citizen scientists. Dr. Brennan compellingly argued that massive data resources offer a “foundational substrate” for knowledge and discovery, and that the All of Us data set will be a prime factor in data-driven biomedical discovery.

Dr. Brennan is focused on a future in which myriad data-rich resources are widely available. She spoke about radical new possibilities for understanding health rather than focusing primarily on the study of disease states. But a diverse data set is key to success, and building a representationally diverse cohort of over one million people contributing data and biosamples will not be easy. The massive scale of the project is simply mind-boggling.


Patti Brennan writes regularly about the value of that ambitiously imagined, data-driven future on her blog, NLM Musings from the Mezzanine. “[W]e released NLM’s strategic plan, A Platform for Biomedical Discovery and Data-Powered Health. Concurrently the National Institutes of Health announced a draft Strategic Plan for Data Science.”

Precision Medicine

“[P]recision medicine is ‘an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.’ …It is in contrast to a one-size-fits-all approach, in which disease treatment and prevention strategies are developed for the average person, with less consideration for the differences between individuals.”

From Genetics Home Reference


All of Us and Public Librarians
Public librarians may play a role in helping to raise awareness of the All of Us Research Program, and Dr. Brennan raised the question of how that role could be fostered. Toward the end of her talk, she posed the question of what can be done to assist public libraries, and I’ll be interested to see what sort of outreach takes place. Public librarians, however, do not need to wait for direction. MLA’s Consumer Health Information Specialization (CHIS) offers an excellent starting point.

I truly enjoyed the CHIS courses I took, and after completing Level I requirements, I pushed a little harder and earned a Level II certificate. I learned a lot, and I’d encourage my public library colleagues – not just librarians, but paraprofessionals as well – to take an introductory course. Building on my public service skills and more effectively helping patrons achieve greater health literacy is the greatest benefit of CHIS coursework. There is no charge for the courses; you can pace yourself. And there’s no pressure to complete work on a certificate. The bottom line is that the benefits are well worth the effort, for us and for our patrons!


“By earning your CHIS, you acquire skills and knowledge needed to become a confident, expert provider of health information to your community.” Learn more about CHIS at the Medical Library Association website. NNLM offers a sponsorship which covers the CHIS application fee for library personnel who take the required number of courses.

CHIS Courses

  • Beyond an Apple a Day: Providing Consumer Health Information at Your Library
  • Stand Up for Health: Health and Wellness Services for Your Community

Find more CHIS opportunities by browsing the list of all NNLM classes.

Categories: Data Science

NIH Releases Inaugural Strategic Plan for Data Science!

Mon, 2018-06-04 18:04

Storing, managing, standardizing and publishing the vast amounts of data produced by biomedical research is a critical mission for the National Institutes of Health. In support of this effort, NIH has just released its first Strategic Plan for Data Science that provides a roadmap for modernizing the NIH-funded biomedical data science ecosystem. Over the course of the next year, NIH will begin implementing its strategy, with some elements of the plan already underway. NIH will continue to seek community input during the implementation phase.

Accessible, well-organized, secure, and efficiently operated data resources are critical to modern scientific inquiry. By maximizing the value of data generated through NIH-funded efforts, the pace of biomedical discoveries and medical breakthroughs for better health outcomes can be substantially accelerated. To keep pace with rapid changes in biomedical data science, NIH will work to address the:

  • findability, interconnectivity, and interoperability of NIH-funded biomedical data sets and resources
  • integration of existing data management tools and development of new ones
  • universalizing innovative algorithms and tools created by academic scientists into enterprise-ready resources that meet industry standards of ease of use and efficiency of operation
  • growing costs of data management

To advance NIH data science across the extramural and intramural research communities, the agency will hire a Chief Data Strategist. This management function will guide the development and implementation of NIH’s data science activities and provide leadership within the broader biomedical research data ecosystem. Jon R. Lorsch, Ph.D., director of the National Institute of General Medical Sciences, is currently available to comment on this strategic plan.

Categories: Data Science