Watch All About It!

Guest post by Bart Trawick, PhD, director of the Customer Services Division at the National Library of Medicine’s National Center for Biotechnology Information, National Institutes of Health.

NLM’s PubMed is the most heavily used biomedical literature citation database in the world. PubMed provides free access to more than 30 million citations and is searched by more than 2.5 million users daily. It is a critical resource for helping researchers, health care professionals, students, and the public share information and learn more about the latest developments in life sciences.

Earlier this year, NLM launched an updated version of PubMed with an enhanced design that provides advanced technology to improve the user experience on mobile as well as desktop devices. This modern interface includes updated web elements for easier navigation and enhanced search results, including previews with highlighted text snippets that can help you scan your results.

Instead of telling you more about these new features and how they work, I invite you to check out a few of them in this video.

Click to watch and learn more about a few of PubMed’s exciting features.

Video Transcript (below):

PubMed is the most heavily used biomedical citation database in the world, guiding over two and a half million users per day to the latest advances in life sciences research. We’re constantly improving PubMed to meet the needs of its diverse user base and to take advantage of ever-evolving internet technologies and standards.

The latest version of PubMed, released in May 2020, is the product of hundreds of hours of stakeholder engagement and research undertaken to give you a better experience.

And it’s not the first time we’ve made big changes.

From its humble beginnings in 1997, PubMed now comprises more than 30 million biomedical literature citations from MEDLINE, life science journals, and online books. These citations may include links to full-text content in PubMed Central and publisher websites to take you directly to the information you need.

To be sustainable going forward, the latest release of PubMed required major changes including new databases, web architecture and cloud delivery. Combined, these changes resulted in a much more resilient version of PubMed with a modern design that looks and works great on your desktop, your laptop, and your mobile device!

We realize this feels like a big change, but we’ve been working hard to help everyone make the transition to the new site and have continued to make improvements along the way.

Here are a couple new and revamped features designed to improve the user experience.

The new Cite button makes it easy to retrieve styled citations you can copy and paste into a document or download an .nbib file to use with your reference manager software.

Using the Cite button for an item will open a pop-up window where you can copy the citation formatted in four popular styles.

Automatic Term Mapping, also called “ATM”, was present in the legacy PubMed, but it’s been expanded to include additional British and American spellings, singular and plural word forms, and other synonyms to provide more consistent and comprehensive search retrieval.

We’re always looking for ways to improve PubMed. Just as we’ve done for the past 24 years, we’ll continue to add features and data to stay current as technology, publishing standards, and our users’ needs evolve.

Please think about other ways that NLM can help you, and share your ideas  with us.  

Headshot image of Bart Trawick, PhD

As director of the Customer Services Division, Dr. Trawick works to connect customers with the vast information resources available from NLM’s National Center for Biotechnology Information. He has also worked to support the National Institutes of Health Public Access Policy since its establishment in 2005. Dr. Trawick is a graduate of Texas A&M University and the University of Texas Health Science Center at Houston.

A New Era of Health Communications

I’ve been reflecting on how communications has transformed our lives, particularly since the COVID-19 pandemic radically changed our ability to interact with others.

Before NLM’s physical workspace shifted to maximum telework, I was walking to work when I passed a strange sight — the last vestiges of pay phones on the National Institutes of Health campus! Those decommissioned pay phones got me thinking about how technology changes over time, how essential communication technology has become, and how NLM’s approach to providing trustworthy biomedical data and health information must evolve as methods of delivery change. As technology advances, we have more choices and greater sophistication in the methods we use to meet our responsibility to deliver biomedical data and health information, as well as in the tools we use to interrogate that information.

Payphones sit outside of the National Library of Medicine, having been removed from use in the building.

The Lister Hill National Center for Biomedical Communications (LHNCBC), now more than 50 years old, provides a case study of how NLM’s efforts to communicate information have been transformed.

LHNCBC was established by a joint congressional resolution in 1968 to stimulate the application of modern communications technologies to the challenges of delivering health information worldwide to support health care services and enhance medical education.

In that same decade, push-button telephone pads were replacing rotary dials, and the Trimline telephone, with the earpiece, mouthpiece, and dial pad in the handset, was introduced. The ARPANET, the early version of the packet-switching internet, appeared soon after. Just as the Trimline phone presaged the design of mobile phones, the early design of LHNCBC laid the foundation for robust innovation in the use of telecommunications tools, computer networks, and high-performance visualization to deliver health information and ensure its use.   

An intramural division of NLM, LHNCBC develops advanced health information resources and software tools that are widely used in biomedical research and by health information technology professionals, health care providers, and consumers. As it seeks to improve access to biomedical information for individuals around the world, LHNCBC conducts and supports research and development on the dissemination of high-quality imagery, medical language processing, high-speed access to biomedical information, intelligent database systems development, multimedia visualization, knowledge management, data mining, and machine-assisted indexing.

In 1994, it launched the Visible Human Project, a landmark accomplishment that made a complete, anatomically detailed, three-dimensional representations of a human male body and a human female body publicly available. 

Current LHNCBC researchers come from a variety of disciplines, including medicine, computer science, library and information science, linguistics, engineering, and education. The Biomedical Informatics Training Program brings together talented individuals to learn from and collaborate with research staff.

Research and development conducted by the interdisciplinary teams across LHNCBC has led to many advances in biomedical communication and information dissemination, such as:

  • Consumer Health Question Answering — This project involves research on both the automatic classification of customer requests and the automatic answering of consumer health questions.
  • Discoveries from Mimic II/III and Other Sources — This effort examines and attempts to validate controversial findings from smaller-scale clinical studies through the interrogation of de-identified medical records and information from health information exchanges. Researchers also conduct retrospective epidemiological studies in areas that lack clinical trials.
  • Open-i — This experimental multimedia search engine retrieves and displays bibliographic citations and their related images by linking to images based on image features.
  • Unified Medical Language System® (UMLS) — This tool integrates key health care terminologies, classifications, and coding systems used by clinicians, billing systems, insurance companies, and researchers. Sources developed include the Metathesaurus®, Semantic Network, and SPECIALIST Lexicon. The UMLS supports health care communication through interoperability, specifically, the mapping of key terms from one vocabulary system to another.

The changes to LHNCBC since its creation in 1968 parallel changes in telecommunications over the past 50 years. Early work at LHNCBC demonstrated how technological advances such as fiber optic networks and semiconductors could be put to best use by the health care sector. Today, LHNCBC continues to improve health through methodological advances in clinical data science and health informatics. We recognize that contemporary communication relies on interoperable data, scalable methods and translation of discovery into operations.  

As health care becomes more highly distributed and NLM resources are increasingly used by individuals around the world and beyond, LHNCBC will continue to be a partner in accelerating health communication.

What trends in health communication do you see ahead? How do you think COVID-19 will shape health communications?

The NIH Preprint Pilot: A New Experiment for a New Era

Guest post by Kathryn Funk, program manager for NLM’s PubMed Central.

Over the last several months, we have seen an increase in demand from the research and library communities for broader discovery and distribution of COVID-19 related literature, including early results posted as preprints. Preprints are complete, public drafts of scientific documents that are not yet peer reviewed. They are playing a key role in accelerating dissemination of research on the SARS-CoV-2 virus and COVID-19.

Recognizing the growing interest in preprints, NLM is today launching the first phase of the NIH Preprint Pilot, which will test the viability of making preprints searchable in PubMed Central (PMC) and, by extension, discoverable in PubMed, starting with COVID-19 preprints reporting NIH-supported research.

To be clear, NLM is not building a preprint server for NIH investigators, nor are we developing a comprehensive preprint discovery resource. Rather, through this pilot, we plan to add a curated collection of preprints from eligible preprint servers to our established literature resources. In doing so, our goal is to improve scholarly communications by accelerating and expanding the findability of NIH research results.

With the encouragement of NIH leadership, NLM has been exploring ways to leverage its literature databases to help accelerate the discoverability and maximize the impact of NIH-supported research via preprints. The planned pilot builds on guidance released by NIH in March 2017, which encouraged NIH investigators to use preprints and other interim research products to speed the dissemination of research and enhance the rigor of their work through public comments and new scientific collaborations.

Interest at NIH in the potential of preprints to improve scholarly communication long predates the 2017 guidance. As author Matthew Cobb recounts in “The prehistory of biology preprints: A forgotten experiment from the 1960s,”Errett C. Albritton, an administrator in the NIH Office of Research Accomplishments, established an informal network for the circulation of preprints and other scholarly communications by post to the group’s members. Although this initial “experiment” ended in 1967, support for the open sharing of scientific knowledge has continued at NIH through efforts such as the NIH Public Access Policy, which this pilot seeks to now complement.

Phase One Focus: COVID-19

In the first phase of the current pilot, NLM will make use of the NIH Office of Portfolio Analysis COVID-19 Portfolio tool to help identify preprints relating to the SARS-CoV-2 virus and COVID-19 pandemic. NLM will select preprints that either list an NIH-affiliated author or acknowledge NIH grant support. To accelerate discovery, preprints will be loaded and made searchable in PMC and PubMed once identified as in scope, without additional processing.  Standard XML versions will be loaded once the conversion process is completed. This workflow allows for rapid inclusion of preprints in the pilot without asking NIH investigators to separately submit them to PMC.

Recognizing that users come to NLM resources with varying levels of familiarity with scholarly communication practices, we want to make sure that researchers, clinicians, and the public can easily distinguish between preprints and peer-reviewed journal literature. Preprint records in PMC and PubMed will be flagged with large banners that clearly identify them as preprints. The banners will explain that the papers have not been peer reviewed and link to information about the pilot for additional context. Those who want to view only peer-reviewed journal literature will be able to exclude preprint records from search results in PMC using newly created filters.

We’ll closely monitor the early outcomes of the first phase of the pilot as we test and refine our workflows. We hope to be able to expand our scope in the next phase of the pilot to include the full spectrum of NIH-funded research, allow NIH investigators to identify their preprints through simplified reporting in My Bibliography, and establish more automated and faster curation workflows.

NLM will continually monitor the impact of the pilot on the scholarly communications landscape, including how research results are shared, discovered, disseminated, and reported, and evidence of increased awareness and emerging best practices around preprint sharing.

We expect the pilot will run for a minimum of 12 months to give us sufficient time to examine the use of preprints and their importance to scholarly communications in biomedical science. Feedback from stakeholders and lessons learned will inform future NLM efforts related to preprints.

PMC turned 20 in February, and its story over those two decades has been one of innovation, evolution and expansion, as we strive to build a collection at NLM that represents “the intellectual content and diversity of the world’s biomedical literature, data, and other research objects and information” and to foster open science practices. In launching this new preprint experiment in PMC, with an initial focus on COVID-19-related preprints, NLM hopes to continue to accelerate and expand access to relevant research in response to the ongoing public health emergency response efforts and to learn more about the impact of accelerated discovery and open sharing of research results on scholarly communications.

Tell Us What You Think!

We encourage you to learn more about the NIH Preprint Pilot and review the pilot overview and related FAQs.

As this new experiment unfolds, please feel free to send feedback to pmc-preprints@ncbi.nlm.nih.gov.

casual photo of Kathryn Funk
Kathryn Funk is the program manager for PubMed Central. She is responsible for PMC policy as well as PMC’s role in supporting the public access policies of numerous funding agencies, including NIH. Katie received her master’s degree in library and information science from The Catholic University of America.

The Pursuit and Power of Alignment

Guest post by Valerie Schneider, PhD, staff scientist at the National Library of Medicine’s National Center for Biotechnology Information, National Institutes of Health.

As a staff scientist at NLM, I’ve found that our strategic plan has become a valuable framework for organizing our mission and providing direction and focus—especially when we’re talking about data science.

A recent project at NLM’s National Center for Biotechnology Information (NCBI) highlights why it’s important to ensure alignment between projects and strategy.

As host to the world’s largest repository of biological sequence data, NCBI provides access to data that are critical to understanding and advancing human health. While users have been searching NCBI’s sequence databases long before the strategic plan was developed, it might be easy to overlook how an effort like the strategic plan has anything to do with the larger picture. When you look, though, it’s easy to see the relationship.

Providing a Common Search Experience

Connecting the resources of a digital research enterprise and advancing research and development in biomedical informatics and data science are just a few of the important objectives in NLM’s strategic plan. We’ve improved the experience of users searching for several types of common sequence-associated data by providing a more comprehensive interpretation of their queries and a new results interface that provides easy access to NCBI’s best results, regardless of the database in which they search.

Our team tackled this effort through extensive user interviews, iteratively developing solutions, and monitoring the usage of those solutions.

We improved searches for the reference set of genes and genomes in all species across multiple NCBI databases by supporting common language queries and using features like auto-suggest. We enhanced the ability to search and access clinically important datasets, such as human variations housed in ClinVar and dbSNP, NCBI’s variation databases, as well as resources with information about antimicrobial resistance genes and viral pathogens.

We also created displays that aggregate the results from different databases and enable easy downloads of data and access to analysis tools. Our new interactive graphics and web page displays allow for the visualization of sequences and the analysis of homologous gene sets. Knowing that NLM users rely on different technologies to access data, we ensured that the displays work on both traditional computers and mobile devices.

Since the first release of these search enhancements in late 2018, they are now triggered in a quarter of all searches in the scoped databases. We’ve seen a 300% increase in their use, with more than 300,000 users clicking on the content they offer in just the month of October 2019. These products have provided results for over 500,000 searches that previously would have returned no content. Regular monitoring of their use helps us make sure that we continue to facilitate search and deliver high-value data.

NLM’s strategic plan gave us the user-centered framework in which to execute the goals of this project. So much of the work we do at NLM is consistent with the goals and specific objectives of the plan — it provides a structure for evaluating our work and making sure that we continue to be forward-looking.

And the strategic plan helps me, as a staff scientist, to identify new areas for work that will best enable NLM to continue delivering a platform for biomedical discovery and data-powered health.

To stay up to date on NCBI projects and research, follow us on Twitter.

Photo (headshot) of Valerie Schneider, PhD
Valerie Schneider, Ph.D.

Valerie Schneider, PhD, is the deputy director of Sequence Offerings and the interim head of the Sequence Delivery 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, the international collaboration tasked with maintaining the value of the human reference genome assembly.

Ukuleles and Fishing Poles?

A living library helps you do.

Well, there goes the Wall Street Journal again. Just when we think they’re all about business, they do another feature in support of libraries of the future. This time Lucette Lagnado showcased libraries who lend everything from fishing tackle to musical instruments (subscription required for article).

Is this just a marketing ploy to pull the unsuspecting public into a library, only to have them leave with a fishing pole and a good book? Maybe, but maybe there’s more to it.

Here at the National Library of Medicine we regularly look for ways to help our patrons make better use of our resources. Toward that end, we carry out regular outreach to communities and audiences across the country and across the spectrum, from medical professionals and scientific researchers to students and the general public.

Outreach, by definition, means “to reach further than,” and in conducting outreach, we take this library further into those communities. In turn, the members of those communities are able to go further themselves, to learn more and to do more than they could have without us.

As part of our strategic planning process we are conducting an audit of the many approaches to outreach we employ. We send staff to powwows held by Native American nations and tribes, bringing on-the-spot coaching to attendees to help them find relevant health resources. We create YouTube videos to teach scientists how to effectively use dbGap, our best-known and most highly used database of genetic sequences. Through our National Network of Libraries of Medicine, we attend community meetings and health fairs to ensure people everywhere know about our valuable, authoritative health information. We make informative websites that walk users through the best ways to search PubMed, and we publish a magazine as a free, trusted consumer guide to the latest medical research and quality health information coming out of NIH and NLM.

At first pass, these efforts look like NLM has taken on a health information mission, just like the libraries visited by Ms. Lagnado seem like music rooms.

But look deeper.

What we are actually doing is bringing the library to life—ensuring NLM’s resources are accessible not only in the traditional, well-understood ways of reading and reflection, but by ensuring those accessing our resources have the skills to use them.

After all you can’t catch a fish by reading a book about fishing, and you can’t play the ukulele by simply looking at a musical score. You need to do, and the new “libraries of things” support that.

And when it comes to NLM’s vast resources, we help you do—to effectively find what you need, assess what you find, and apply what you learnto help us all reach further and do more than we did before.