“And the Altman Goes to…”

NLM’s Role in Driving Progress in Translational Bioinformatics

Guest post by Dr. Valerie Florance, Director of the NLM Division of Extramural Programs.

How can you discover the cool stuff happening in translational bioinformatics?

Check out Russ Altman’s “Year in Review.”

Each year since 2007, Altman, a professor of bioengineering, genetics, medicine, and biomedical data science at Stanford, has hosted a popular plenary session at the annual joint summit on Clinical Research Informatics and Translational Bioinformatics sponsored by AMIA, the American Medical Informatics Association. Entitled “Translational Bioinformatics: The Year in Review,” this lively talk provides an overview of scientific trends and publications, celebrating progress and highlighting opportunities in research focused on informatics and data science methods that link biological entities to clinical entities.

It’s not exactly the Emmys, but Altman’s talk does bestow minor celebrity status on those acknowledged—and more importantly, it draws attention to new data collections, new software tools, and new directions for a field that increasingly impacts real problems in biology and medicine.

To build the list of candidate papers, Altman solicits recommendations from scientific colleagues. He then enlists volunteers from AMIA’s student working group to review and score the articles based on three basic criteria: informatics novelty, application importance, and presentability.

This year the student team scored over 285 articles, out of which Altman chose 28 to present at the joint summit and another 32 to receive a shout-out. This and past years’ honorees are enshrined on Altman’s blog.

After each meeting, NLM’s grant program staff comb through Altman’s presentation to identify work that builds on or highlights NLM-funded research. The process is not exact, relying on the articles’ acknowledgements of support to identify funding sources, but, like Altman’s talk itself, it’s something to go on, a back-of-the-envelope way of seeing where NLM dollars are having an impact and driving the science forward.

Of course, these papers commonly have multiple authors and multiple sources of funding. Furthermore, for the data scientists and informaticians supported by NLM, their methodological work may not be the focus of the article, but that work nevertheless contributes fundamentally to the reported results.

Of the 28 articles Altman presented this year, five acknowledged NLM grant support, while five additional NLM grantees secured one of Altman’s 32 shout-outs [total: 10 of 60 (16.7%)].

The following three examples from Altman’s list give a sense of the kind of work—and impact—NLM grants and grantees are having.

This research was funded by NIH grants from four different NIH Institutes, and by the Intramural Research Program of the NIH National Human Genome Research Institute.

Although Sean Mooney is not listed as a co-author, the article acknowledges his NLM-funded grant, “Informatic Profiling of Clinically Relevant Mutation” (1R01LM009722). Initially issued in 2007, Dr. Mooney’s award is still active and has produced 53 publications with more than 780 citations (Thomson Reuters).

The funded research develops novel methods to identify patients at risk for complex trait disorders, with a long-term goal of creating a whole genome interpretation engine based on data in public resources. Dr. Mooney’s academic background is computational modeling and biochemistry.

This paper acknowledges support from three different NIH Institutes and the National Science Foundation.

Co-author Marylyn Ritchie received NLM funding from 2009-2013 for the grant “Analysis Tool for Heritable and Environmental Network Associations” (1R01LM010040). Her work resulted in 33 publications with more than 151 citations (Thomson Reuters).

The project helped develop the ATHENA framework, which uses machine learning to incorporate biological information from databases with diverse data types to detect disease susceptibility driven by gene-gene and gene-environment interactions. Dr. Ritchie’s academic background is applied statistics and statistical genetics.

This work was funded by five different NIH Institutes and Pfizer.

The paper acknowledges Russ Altman’s NLM grant currently focused on “Text Mining for High-Fidelity Curation and Discovery of Gene-Drug-Phenotype Relationships” (5R01LM005652). There are 98 publications attributed to this grant, with 620 citations (Thompson Reuters).

Altman, an MD, PhD with academic training in molecular biology and medical information sciences, uses computational natural language processing to extract semantically precise knowledge about drugs, genes, and phenotypes.

In 1997, Altman’s research earned him the Presidential Early Career Award for Scientists and Engineers (PECASE), the first NLM grantee to earn that distinction.

Now, twenty years later, Dr. Altman is encouraging other scientists by featuring some of the innovative work happening in translational bioinformatics.

Whether funded by NLM or not, we expect this research to move the science forward, and who knows? Maybe something more than an Altman lies in the future for these researchers. Stay tuned.

Get Ready for Tornado Season

Information and readiness build resilience.

Guest post by Stacey Arnesen and Florence Chang, NLM Specialized Information Services.

The red pickup anxiously plowed through the corn field, heading toward the dark, ominous funnel, an F5-class tornado. Despite their many failed attempts, Jo and Bill were ready this time. On the truck bed was “Dorothy IV,” Jo and Bill’s invention, carrying thousands of data-collecting sensors. As the truck plunged into the swirling monster, Dorothy IV released the sensors, twirling and blinking like pixie dust. Streams of data collected by the sensors started flowing into a computer designed to make sense of the millions of data points regarding wind speed, air temperature, rotational force, and other elements of the storm.

This scene from the 1996 movie “Twister,” starring Helen Hunt and the late Bill Paxton, might have seemed a bit futuristic twenty-one years ago, but it was grounded in the science of the day. NASA and NOAA (National Oceanic and Atmospheric Administration) have collected data, shared data, and used data to predict the weather and make meteorological discoveries for decades before “Twister” brought storm-chasing and the work of the National Severe Storms Lab (NSSL) to the public’s attention.

Thanks to that research, today’s Doppler radar system uses sophisticated algorithms and modeling to monitor the weather and detect tornadoes. Advances in mobile technology and social media have also opened new channels for data exchange and communication, resulting in such apps as Wireless Emergency Alerts from NOAA and NSSL’s mPing, which crowdsources weather observations. Together, these early warning systems save lives and prevent injuries by giving people more time to take shelter before a tornado strikes.

Even with these advanced detection and warning systems, preparedness for tornadoes is still crucial. FEMA recommends that families start by assembling an emergency preparedness kit and creating a household evacuation and shelter plan. These will help you stay safe during the storm and survive on your own afterward until help can arrive.

NLM’s Disaster Information Management Research Center (DIMRC) suggests going one step further and packing a “digital go-bag” on your mobile device. Apps from FEMA, the American Red Cross, the National Weather Service, and NLM will ensure you have helpful and current information at your fingertips, from up-to-the-minute, localized weather warnings to first aid instruction and post-storm tips. You can also help with situational awareness and emergency response by submitting photos of damaged areas to FEMA.

Librarians as Information First Responders

Information is key during an emergency, which highlights an important role for libraries and librarians: as information first responders.

New Jersey State Librarian Mary Chute noted that disasters and other emergencies can turn a library into a “a safe haven where librarians, skilled in customer service and effective communications, can help those struggling to cope with unusual and stressful situations…and  offer critical services to help support police, firefighters, and medical personnel.”

In 2011, that role played out in Springfield, Massachusetts where, following a tornado, the libraries offered a space where community members without electricity or with damaged homes could gather to connect with each other and with essential services. A year later, following Hurricane Sandy, libraries were often the go-to place, and then-FEMA Administrator Craig Fugate tapped into the idea of library-as-community-builder by encouraging parents to read to anxious children. Readers tweeted their top picks using the hashtag #StormReads.

To foster the role of librarians as partners in disaster management, NLM, together with the Medical Library Association, developed a Disaster Information Specialization for those looking for ways to support their institutions or communities during such emergencies.

Who knows? Maybe the sequel to “Twister” will have librarians in the lead. (Hmmm, now we’re wondering who should play us.)

Florence Chang and Stacey Arnesen smilingGuest bloggers Florence Chang and Stacey Arnesen work in the NLM Division of Specialized Information Services.

Photo credit (tornado, top): Brent Koops, NOAA Weather in Focus Photo Contest 2015 [Flickr (CC BY 2.0)]

The Future’s So Bright I Gotta Wear Shades

And that future is all about you!

We’re halfway through the strategic planning process at NLM, with the second of four panels convening last week to explore the future of the public’s health.

Like the other topical panels, invited experts from around the US joined us to share their unique and important perspectives. I am grateful for the opportunity to glimpse the visions of these great leaders, because each meeting gives me new insights and inspires new directions, new possibilities, for the National Library of Medicine.

The topic of public health covered by the panel includes personal health management, clinical care services, and community and public health. We did not separate these in the discussion because people in health or illness pass through each of these care environments as they traverse the trajectory from health to illness and back again.

As our experts shared their visions of what might happen in or across their various sectors over the next 10 years, the message was strong: The future of health lies in the hands of the people who will experience those health journeys. The public’s health, whether experienced in a public health clinic, a hospital bed, or a patient’s home, is going to be increasingly driven by the vision, skill, preferences, and choices of the person, not the professional!

It became immediately clear to me that the library designed to support the intensive care unit in 1995 will be ill-equipped to support a community-situated, patient-centric health care environment in the next decade.

The library that supports acute care rests on several premises:

  • Biological knowledge dominates.
  • Point-of-care decision making is the rule.
  • Records became archives of the care experience.

The future of health lies in the hands of the people who will experience those health journeys.

With a person-driven model, the information needed for care is simultaneously more broad—encompassing social, behavioral, and environmental factors—and more precise—focused on individuals, not the statistical average. We must also reconsider how that information is delivered, so it aligns with the individual’s values regarding heath and health care and is relevant to his or her life experiences and understanding of illness.

So what needs to happen to NLM to make it a library that accelerates personal health, person-centered care, and public health?

We need to collect new kinds of information, such as studies that help us characterize health and illness in terms of the patient. We need to build new filters and integrate special search terms so the process of locating that information aligns with how people experience and understand their own health issues. Finally, we must present that material in a way that is both actionable and comprehensible by the layperson, which might call for translation services or plain language interpretations.

As we design NLM’s future, please let us know what you know. How will care practices and knowledge development in your domain change over the next five years? And how can NLM help you meet those challenges?

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.

“Rock Star” Librarian—Now That’s a Stereotype I Can Get Behind!

Earlier this month, the Wall Street Journal published a piece by Ellen Gamerman with the headline “The ‘Rock Star’ Librarians Who Choose What Your Kids Read” (subscription required).

The article highlighted how some librarians use social media, including Twitter and blogs, to recommend children’s reading selections—and end up with their own bit of low-level fame along the way.

As many commenters pointed out, this practice does raise some concerns, including adults choosing reading materials for kids, but to me, one message comes through loud and clear: new librarian stereotypes are emerging—and this is GOOD!

Those of you who follow me on Twitter or read a recent interview of me in The Washington Post know that stereotypes of librarians (and nurses) remain and are not always positive. Even when employed good-naturedly, these stereotypes can be unfair or untrue. I’d like to see them go away, but until they do, I suggest we undercut negative stereotypes by cultivating positive ones.

With that in mind, I’m all for the “rock star” librarian idea.

The National Library of Medicine relies on librarians here and in the field—in public libraries, hospital libraries, academic research centers, and K-12 schools. These librarians help people discover and use the quality health information NLM provides to stay healthy, manage illness, and learn about personal or public health issues.

The librarians in the 6,500 or so libraries linked through the National Network of Libraries of Medicine have a presence in almost every county in the United States! They reach out to health professionals and the public in their regions to assess information needs and provide resources. And they do it in ways that work for those audiences—whether via community meetings, webinars, training classes, or face-to-face consultations. These librarians are our rock stars.

What better term to use to describe the 21st century librarian!