“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.

Leading in Transitions

Maintaining continuity in a time of change

Those of you watching the calendar have probably figured out that I’ve been on the job as the NLM Director for just about five months. My past 30 years were spent in academe, and I figured the biggest transition I would be facing was from academic to Federal employee—daunting but doable, I thought!

I had not figured on the difference between my transition from academic to fed and THE TRANSITION, the change brought about when a new president takes over for a sitting president and the reshuffling in the House and Senate that accompanies it. The logistics of a presidential transition are many—with a good percentage actually completed by October—including preparing briefing books for the incoming administration.

This task is more challenging than it might sound. Putting together a briefing book means distilling this $400 million operation down to a 3.5-page summary detailing our goals, staffing, and key actions for the near future. None of this would have been possible for a newbie without the diligence and insights of Betsy Humphreys, our NLM Deputy Director.

Beyond NLM, it seems to me that the NIH and the entire Department of Health and Human Services (DHHS) is experiencing a mixture of business-as-usual, excitement about change, and curiosity about where a new DHHS Secretary and a whole new administration (with 4,000 new political appointees) will take us.

So what is my role in all of this?

My primary job is to ensure adequate resources for the men and women who work here to create and manage our products and services (such as PubMed, the Common Data Elements Repository, the UMLS, PubChem, ClinVAR, TOXNET, etc.), preserve our historical collections, conduct research, and develop new ways to document clinical trials. I also need to be an advocate for the NLM in NIH-wide discussions about how to foster discovery and support clinical practice in a time of uncertain direction. I must be mindful of my own tolerance for ambiguity, being sure to listen to the concerns of staff and colleagues, respond with confidence, and provide reassurance in a realistic manner.

No leadership job comes with a crystal ball, and my personal opinions about how the future will pan out do not serve as a guide for action. What does guide me is the wisdom arising from the strong NLM leadership team, formed prior to my arrival and now pivoting to guide me as I lead the Library not only in anticipating our third century but also in transitioning to a new administration. The NLM enjoys broad respect and acceptance, so I expect our core mission to persist, but frankly, I too am curious about what the future holds.

What do you think this transition will bring us?

Holidays Greetings from the Mezzanine!

Like most busy and productive workplaces, the NLM celebrates those times when social events intersect with everyday work. Just now, we are pausing to celebrate the Judeo-Christian holidays of Christmas and Hanukkah. Decorations are up, treats are appearing, and everyday greetings are complemented with good wishes for the holidays and the new year.

Arising from my family traditions and beliefs, I take this time to extend my greetings for a Merry Christmas and a Happy New Year to you, your friends, and your families. In our large family of 10 children, Christmas was a time of giving and excitement, with crafts-leading-to-gifts, secret presents hidden till that special morning, and participation in the church traditions of our community.

Although perhaps the most visible holidays mixing religious ideas and social events, Christmas and Hanukkah are but two of the range of holidays practiced by different cultures and religious sects recognizing the passage of time, preparation for the future, and attention to fundamental faith tenets. Here at the NLM we have staff from nearly every corner of the globe. In Library Operations alone, we have staff who, collectively, can speak 34 languages other than English, and across the Library my colleagues’ ages span from late teens to over 80. While we are united in the goals of our work, we recognize and respect that among us are people who hold a wide range of beliefs and adhere to different traditions that mark the passing of time and visions of the future.

So, as I extend and receive holiday greetings, I try to be mindful that to some, other times and other events provide more meaningful signals in their lives of what Christmas means to me. I encourage you to commit yourself, at least once in the next year,  to learn of the traditions of one of your colleagues–this will extend our holiday greetings year round!

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