Current Affiliation: Director of the Center for Data to Health, Oregon Clinical & Translational Research Institute, Oregon Health & Science University; Director of Translational Data Science, Linus Pauling Institute, Oregon State University
Education: PhD, Neuroscience, University of Wisconsin
BA, Chemistry, Reed College, Portland, Ore.
How do I describe my work to those outside the field …
The first thing I tell people is that we aim to improve rare disease diagnosis and discovery by making all the data count - whether that data is from humans or from model organisms like mice, or even from unusual non-model organisms like platypus. Then I ask if they have ever used Amazon, because when you're looking at one thing on Amazon, the site seems to know that you might be interested in this other thing, and you actually are! That's what we do for medicine; we tell the computer how to associate things in a logical and intuitive way that a machine can understand such that when it presents it to the user, it just works.
Years of experience:
I started working in informatics in 2004; however, a lot of what my group does is not what most people first think of when they hear the word 'informatics'. Our work falls into three interdependent categories: biocuration, ontology development, and data harmonization. Biocuration involves taking knowledge from sources such as the medical literature, electronic health records, and research data, and transforming it into a standard, quality-controlled, and--most importantly--computable format. The biocuration community is small, but vibrant and growing, and the work biocurators do is a necessary precursor to most informatics pipelines. Our group also works on the development of ontologies to model knowledge in a computable manner. Under the hood, Amazon logically defines "azure-colored platform shoes" and "turquoise sandals" as both being types of shoe and both being shades of blue. Our third area of expertise builds on the curation and ontology work to integrate and harmonize data. This aspect of our work began when we started utilizing genotype-phenotype data from across species to assist in rare disease diagnosis and mechanistic discovery.
My background was in neuroscience and developmental genetics, molecular biology, and toxicology. I loved many aspects of bench science, but when I got pregnant in 2004, I decided to switch gears. I had been moonlighting as a biocurator for the zebrafish database, and when a full time opening came up, I took it. The career move to biocuration gave me a deep appreciation for how underutilized the data were in disease research, and I started working with one of my long-standing collaborators, Chris Mungall, at Lawrence Berkeley National Lab. We developed the technology over the course of four years; then in 2009, we published a first seminal paper that showing that in the absence of genomic data, comparison of phenotypes could be used to identify candidate genes for diagnosing rare disease. That paper got the field to think beyond solely genomic-based diagnostics and to start incorporating phenotypes as well.
What are your ambitions? At the end of your career, what do you hope to have accomplished?
I would like to further accelerate the speed and precision of rare disease diagnosis. I would also like to use informatics to reduce healthcare inequities. For instance, one of the things we are doing to address both of these things is to improve the diagnosis of rare disease patients in rural areas. According to one study, only 10 percent of the expected rare disease incidence was being diagnosed in these rural settings. Sanford Health, which serves millions of patients in the rural U.S., is partnering with us to bring widespread usage of our technologies to improve patient diagnoses and healthcare.
Who or what are your "key sources" in the informatics field?
I find great pleasure and inspiration from my colleagues, specifically Chris Mungall (LBNL), who first introduced me to the world of ontologies back in 2004. I have also been driven to new interests and successes by my other co-PIs on the Monarch Initiative, specifically Peter Robinson (Jax), Damian Smedley (QMUL, Genomics England), Tudor Groza (Garvan), and David Osumi-Sutherland (EBI). More recently our collaboration with Maureen Hoatlin (OHSU), Stan Ahalt (RENCI), Chris Chute (JHU), and Andrew Su (Scripps) on the NCATS Biomedical Data Translator has also provided new focus on how we share and use data for mechanistic discovery and patient stratification in novel ways.
I have also found great direction in my science from my collaboration with Julie McMurry, whose ability to illustrate and refine my ideas have made our science more innovative and effective. Pictures really do say a thousand words.
Articles that spotlight my research interest
Vasilevsky N, (~30 authors)….. Haendel M. (2018) Plain-language medical vocabulary for precision diagnosis. Nature Genetics. In press
Kohler S, Vasilevsky NA, Engelstad M, …., Groza T, Smedley D, Mungall CJ, Haendel MA, and Robinson PN. (2016) The human phenotype ontology in 2017. Nucleic Acids Research, 2016 1-12 doi: 10.1093/nar/gkw1039. PMC5210535.
Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall CJ, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med. 2016 Jun;18(6):608-17. PMC4916229
Mungall CJ, McMurry JA, Kohler S, ……, Robinson PN, and Haendel MA. (2016) The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research, 2016 1 doi: 10.1093/nar/gkw1128. PMC5210586
Haendel, MA, Balhoff, JP, Bastian, FB, Blackburn, DC, Blake, JA, Bradford, et al. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014 May 19;5:21. PMC4089931
Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA. (2013) On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ. Sep 5;1:e148. PMC3771067
*Washington, N. L., *Haendel, M. A., Mungall, C. J., Ashburner, M., Westerfield, M., & Lewis, S. L. Linking human disease to animal models using ontology-based phenotype annotation. PLOS Biol. 2009 Nov;7(11):e1000247. PMC2774506 *co-first author
Hobbies/Interests outside AMIA...
I'm a cook and a baker, and I love to cook food I've gathered, hunted, or grown in my garden. I have a very large garden and I also do a lot of wild mushroom and muscle picking, and my husband hunts, so we do a lot of our own sausage making. Also, I just learned how to make sourdough bread. So, anything having to do with harvesting, cooking, or eating delicious food is right up my alley.
AMIA is important to me because ...
AMIA is important to me because it is one of the primary societies that brings together informatics disciplines across the translational spectrum; it is also a very safe and productive space to promote women. For example, my colleague, Jessie Tenenbaum, has done a lot to promote women in informatics. She was the founder of the WINE event - Women in Informatics Networking Events that happen at AMIA every year.
I am involved with AMIA ...
I was a co-chair of TBI this year, and have attended most AMIA TBI meetings over the past decade.
It may surprise people to know ...
Just like wanting to make all the data count, the same goes for food. I guess it is consistent with my survivalist tendencies, but I can't allow food to go to waste. I'm a card-carrying member of the clean plate club and even made venison from deer and elk that have been hit by cars.