Loss of an Early Informatics Visionary

I am saddened to learn of the passing of Dr. Burton "Bud" Rose due to complications of Covid-19. Dr. Rose was the creator of the well-known UpToDate online medical information system, which is used by clinicians around the world. I played a tiny role in the development of UpToDate by programming its first search capability. In the late 1980s, I was a postdoctoral fellow in medical informatics at Brigham & Women's Hospital, working in the lab of my mentor, Dr. Robert Greenes. Dr. Rose, a kidney specialist, came to Dr. Greenes seeking help to add a searching capability to a collection of "cards" of information about kidney diseases he had collated in an Apple Hypercard Stack. My research had been focusing, then as now, on information retrieval (search) systems. It was relatively straightforward to connect a simple system I had programmed to index and retrieve from the information in the cards. It was a marvel at the time to be able to type in a few words and get medical information, years before the onset of the World Wide Web and Google.

I ultimately finished my fellowship and moved on to Oregon in 1990, and the development of UpToDate was taken over by a fellowship colleague, Dr. Joseph Rush, who stayed on the project for years as it matured into a commercial product that expanded to all of medicine. In 2008, UpToDate was acquired by the large publisher, Kluwer. I had not seen Dr. Rose in many years, but he continued to be a vibrant clinician and educator until his recent retirement.

UpToDate is still widely used and revered in medical settings around the world. I believe its real value is in its content. While its modern search functionality is excellent, what really draws clinicians to it is the quality of its content that can be used to make clinical decisions based on rapid access to high-quality information.

Virtual Informatics Course for Medical Students Progresses

My virtual informatics course for medical students is starting its third offering this week, and the uptake has been great. We hope to keep offering the course through the OHSU spring academic quarter, which runs through early June.

The primary impetus for the course is that medical students have been sidelined from clinical experiences due to the need to protect their health as well as conserve personal protective equipment (PPE) for physicians, nurses, and others taking care of patients.

The usual 10-week course has also been organized into a 4-week block format for medical students. Students are required only to complete the weekly multiple-choice assessments and not a term paper or final exam. The course has been offered not only to OHSU medical students but also to any medical student from any US allopathic or osteopathic medical school. External students register for the course through their own institutions, who send us lists of students to enroll in the course.

The medical student course has been offered in weekly waves. The first course started with 17 OHSU medical students. The second two offerings include 62 medical students from 11 different medical schools: Dartmouth College (2), Northwestern University (1), University of Iowa (6), University of North Dakota (2), University of Rochester (15), City University of New York School of Medicine (2), Emory University (12), University of Miami (3), Philadelphia College of Osteopathic Medicine (9), Quinnipac University (1), and Stony Brook University School of Medicine (9). We anticipate additional waves of students from additional medical schools over the next few weeks.

TREC-COVID: A New Information Retrieval Challenge for Covid-19

Calling all information retrieval (IR) and biomedical informatics researchers interested in IR! My colleagues and I are pleased to announce  a new research challenge related to Covid-19. TREC-COVID aims to develop and evaluate methods to optimize search engines for the current and rapidly expanding number of scientific papers about Covid-19 and related topics. A group of information retrieval (IR) researchers from the Allen Institute for Artificial Intelligence (AI2), the National Institute of Standards and Technology (NIST), the National Library of Medicine (NLM), Oregon Health and Science University (OHSU), and the University of Texas Health Science Center at Houston (UTHealth) have organized the challenge. A press release and official Web site for the project have been posted. Although not official to the project, I am also maintaining a page about the project.

TREC-COVID applies well-known IR evaluation methods from the NIST Text Retrieval Conference (TREC), an annual challenge evaluation that evaluates retrieval methods with data from news sources, Web sites, social media, and biomedical publications. In an IR challenge evaluation, there is typically a collection of documents or other content, a set of topics based on real-world information needs, and relevance assessments to determine which documents are relevant to each topic. Different research teams submit runs of the topics over the collection from their own search systems, from which metrics derived from recall and precision are calculated using the relevance judgments.

The document collection for TREC-COVID comes from AI2, which has created the COVID-19 Open Research Dataset (CORD-19), a free resource of scholarly articles about COVID-19 and other coronaviruses. CORD-19 is updated weekly, although fixed versions will be used for each round of TREC-COVID. It includes not only articles published in journals but also those posted on preprint servers, including bioRxiv, medRxiv, and others.

Because the dataset (along with the world's corpus of scientific literature on Covid-19) is being updated frequently, there will be multiple rounds of the challenge, with later ones focused on identifying newly emerging research. There may also be other IR-related tasks, such as question-answering and fact-checking. The search topics for the first round are based on those submitted to a variety of sources and were developed by myself, Kirk Roberts of UTHealth and Dina Demner-Fushman of NLM. Relevance judgments will be done by people with medical expertise, such as medical students and NLM indexers. I am overseeing the initial relevance judging process, which is being carried out by OHSU medical students who are currently sidelined from clinical activities due to the Covid-19 crisis.

The Easiest of Times, the Hardest of Times

To paraphrase Charles Dickens,  these Covid-19 times are the easiest and hardest of times.

For me personally, the Covid-19 crisis so far has been relatively easy. Because of this, I have gratitude and also note my fortunes could change at any time. So far, none of my immediate family, friends, or colleagues has become infected or fallen ill. We are comfortably ensconced in our house, have access to just about all of life's essentials, and can enjoy the outdoors, including my own running, with careful physical distancing. Spring is arriving, and the weather over the last few days has been wonderful.

Likewise, my work life has for the most part gone on as usual. I actually have extra work in managing for the future of my department in the emerging financial recession and its impact on my academic medical center. But since my life is already highly virtual, my work has been relatively easy to carry on. For many years, almost all of the teaching I have been doing is already online. My other academic work, especially my informatics research, is also mostly virtual. I have also used this opportunity to offer up additional virtual teaching to other programs within and outside my university, and have become involved in one of many Covid-related informatics research initiatives.

But these times are still extremely hard. It is sad to watch and read the news, and see the statistics. It is difficult to see those succumbing to the virus and that impact on their families and friends, especially since better early management could have prevented some of that. I cannot say enough words of gratitude I have for frontline workers who are the true heroes of this pandemic, from those in healthcare to those in public safety, grocery stores, and other essential businesses. It is also difficult to see the economic impact, especially on those who cannot easily convert to remote work like I can. I also have tremendous worry not only for the recovery of public health and economy as well as inadequacies it has exposed in our healthcare system and the larger social support that society must provide.

It is easy to express my usual optimism being in my situation. While we must honor and protect those who have been impacted by this pandemic, we must also think of how we must also restructure society to insure not only a better approach for crisis times but also when times are good yet not everyone can benefit. 

A Virtual Course in Biomedical and Health Informatics for Medical Students

Medical students from around the US (and the world) have had their education displaced by the Covid-19 pandemic. In many places, there is either desire to keep them away from risk or to preserve personal protecting equipment (PPE) to physicians, nurses, and others directly involved in patient care. As such, the medical education community has worked to identify virtual educational experiences for medical students.

Our contribution is a virtual course in biomedical and health informatics. Readers familiar with my work will recognize the content of this course as emanating from the introductory course in the Oregon Health & Science University (OHSU) Biomedical Informatics Graduate Program. This course is also used in OHSU's offering as part of the American Medical Informatics Association 10x10 ("ten by ten") program. The syllabus for the course details on how medical schools can enroll their students.

We are implementing the course as a 4-week medical student elective, which is awarded 2 credits at OHSU. The course has about 40 hours of lecture, and we anticipate another 40 hours spent on discussion forums, multiple-choice self-assessments for each unit, and optional readings. The course is graded as pass-fail, and passing requires completion of all of 10 units and their self-assessments over the 4 weeks of the course. Due to high demand, we are limiting enrollment to students in US-based allopathic and osteopathic medical schools.

One new offering of the course will begin each week starting Monday, April 6. We will enroll as many students as we have in a single section, and make all of the content available to them for the duration of the 4 weeks. We will make use of the discussion forums built into our LMS to answer questions they have, and raise a few questions for them to answer. At the end of 4 weeks, the course will end, and those who have completed all of the work will receive a passing grade, which we will report back to the contact from each school.

We are asking each medical school handle student enrollment and credit themselves. In other words, we will make the course available through our learning management system (LMS) at OHSU, but we will ask each school to provide us a list of students to enroll and each will get a login to the course. After the course is done, we will report back to the schools on whether each student completed the course or not. We would like for medical schools that participate to handle giving students credit (probably through some sort of self-study elective).

We also prefer that there be a single point of contact for each school with which we communicate. To capture this information, we have created an online survey that asks for the point of contact (please use a university email address), estimated number of students (initially up to 20 per school - we may be able to accommodate more later), and preferred dates (which we may need to change to balance load). After the survey is completed, someone from our staff will contact the schools to work out the details.

In addition, for those interested in less than a full course on informatics, we have an open Web site that provides some of the materials and is being used by some medical schools.