Wednesday, October 6, 2021

Certification for the Rest of Informatics

After several years of planning, professional certification is coming to the rest of the informatics field, i.e., moving beyond just board certification for eligible physicians. While certification is somewhat easier to apply in the context of the physician board model, the American Medical Informatics Association (AMIA) has now rolled out the AMIA Health Informatics Certification (AHIC, formerly Advanced Health Informatics Certification). Those who are certified will be designated as ACHIP, the AMIA Certified Health Informatics Professional. A section of the AMIA Web site provides detailed on the certification, eligibility for it, applying for and taking the exam, and recertification.

While AHIC is open to all who have a master's or doctoral degree in health informatics or a related discipline, the certification process is not conferred upon initial completion of one's education. Rather, individuals also need to have completed qualifying work experience to be eligible for certification. This is different from some fields, such as medicine, including the clinical informatics subspecialty, where one takes the board certification exam shortly after completing formal training. There are a number of healthcare disciplines that require significant work experience for certification, such as some of the advanced certifications offered by the American Nurses Credentialing Center.

The qualifications for AHIC are listed in a table on the AHIC Web site. There are two tracks of eligibility. Track 1 is for those who have a graduate degree in a health informatics-related area, e.g., health informatics, biomedical informatics, nursing informatics, public health informatics, translational bioinformatics, etc. Track 2 is for those who have a graduate degree in a related field, e.g., health professions such as nursing, pharmacy, and medicine, and other fields such as computer science and public health. The work time required for those in Track 1 is 50-100% work time over the last four of six years or 20-49% time over the last six of eight years. The work time required for those in Track 2 is 50-100% work time over the last six of eight years or 20-49% time over the last eight of 10 years.

The certification process is being developed and managed by the Health Informatics Certification Commission (HICC), a 14-member commission that is part of AMIA yet has considerable autonomy from AMIA, especially with regards to AMIA's educational programs. The HICC is responsible for eligibility, examination development, and recertification requirements for AHIC.

The first offering of the certification exam is taking place this fall. The outline of exam topics follows  the health informatics workforce analysis commissioned by AMIA (Gadd, C.S., Steen, E.B., Caro, C.M., Greenberg, S., Williamson, J.J., Fridsma, D.B., 2020. Domains, tasks, and knowledge for health informatics practice: results of a practice analysis. J Am Med Inform Assoc 27, 845–852., just as the clinical informatics subspecialty exams now uses the complementary clinical informatics subspecialty workforce analysis for its exam blueprint.

The two questions someone enrolled in or contemplating seeking a degree in informatics will likely ask are: (1) Is this certification process for me? and (2) Will it benefit my career? Since this form of certification is new for professionals who work in informatics, the benefits at this time are unknown. The main drivers of the uptake will be employers who make hiring decisions that are influenced by job candidates having the certification. Similar to the clinical informatics subspecialty, we will probably see a gradual uptake of the AHIC over time. It may never be an absolute requirement for a job but it will be an important "feather in one's cap" when competing with others for a given position.

Tuesday, August 24, 2021

Scientific Rankings for the Informatics Professor

While I agree with those who argue that scientific rankings, especially based on bibliographic citation indicators, are limited in their measurement of a scientist's impact, I must admit a certain fascination with them. Perhaps that stems from my interest in dissemination and retrieval of scientific information generally. And perhaps also, because I enjoy writing and tend to measure well by these metrics.

I do show up in most rankings of my primary and related scientific fields. As I consider my primary scientific discipline to be biomedical informatics, I can report that I rank 57th on one list of researchers in the field. On another more focused list of those who work in medical informatics, I rank 14th, although my ranking falls to 33rd when the list is less focused (details below - also see [1,2]). I am also on a global list of the top 1000 computer science and electronics researchers, where I rank 932nd globally and 569th among Americans. On a more focused computer science list for the information retrieval field, I rank 23rd.

A description of how these rankings are calculated gives some perspective into my positions on them. All of these rankings make use of the well-known citation measure, the h-index, although one uses additional factors. The h-index is a measure of the number of one's publications that have been cited by at least that same number of publications. So for example, if one has 15 papers that have been cited 15 or more times, their h-index is 15. There are two main public sources of h-index values that are most commonly used, which give different results due to the way they are calculated. The two are Google Scholar and Scopus, the latter an arm of the scientific publishing conglomerate, Elsevier. The Google Scholar h-index is usually higher than the Scopus h-index due to the former including a wide variety of academic products, such as conference proceedings, books, non-peer-reviewed reports, and other publications on the Internet, whereas the latter is limited to journal publications. As the Google Scholar value is also generated automatically, it is more likely to contain erroneously included papers, especially when author names are ambiguous. My current Google Scholar and Scopus h-index values are, as of this writing, 75 and 46 respectively.

Obviously the h-index is related to the duration of one's career, and as citation patterns vary in different fields, one must compare the h-index of different individuals with caution. With those caveats, we can explore further my own ranks. The list of biomedical informatics researchers is maintained by Allison McCoy of Vanderbilt University. One concern about this list is that it contains a number of researchers who, although published in the biomedical informatics literature, do not primarily work in the biomedical informatics field. This list is generated from software developed by Jimmy Lin of University of Waterloo, who maintains the list of information retrieval researchers (and several other fields within computer science). The list of top worldwide computer science researchers is maintained by a Web site devoted to computer science research, Guide2Research.

An additional ranking in which I appear is one compiled by John Ioannidis of Stanford University and colleagues [1,2]. This analysis includes the top 100,000 scientists across all fields, with additional enrichment from those in the top 2% of their field but not in the top 100,000. Unlike the other sources, this analysis is fixed, with data through 2019 and taking more factors into account than just the h-index. A composite C-score is made up of six factors measured from citations through 2019 and excludes self-citations:

  • h19 (ns)    h-index as of end-2019
  • hm19 (ns)    hm-index as of end-2019
  • ncs (ns)    total citations to single authored papers
  • ncsf (ns)    total citations to single+first authored papers
  • npsfl (ns)    number of single+first+last authored papers
  • ncsfl (ns)    total citations to single+first+last authored papers

The rationale for this more complex measure is based on observations that (a) in some fields, many papers have vast numbers of authors, (b) these large numbers of authors give great weight to measures based purely on citations, (c) many Nobel laureates do not rate highly in simple citation measures such as h-index, (d) many of those who rank highly in simple citation measures have few or no first-authored or last-authored papers, and (e) Nobel laureates rank higher when more complex measures such as a C-score are employed.

In this cast of more than a hundred thousand, my C-score of 3.938 gives me an overall rank of 22,034, which is based on 241 papers published and 6109 citations to them through 2019. As noted above, I rank 15th among those whose primary field is medical informatics. There are also others for whom medical informatics is listed as their secondary field, and when combined with those for whom it is primary, my ranking is 34th(?). There is a separate ranking for those whose primary field is bioinformatics. 

I can also extract out all researchers in the ranking from my institution and its affiliates (Oregon Health & Science University, OHSU School of Medicine, Oregon National Primate Research Center, and Portland VA Medical Center) and note that I rank 49th out of 256 included in this list. (I am also pleased to note that 10 people from my department make it on to the overall OHSU list, including Roger Chou, Heidi Nelson, Mark Helfand, Joan Ash, Cynthia Morris, Paul Gorman, Rochelle Fu, Linda Humphrey, and Aaron Cohen.)

One interesting aspect of the Ioannidis et al. analysis is that I rank better using the composite score than just by my h-index. Based solely on the h-index, I would rank only 131st for OHSU and 37th in the primary medical informatics list. My C-score is improved by my relatively higher number of first-author and single-author papers, and citations to them. I also must have fewer co-authors on my papers than my colleagues at OHSU and in informatics, as I do better with the hm-index, which adjusts for the number of authors on a paper. At OHSU in particular, where I rank 49th overall and 131st by h-index, I rank 51st in hm-index, 37th in citations to single-authored papers, and 41st in citations to single- and first-authored papers. My 104 single- and first-authored papers rank me 22nd at OHSU. My data for the Ioannidis et al. analysis is available in a spreadsheet (Enjoy!).

On a final note, I am pleased to report that citation indices are a family affair for me. My daughter Alyssa Hersh, MD, MPH is currently a resident in Obstetrics & Gynecology at OHSU. She is also a rising researcher, and as of this writing has a Google Scholar h-index of 6 and a Scopus h-index of 4. I have no doubt she will surpass my current citation metrics long before she reaches my current age!


[1] Ioannidis, J.P.A., Klavans, R., Boyack, K.W., 2016. Multiple Citation Indicators and Their Composite across Scientific Disciplines. PLoS Biol 14, e1002501.

[2] Ioannidis, J.P.A., Boyack, K.W., Baas, J., 2020. Updated science-wide author databases of standardized citation indicators. PLoS Biol 18, e3000918.

Wednesday, July 14, 2021

Translational Artificial Intelligence: A Grand Challenge for AI

The potential for artificial intelligence (AI) to transform biomedicine and health is immense, yet at this time that potential remains largely unfulfilled. As I have noted in this blog over the years, there have been many impressive achievements in applying AI to biomedical and health data using clean and well-curated data sets, yet its use in every day medical care or health pursuits is modest. I have noted the reasons for this gap over the years in various postings, namely in the need to move capabilities beyond prediction to the ability to take action on them and the importance of showing actual clinical value, whether in leading to better health outcomes or care delivery. Failure to achieve these will relegate AI to the same fate as its first generation in the last century.

The premiere biomedical research agency in the US, the National Institutes of Health (NIH), has recognized the need to advance the science of AI in biomedicine. As such, the NIH has launched a new initiative, Bridge to Artificial Intelligence (Bridge2AI), which aims to "propel biomedical research forward by setting the stage for widespread adoption of artificial intelligence (AI) that tackles complex biomedical challenges beyond human intuition."

I applaud this program, and hope it will address the larger picture of translating current advances in AI into algorithms and systems that truly lead to improved health outcomes and care delivery. Along the way, it will hopefully address other issues related to AI, such as deploying AI ethically, focusing on solving important problems, and developing human expertise, not only of those who implement and evaluate AI systems but also the clinicians who employ them in their professional practice and patients who understand the benefits and limitations.

The Bridge2AI program recently hosted a virtual workshop series. One of these was devoted to enumerating grant challenges for AI in biomedicine. Participants were allowed to suggest grand challenges related to any aspects of the problems or solutions. I submitted a grand challenge focused on what I perceive is the need for translational AI, i.e., building on the successes in the "basic science" of showing the predictive value of algorithms to studying and ultimately deploying evidence-based AI in the real world. My grand challenge was one of 25 accepted by the meeting organizers for presentation to workshop attendees. We were allowed to use one slide, which is shown below.

To reiterate from my slide and presentation, I noted that most AI and machine learning research is still at the "basic science" stage of the biomedical research pipeline. Advances have been made with clean and well-curated data sets in simulated settings. Just as drugs and devices must progress from the lab to patient care, AI advances must do the same. In other words, moving from prediction to prescription and providing value. There are all sorts of potential ethical issues that must be addressed in the translational activities, such as balancing privacy protection vs. the public good, identifying and eliminating bias in data and algorithms, and ensuring the resulting actions do not exacerbate groups that have historically been discriminated against in health and healthcare. It is also critical that the "people perspectives" are addressed to develop the expertise in scientific as well as sociotechnical issues, including patients/consumers, clinicians, and researchers. In particular, appropriate education must be provided for clinical users and leaders to maximize value and minimize harm from these approaches. I am hardly the only person to hold these views, and a number of others have articulated the importance of AI providing real-world value in its application in biomedicine and health.[1-3]

One concern I have for Bridge2AI is that the first round of funding opportunities is focused on data generation projects. Generating high-quality, ethically-sourced, and relevant data is of course necessary, but is not sufficient. In fact, I have a hard time aligning what is proposed in my grand challenge with this initial funding opportunity. I hope that Bridge2AI will broad the focus of research and usher in translational research and ultimately demonstrates its true potential to improve human health.


1. Allen, B., Agarwal, S., Kalpathy-Cramer, J., Dreyer, K., 2019. Democratizing AI. Journal of the American College of Radiology 16, 961–963.
2. Wiens, J., Saria, S., Sendak, M., Ghassemi, M., Liu, V.X., Doshi-Velez, F., Jung, K., Heller, K., Kale, D., Saeed, M., Ossorio, P.N., Thadaney-Israni, S., Goldenberg, A., 2019. Do no harm: a roadmap for responsible machine learning for health care. Nat. Med. 25, 1337–1340.
3. Faes, L., Liu, X., Wagner, S.K., Fu, D.J., Balaskas, K., Sim, D.A., Bachmann, L.M., Keane, P.A., Denniston, A.K., 2020. A Clinician’s Guide to Artificial Intelligence: How to Critically Appraise Machine Learning Studies. Transl Vis Sci Technol 9, 7.

Friday, June 4, 2021

Virtual Graduation Message for 2021 OHSU Biomedical Informatics Graduates

I never imagined before 2020 that I would ever take part in a virtual graduation ceremony as I did in 2020, and now it is hard to believe that I am doing the same in 2021. As I noted last year, one of my favorite activities of the academic year is the Convocation and Hooding Ceremony, where we honor graduates of Oregon Health & Science University (OHSU), including those graduating from the OHSU Biomedical Informatics Graduate Program. Despite the pandemic over the last year and a quarter, we have 33 graduates this year from our PhD, Master of Science and Graduate Certificate programs. Since the programs inception in 1996, we have awarded 905 degrees and certificates to 815 people. I am very proud of all they accomplished during their time at OHSU and now beyond in various academic, industry, government, and other settings.

This year’s annual OHSU Convocation and Hooding Ceremony will take place virtually on Sunday, June 6, as noted in our department blog. Here is the transcript of my video message to the Class of 2021 graduates of the OHSU Biomedical Informatics Graduate Program:

It gives me great pleasure to welcome the 2021 graduates of the OHSU Biomedical Informatics Graduate Program to this year’s virtual Commencement ceremony. I never thought we would have a second virtual Commencement this year, but the pandemic is not yet fully behind us. With more and more people getting vaccinated each day, however, I am confident that next year’s ceremony will be in person, and I hope OHSU finds a way for those participating virtually the last couple years to take part in person in some way. If nothing else, we will celebrate next year at our annual DMICE banquet around graduation time that all alumni are always invited to attend. I do miss the pomp and circumstance of graduation, and getting to wear regalia and march in the procession.

As many of you know, the annual Commencement ceremony is an important event for me, as I enjoy every year celebrating the success of our graduates and their moving on to new paths in their lives. We have been awarding degrees and certificates from our program since 1998, and only once have I had to miss Commencement.

In any case, most of you are now moving from your studies into jobs where the contributions of informatics are more critical than ever. Just as the pandemic has exposed problems in our healthcare system, it has also exposed limitations in our data and information systems. It is critical for all informatics graduates, and everyone else in the informatics field, to keep improving how we use data and information, not only to overcome COVID-19 but also to improve health, health care, public health, and biomedical research generally. From bio- to imaging to clinical and public health informatics, the challenges have never been greater. I am confident that you all have the talent, and the knowledge and skills you have acquired in your studies, to meet those challenges.

I am pleased to report that with the 33 of you graduating today, our program has now awarded over 900 degrees and certificates dating back to 1998. These include 398 master’s degrees and 34 PhD degrees. Our graduates have achieved success in academia, industry, government, and just about every other place where informaticians work. Your success is one of the main aspects of our work that gives faculty and staff great satisfaction.

Let me close as always to remind you that even though you are moving on from OHSU and DMICE, we are still here for you and hope you will keep in touch with us as your careers develop and prosper.

Thursday, April 8, 2021

Response to NIH RFI: Comments and Suggestions to Advance and Strengthen Racial Equity, Diversity, and Inclusion in the Biomedical Research Workforce and Advance Health Disparities and Health Equity Research

In addition to its public health problems, the COVID-19 pandemic has exposed other fault lines in society, not the least of which is systematic racism that still pervades American society. A more equitable society would ensure diversity and inclusion in all aspects of life, including in healthcare and in biomedical research. The National Institutes of Health (NIH), the premier US federal agency that funds biomedical research, has recognized the need for its activities to be more inclusive of all Americans from every background. Not only must biomedical research reflect the health issues for the entire US population, its workforce should ideally reflect the ethnic and racial makeup of our larger society. The NIH recently issued a request for information (RFI), asking for Comments and Suggestions to Advance and Strengthen Racial Equity, Diversity, and Inclusion in the Biomedical Research Workforce and Advance Health Disparities and Health Equity Research. This posting contains the comments I submitted in response to this RFI.

While others will likely comment on the need for biomedical research itself to address health disparities and move toward health equity, it is equally important to address the needs of the biomedical research workforce that will contribute solutions to these problems. The NIH has already made a tremendous commitment to diversity and inclusion, including in building career pathways the biomedical research workforce, but additional efforts must be made to facilitate access to these programs by extramural researchers and leaders.

One example is the Building Infrastructure Leading to Diversity (BUILD) Initiative, which has a prominent program in our region.

Nonetheless, there are still challenges for engaging the potential future biomedical research workforce. My particular concern is how to increase diversity and inclusion among faculty of academic health science centers.

One of the challenges is explaining to young minds the opportunity and the work of biomedical research. While most young people are familiar with healthcare professionals - i.e., physicians, nurses, and pharmacists - fewer are familiar with the work and importance of researchers. Schools and communities themselves may not be aware of career opportunities. There should be resources committed, and easy-to-use tools made available, so that academic health science centers and others can disseminate information about careers and the rewarding work of biomedical research.

A second challenge is for researchers themselves to have the time to engage in such mentoring and teaching. As demands for productivity by biomedical research faculty in academic health science centers increase - i.e., keep grants funded and students taught - there is less time in their busy schedules for this critical activity. Such activity is also unlikely to "count" toward promotion or lead to that next grant. There should be standards for promotion committees in academic health science centers to require diversity and inclusion outreach. Of course, this must not be an "unfunded mandate," and instead be an activity that has committed time from institutions.

A third challenge is that success in biomedical research typically requires a graduate degree. As such, the road to college and then graduate or professional school is long and can be expensive. There must be pathways for students, especially for those of limited resources with few parental or other role models, to be helped through that long path. There should be opportunities provided, along with appropriate mentoring, for students to enable them to stay engaged during the long journey. Students should not only be given sustained exposure, but also be taught knowledge and skills along the way.

My own work is as an academic faculty in biomedical and health informatics, where I daily experience the satisfaction of research and teaching. While my field has made some strides in diversity and inclusion, it still has a long way to go to reflect our the racial and ethnic distribution of our larger society. Many who want to spend time engaging with future diverse researchers and professionals in the field need help in overcoming the above barriers. This leads to questions that must be answered:

  1. How do we engage with schools, community organizations, and others to expose high school and perhaps even younger students to biomedical research?
  2. How do we provide academic faculty with the protected time and academic credit for this work of critical importance?
  3. How do we develop pathways to sustain the interest and achievement for students, especially those from backgrounds that include little exposure to higher education?

We can and should require our academic health science centers and their faculty and others to engage with historically underrepresented groups in biomedical research, but make sure that they have the time and the tools, with milestones and outcomes measured, to achieve these goals. This should consist of:

  1. The availability of resources and tools to engage young minds in the possibilities for careers in biomedical research
  2. Expectations and protected time for existing faculty to devote effort to engaging with young students, including requirements to achieve promotion
  3. Developing pathways to sustain interest and achievement toward careers in biomedical research

By making diversity and inclusion efforts an expected activity of all biomedical research faculty and providing such faculty the resources and opportunities, we can achieve the shared aim of the biomedical research workforce and its activities reflecting the larger population of our country.

Thursday, February 25, 2021

A New OHSU Course in Applied Clinical Data Science and Machine Learning for Health & Clinical Informatics (HCIN) Students

I have written over the years about the need for all who work in biomedical and health informatics to have appropriate knowledge and skills in data science, machine learning (ML), artificial intelligence (AI), and related topics. I am now excited to announce that our OHSU Biomedical Informatics Graduate Program is launching a new course in Applied Clinical Data Science and Machine Learning for Health & Clinical Informatics (HCIN) majors.

The goal of this new course is not to provide students with the mastery of ML and AI tools and techniques; rather, it is to provide a conceptual understanding of their practical application in health and biomedicine. The course is not meant to be a substitute for the sequence of courses available in the other major in our program, Bioinformatics & Computational Biomedicine (BCB), whose offerings delve far more into the theory, mathematics, and programming of these topics and include:

  • BMI 551/651 - Statistical Methods
  • BMI 531/631 - Probability and Statistical Inference
  • BMI 543/643 - Machine Learning
  • BMI 525/625 - Principles and Practice of Data Visualization

The new HCIN course will be focused on applied data science and machine learning, with a focus on clinical data sets as well as clinical issues and challenges in their application. While the course will have some programming activity (requiring Python programming as a prerequisite), it will focus on a hands-on, high-level view of the different types of machine learning methods and their applications. It will also cover the topics of data management and selection, pitfalls in building and deploying models, and critical appraisal of clinical machine learning literature. The course will aim to provide an in-depth understanding for those who will work alongside experts who develop, build models, implement, and evaluate machine learning applications in health and clinical settings.

The textbook for the course will be: Hoyt, R. and Muenchen, R. (Eds.), 2019. Introduction to Biomedical Data Science, The course syllabus provides further details on the topics to be covered.

The content of the course will be based on a combination of what faculty and students believe is most important for a course like this. Among the topics that be included are:

  • Data sources - electronic health records, registries (e.g., N3C, AllOfUs), patient-generated, social media, public health
  • Data preparation (wrangling) - cleaning, quality analysis, feature selection, de-biasing
  • Exploratory data analysis - summaries, correlations, visualizations
  • Machine learning approaches and models - supervised, unsupervised, reinforcement, deep learning
  • Software and tools available
  • Common pitfalls and misunderstandings of applying machine learning
  • Critical appraisal of clinical machine learning literature
  • Ethical issues and challenges

The 3-credit course will be taught in the OHSU spring academic quarter, which runs from late March to early June. The lead instructors will be Steven Chamberlin, ND and myself, with other department faculty contributing. As with all courses in the HCIN major, it will be mostly online and asynchronous, with some option synchronous activities (which will be recorded for those not able to attend). This course will be different from to complementary to other data science-related courses in the HCIN major, including:

  • BSTA 525 - Introduction to Biostatistics
  • BMI 540/640 - Computer Science and Programming for Clinical Informatics
  • BMI 544/644 - Databases
  • BMI 524/624 - Data Analytics for Healthcare
  • BMI 516/616 - Standards/Interoperability in Healthcare
  • BMI 537/637 - Healthcare Quality
  • BMI 525/625 - Principles and Practice of Data Visualization

I will be excited to see how this course is accepted and how it evolves based on feedback of students and others. I suspect there will be interest beyond our graduate program.

Monday, February 22, 2021

Vaccinated and Vaccinating: The End May Be Near?

I was delighted to learn in early January that my institution, Oregon Health & Science University (OHSU), made the decision like many medical centers to offer the SARS-CoV-2 vaccine to all employees, not just those at the front line of care delivery. I received my first and second doses of the Pfizer vaccine on January 2nd and 23rd. I had some minor malaise the day after the second dose, but was thrilled to have received the vaccine.

I also decided that since I received an early dose, I would do everything I could to support the national and global effort to disseminate the vaccine. To that end, I have volunteered to work shifts at the OHSU Portland International Airport Vaccine Clinic. While I thought I might put my medical training to use giving injections, it turns out that the greater need was for registration and check-in personnel. I suppose it is most appropriate for the Chair of the informatics department to be checking in and scheduling follow-up appointments in Epic for those coming for their shots. But I actually enjoy the job I am doing at the site, interacting with people driving through the site and expressing gratitude they are able to get vaccinated. It is also nice to put on a friendly face for our university.

Overall, I feel a sense that the end may be near for the worst of this pandemic that has upended our lives. While the complete end will not come any time soon, and we will likely need to be vigilant about SARS-CoV-2 for years to come, I am hopeful that the vaccine rollout will continue at a strong pace and allow us to gradually resume more normal living. I am also encouraged that the COVID-19 numbers of cases, hospitalizations, and deaths are trending downward, and that we have new science-driven leadership in our federal government.

Looking ahead, I yearn to be around people at work, in social settings, and, yes, traveling. Regarding the latter, it has been almost a year since I have been on an airplane, although I am planning to visit my elderly stepfather, my last living adult relative, next month in Florida. He will have received his second dose a couple weeks before I visit.

There are many unanswered questions about what life will be like in the long run. Will work move to a more virtual arrangement? What will come of city centers that have been hurt by the pandemic and resulting economic and social upheaval? What will come of academic meetings and conferences, many of which probably could be done more virtually? Even though I spend a great deal of work time in front of a computer, I am still a social being. Social media has taken the sting off of the interpersonal isolation, but there is nothing like being around other people, and I am hopeful that much of that will eventually return. We will see as 2021 unfolds.

Thursday, December 31, 2020

Annual Reflections at the End of 2020

Since the inception of this blog in 2009, I have ended each year with a post reflecting back on the year. In the early years, a good deal of the focus of this blog was on the HITECH Act, especially its workforce development provisions. Later on, there were other topics such as the clinical informatics subspecialty and emergence of data science. And many more.

And now, the end of 2020, which has been a year like no other. The COVID-19 pandemic has upended our lives and society. It has not only created a public health emergency, but also uncovered other fault lines in our society, from systemic racism to political leadership more focused on personal aggrandizement than solving real problems in society.

Despite these challenges, other aspects of 2020 were successful. From a professional standpoint, my research and educational work barely missed a beat. I mostly publish as a senior author these days, and my name appeared in that position in a number of publications. I maintained my educational work as well, not only directing the OHSU Biomedical Informatics Graduate Program but also adding teaching that was needed to fill in for lost opportunities in the pandemic, especially for medical students.

I spent a fair amount of time in 2020 trying to reflect on gratitude, especially the value of the continuity of family and friends. There is no question that having a lifetime of friends and colleagues made the (hopefully temporary) transition to virtual life more tolerable. While life on the other side of COVID-19 will no doubt be different, I do look forward to returning to in-person interaction and being able to travel.

This all said, I am optimistic going into 2021. Vaccines are being rolled out, starting first with frontline workers and high-risk populations and then later to the rest of us. A new US political leadership promises a return to decision-making based on science and human dignity. And the need for the research and education in informatics will be needed more than ever.

Monday, December 28, 2020

Kudos for the Informatics Professor - Summer/Fall 2020 Update

You might not know it from the presence of the COVID-19 pandemic, but I was quite busy and productive since being relegated to virtual work since mid-March of 2020. In the last of my periodic kudos postings, I described all of what I accomplished in the first half of 2020, some of which took place during the early dark days of the pandemic. In the rest of 2020, I have published a number of scientific papers and book chapters as well as given a number of talks, some in distant places, albeit virtually.

Here is a list of papers published in the latter half of 2020:
I also published a number of book chapters in the second part of this year (in addition to my own book, and stay tuned for some chapters in other books coming in the near future):
Here is a list of talks given since my last kudos posting:
As noted earlier this year, I was elected President of the International Academy of Health Sciences Informatics (aka, The Academy). Since then, OHSU featured a posting about it and I had a chance to represent the Academy in a panel with the World Health Organization and its Director General Dr. Tedros Adhanom Ghebreyesus. The panel took place on December 16, 2020 and was entitled, Digital Health during COVID-19: Opportunities and Challenges. One of the topics I spoke on was the need for training and competence in informatics for both informatics as well as healthcare professionals.
As the pandemic relegated our educational program recruitment to virtual form, I had the opportunity to be featured with other faculty and students in promotional videos for our informatics educational programs:

I am pleased that 2020 turned out to be an academically productive year for me, but I am more than eager to return to normal living as vaccination and herd immunity are achieved for COVID-19 in 2021.

Tuesday, December 22, 2020

Next Year, Immune

There is a famous line at the end of the Jewish Passover Seder, Next year in Jerusalem. While some interpret the phrase literally, to most it means that next year the community will be together and stronger, no matter where in the world everyone is.

As the current COVID-19 pandemic rages out of control, there are some signs of hope. Two vaccines have been approved and are being rolled out across the country and the world. While I am envious of friends who are posting pictures of themselves getting their first injection on social media, I am content to wait my turn in line, as I am not a frontline clinician or other frontline worker, nor do I have co-existing medical conditions that would put me at higher risk for complications if I were to get infected with SARS-CoV-2. I will wait my turn, although I will show up in a heartbeat when my number is called, which I anticipate will be in the spring or summer of 2021.

In the meantime, while we are all waiting to get our vaccine shots, there are other things we can and should be doing, such as wearing masks and social distancing. I have lent my endorsement to another effort, signing my name on to a letter calling for the development of cheap, rapid, and frequently administered antigen tests. The idea of these tests is that if we all test frequently, we can learn if we are infectious and self-quarantine. These tests do not have same sensitivity and specificity as PCR tests, but they are much faster and cheaper, and tend to be positive when one is actively infectious. If we all used these simple paper-strip tests a couple times a week, and just as importantly, self-quarantined when positive, we could keep the virus at bay until we all have herd immunity from the vaccine.

Despite this being one of most challenging years in the history of many of our lives, I look to the future with an optimistic eye. The toll of COVID-19 has been devastating, not only to those who have perished but also the devastated economy and disruption of education, especially for children. But in the end, science will prevail and, over time, the worst of the pandemic will be behind us.

I feel fortunately in having always lived a relatively virtual work life, as noted in this blog last year, and I have had little trouble staying productive in the pandemic. But that does not mean that I miss going into the office, or attending conferences and other events. I am fortunate enough to have a lifetime of friends and colleagues, and keeping in touch with them by social media, videoconferencing, and the like has been easy. I am sure it is different for those without such a long time to build interpersonal bonds, such as those earlier in their careers.

Thus I do look forward to having immunity to SARS-CoV-2, or at least the COVID-19 disease that it causes. I look forward to seeing my family, friends, and colleagues again, and getting to once again visit the world. Travel will likely be different on the other side, not only due to the pandemic but also due to climate change, but I am confident I will again visit so many wonderful people and places around the world.

Friday, November 20, 2020

Assuming the Presidency of the International Academy of Health Sciences Informatics

One of the most enjoyable aspects of my work in biomedical and health informatics is the opportunity to interact with colleagues from around the world. As I wrote early on in the history of this blog, informatics is a field of global truths. Countries may have different healthcare systems and different resources for information technology, but informatics is driven across the planet by the goal of using information and data to improve all aspects of health and healthcare. Those of us in the academic portion of the field are also driven by research to push the boundaries of what can be done and by education to disseminate knowledge to current and future practitioners, researchers, and leaders in the field.

It is from this perspective that I am gratified to have been elected President of the International Academy of Health Sciences Informatics, or the Academy for short. I am assuming this role from my esteemed colleague and friend, Dr. Reinhold Haux, who has served as the Inaugural President of the organization. My main disappointment in starting my role is that I will need to do so virtually due to the COVID-19 pandemic. I would much prefer to have been in attendance with my friends and colleagues from around the world at the Plenary session of the Academy this weekend in Hamamtsu, Japan.
The Academy was established in 2017 by the International Medical Informatics Association (IMIA). As noted on its Web site, the Academy "serves as an honor society that recognizes expertise in biomedical and health informatics internationally. Academy Membership is one of the highest honors in the international field of biomedical and health informatics.  The Academy will serve as an international forum for peers in biomedical and health informatics. The Academy will play an important role in exchanging knowledge, providing education and training, and producing policy documents, e.g., recommendations and position statements.” With the recent election of the Class of 2020, there are now 179 fellows from around the world, diverse in their gender, ethnicity, and nationality.

I have had the pleasure of participating in almost all of the plenary sessions of the Academy so far. I am also guided by the vision for the Academy as published by Dr. Haux [1, 2] as well as the strategic focus document by the initial Board that was recently published [3]. I will draw on the latter document as a launching point activities of the fellows. My guiding principles will be to organize working groups accountable to the larger Academy and to be collaborative and non-duplicative with other informatics organizations and efforts. I look forward to this exciting two-year journey.
1. Haux, R., 2018. Visions for IAHSI, the International Academy of Health Sciences Informatics. Yearb Med Inform 27, 7–9.
2. Haux, R., Ball, M.J., Kimura, M., Martin-Sanchez, F., Otero, P., Huesing, E., Koch, S., Lehmann, C.U., 2020. The International Academy of Health Sciences Informatics (IAHSI): IMIAs Academy is Now Established and on Track. Yearb Med Inform 29, 11–14.
3. Martin-Sanchez, F., Ball, M.J., Kimura, M., Otero, P., Huesing, E., Lehmann, C.U., Haux, R., 2020. International Academy of Health Sciences Informatics (IAHSI): Strategy and Focus Areas, 1st Version. Yearb Med Inform 29, 15–25.

Friday, November 13, 2020

A Fall Conference Year Like No Other

A staple in my life each fall, dating back to 1986, is my annual attendance of what is now called the AMIA Annual Symposium. This year marks my 35th consecutive year of participation. I first attended this meeting when it was still called the Symposium on Computer Applications in Medicine Care (SCAMC).  I was a third-year internal medicine resident at the time, seeking to learn more about the field and how to pursue training in it. Since 1986, I have never missed this meeting each fall.

Of course, the 2020 version of the AMIA Annual Symposium will be like no other. We are in the midst of the COVID-19 pandemic, so like most scientific meetings in 2020, this year's meeting will be virtual. That won't keep me from attending all the meeting's usual events, including the opening session, the induction of fellows (of both ACMI and AMIA), the leadership gala dinner, the association business meeting, numerous scientific sessions, and the closing session. I will also conduct another staple AMIA activity of mine I have been doing since 2005, which is the in-person session that culminates the 10x10 course and will take place virtually this year. Finally, I will be making an appearance at the Oregon Health & Science University (OHSU) virtual booth in the Career Expo portion of the Exhibit Hall (see image below)

Although many activities will be recast in virtual format, there will be others not taking place that I will miss. My colleagues in AMIA are among my best friends in the world. Although my academic work interdigitates with a number of scientific fields, in the end, my primary field is informatics and the AMIA symposium is where the field all comes together. The social aspects of the meeting, from formal activities to hallway conversations, are what makes this meeting most special. I have often joked that walking across the hotel lobby at the meeting usually takes as much as an hour, stopping to say hello to so many friends and colleagues, one after another. And waving hello to so any others riding in opposite directions on the hotel escalators. AMIA also has among the greatest staff for professional organizations, with great longevity and institutional knowledge for putting on great meetings.

Another meeting I have attended almost every fall that typically occurs in proximity to AMIA is the Text Retrieval Conference (TREC). I attended the first TREC meeting in 1992 and have missed a few over the years, but otherwise have attended almost all of them. It has been gratifying to contribute to the leadership of the series of biomedically-oriented information retrieval challenge evaluations. At the 25th anniversary of TREC in 2016, I enjoyed giving an overview talk on all of the biomedical tracks up to that time (starting at just past 50 minutes into the Part 3 of the recorded Webcast). As with AMIA, the social aspects and hallway conversations are also what makes attending the meeting so enjoyable.

Some years I have had to made compromises with AMIA or TREC when they have been the same week but in different cities. Like AMIA, the TREC meeting will be virtual this year as well, and actually spread out over the entire week that also includes AMIA. But one upside to both conferences being virtual is that I can jump back and forth between the meetings.

These virtual conferences come on the heels of some of the early results of COVID-19 vaccines being released in the news media. I do hope that next year at this time, I will have immunity to SARS-CoV-2 as I attend in person both the AMIA and TREC meetings. We will see in retrospect that turns out to be wishful thinking.

Wednesday, November 11, 2020

15 Years of 10x10 ("Ten by Ten")

I like to believe that I have made many contributions to the field of biomedical and health informatics over the years, but I suspect the one that will most define my legacy in the field is the conceptualization and implementation of the first and still flagship course of the American Medical Informatics Association (AMIA) 10x10 program. This year marks the 15th year of the course, which has been completed by over 2700 people, dating back to 2005.

For me, the 10x10 course fulfills the three criteria of the Jim Collins' Good to Great hedgehog. I am passionate about the course as a way to disseminate knowledge of the informatics field. I also believe I am well-skilled in my ability to cover the important areas of the field, making them understandable, and giving the big picture and context of why they are important to biomedicine and health. And finally, the course has a revenue stream that enables me to devote a significant amount of my work time to teach it and keep it up to date.

I have always enjoyed teaching at the introductory level, introducing people to the field. The introductory course that comprises 10x10 came from an introductory course I first taught in the MPH program at Oregon Health & Science University (OHSU), Public Health 549, starting in the early 1990s. When we launched our informatics master’s degree program in 1996, that course became Medical Informatics 510 and it has served as the introductory course (now called Biomedical Informatics 510, or BMI 510) in our Biomedical Informatics Graduate Program to this day. The course has also been taken by students in other disciplines, including medicine, nursing, basic biomedical sciences, public health, and more.

I maintain a Web page that describes the course. It includes a link to the AMIA site where one can register for the next offering. I recently updated my chapter about the course in newly published second edition of Eta Berner's informatics education in healthcare book (Hersh W, Online Continuing Education in Informatics - the AMIA 10x10 Experience, in Berner ES (ed.), Informatics Education in Healthcare: Lessons Learned, 2nd Edition, New York: Springer, 2020, 251-262).

It would probably be a fascinating study to do a word analysis of my slides in the course. It would be interesting to see when various terms came into being used, such as “health information exchange” or “machine learning,” and which ones have faded away, such as “meaningful use.” It might also be interesting to see terms whose frequency have decreased and re-emerged over time, such as “artificial intelligence.” The image below shows a word cloud of the syllabus of the latest offering of the course.
The 10x10 course came about when then-President of AMIA Charles Safran called in 2005 for at least one physician and one nurse in each of the 6000 or so hospitals in the US to be trained in informatics. He asked directors of informatics education programs such as myself how many more students their programs could take. Many said they could increase 2-3 fold. However, as OHSU had already been teaching online since 1999, I told him that with enough lead time, we could expand and educate “all of them.” Rounding off some numbers, I came up with the name 10x10, indicating we could train 10,000 people by the year 2010. Ten thousand people did not show up, although I genuinely believe we could have handled that many with enough advance planning.

We also structured the 10x10 course so that those wanting to get academic credit for the OHSU BMI 510 course and pursue further study in the OHSU Biomedical Informatics Graduate Program. About 10-15% of those taking the course have chosen this option, pursuing the OHSU Graduate Certificate or Master of Science degree. Two of them ended up working all the way to a PhD. Others transferred the credits to educational programs at other institutions.

I offer the course three times a year with AMIA, with the four-month course starting each December, April, and July. The course includes an optional face-to-face session at the end of the course, where those completing the course meet those they have been studying with for the last several month and present their small course projects. I also provide special offerings with other groups, such as the American College of Emergency Physicians and Gateway Consulting in Singapore. The latter has been offered with my colleague KC Lun, PhD and includes 310 of the course's 2700 graduates. I have enjoyed my many trips to Singapore for the in-person session at the end of the course and have come to know the country, its stellar healthcare system, and its strong health IT environment well. I have also provided offerings in Thailand, Israel, Saudi Arabia, United Arab Emirates, and South Africa.

The 10x10 course is part of the fabric of my career. I have an offering of the course running almost all the time and do not foresee stopping this activit I enjoy so much any time soon. I am gratified that it has been an entry point into the informatics field for many of them.

Wednesday, October 28, 2020

What is the Work of Informatics? Integration of Recent Workforce Analyses

In 2006, I published a paper entitled, Who are the Informaticians? - What We Know and Should Know [1]. As my interest in developing educational programs was growing at the time, I was also thinking about the nascent growth of biomedical and health informatics as a profession. Since I had entered the field in the late 1980s, informatics was mostly a research discipline. But with the growth of information technology (IT) adoption in healthcare and other aspects of biomedicine, informatics was becoming a profession that included operational, research, and academic roles and activities.

The last decade (2010-2020) has seen progress in answering my questions from 2006 paper. There has been progress in defining the field on several fronts, although not all efforts have been fruitful. Beginning with the rollout of the HITECH Act, the health IT workforce was viewed as an essential component for success [2]. Professional certification in informatics emerged, first for physicians [3] and soon for others working in the field [4]. The work in preparing for the physician subspecialty led to the development of a core content outline for the field, which would be used among other things for the content of the physician board certification exam [5]. Other efforts led to definitions of competencies for graduate study in biomedical informatics broadly [6] and more focused in master’s-level applied health informatics [7]. One unsuccessful effort was the attempt to become defined in US federal labor statistics through the designation of a Standard Occupational Classification (SOC) code [8]. Health informatics was included in the initial 2018 update of the SOC, but was ultimately left on the proverbial BLS cutting-room floor [9].

A more recent effort has been led by AMIA in conducting two parallel analyses focused on defining the knowledge, skills, and tasks of people who work in informatics [10, 11]. The results have been published in two papers that focus on one narrow and one broader group. The narrow group consisted of physicians in the clinical informatics subspecialty (CIS) [10]. One goal of this effort was to update the core content that was now nearly a decade old and still being the “study guide” for the board certification exam. The larger group consisted of all who work in health informatics (HI), which was defined broadly to include those who work in informatics focused on individual health, healthcare, public health, and research [11].

Interestingly, the workforce analyses conducted by AMIA for the CIS and HI groups led to very similar results. Each found five domains of practice that define the required knowledge, skills, and tasks of informatics practice and research. One interesting yet unsurprising result of the analysis was that four of the domains were relatively similar to those of the original CIS core content [5], while the fifth domain showed the growing importance of issues related to data, including its capture, governance in organizations, and analytics. New uses of the data existed during the time of the original CIS core content but played a small role in the field, such as machine learning and predictive analytics.

I recently took a deep dive into both analyses, with a major aim of identifying the similarities. I describe my findings here (and take any blame for any misrepresentation of this impressive body of work). Both analyses describe the first domain of fundamental knowledge and skills, which include a common vocabulary, basic knowledge across all informatics domains, and understanding of the environment(s) in which the workforce functions. Depending on where an individual works, this may include consumer health, health care, public health, or research settings.

The second domain differs somewhat between the HI and CIS analyses but can be integrated into an overall focus on enhancing health decision-making and improving health care delivery and outcomes. Informatics practice should support and enhance decision-making by clinicians, patients, policy makers, researchers, and public health professionals. It must also analyze existing health processes and identify ways that health data and health information systems (HIS) can enable improved outcomes. Informatics work should also evaluate the impact of HIS on professional practice as well as pursue discovery and innovation. More clinically, informatics practice should be able to develop, implement, evaluate, monitor, and maintain clinical decision support while also supporting innovation in the health system through informatics tools and processes.

The third domain of each analysis can be combined into an overall category of health and enterprise information systems. Informatics practice should include planning, developing or acquiring, implementing, maintaining, and evaluating HIS that are integrated with existing information technology systems across the continuum of care. This should include the clinical, consumer, and public health domains and address security, privacy, and safety considerations. This domain should also include the development, curation, and maintenance of institutional knowledge repositories, also while addressing security, privacy, and safety considerations.

A critical domain is the new addition to the previous four domains of the CIS core content, which can be integrated as data governance, management, and analytics. Practice should include establishing and maintaining data governance structures, policies, and processes. The workforce should be able to acquire and manage health-related data to ensure their quality and meaning across settings and to utilize them for analysis that supports individual and population health while driving innovation. It is also critical to incorporate information from emerging data sources, ensure data quality and meaning across settings, and derive insights to optimize clinical and business decision-making. Although not explicitly mentioned in the overall descriptions of this domain (but covered in the details of practice) are the ability to identify and minimize biases in data and mitigate their impact as well as to implement and evaluate machine learning and artificial intelligence applications in all health-related settings.

The final domain reflects the organizational and management aspects of informatics, with required abilities in leadership, professionalism, and transformation. Informatics practice should be able to build support and create alignment for informatics best practices as well as lead informatics initiatives and innovation through collaboration and stakeholder engagement across organizations and systems.

Although it is valuable to have the requirements for the workforce well-elucidated, the results of the new analyses are hardly surprising. We have known for many years that biomedical and informatics is a sociotechnical discipline, i.e., influenced by the interaction between social aspects and use of technology. We also know from prior explorations of competencies for master’s-level education that foundational knowledge and skills are required from health sciences, social sciences, and information sciences [7]. This new work demonstrates more clearly the work of informatics, and future work will hopefully quantify the different types of professionals and their require knowledge and skills.


1. Hersh, W., 2006. Who are the informaticians? What we know and should know. J Am Med Inform Assoc 13, 166–170.

2. Hersh, W., 2010. The health information technology workforce: estimations of demands and a framework for requirements. Appl Clin Inform 1, 197–212.

3. Detmer, D.E., Shortliffe, E.H., 2014. Clinical Informatics: Prospects for a New Medical Subspecialty. JAMA 311, 2067–2068.

4. Gadd, C.S., Williamson, J.J., Steen, E.B., Fridsma, D.B., 2016. Creating advanced health informatics certification. J Am Med Inform Assoc 23, 848–850.

5. Gardner, R.M., Overhage, J.M., Steen, E.B., Munger, B.S., Holmes, J.H., Williamson, J.J., Detmer, D.E., AMIA Board of Directors, 2009. Core content for the subspecialty of clinical informatics. J Am Med Inform Assoc 16, 153–157.

6. Kulikowski, C.A., Shortliffe, E.H., Currie, L.M., Elkin, P.L., Hunter, L.E., Johnson, T.R., Kalet, I.J., Lenert, L.A., Musen, M.A., Ozbolt, J.G., Smith, J.W., Tarczy-Hornoch, P.Z., Williamson, J.J., 2012. AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline. J Am Med Inform Assoc 19, 931–938.

7. Valenta, A.L., Berner, E.S., Boren, S.A., Deckard, G.J., Eldredge, C., Fridsma, D.B., Gadd, C., Gong, Y., Johnson, T., Jones, J., Manos, E.L., Phillips, K.T., Roderer, N.K., Rosendale, D., Turner, A.M., Tusch, G., Williamson, J.J., Johnson, S.B., 2018. AMIA Board White Paper: AMIA 2017 core competencies for applied health informatics education at the master’s degree level. J Am Med Inform Assoc 25, 1657–1668.

8. Request/Recommendation for New Health Informatics Practitioner Standard Occupational Classification (SOC), 2016.

9. AMIA Washington Download: 12.18.17 Government Equates Informatics with Registrars New Occupation Codes, 2017.

10. Silverman, H.D., Steen, E.B., Carpenito, J.N., Ondrula, C.J., Williamson, J.J., Fridsma, D.B., 2019. Domains, tasks, and knowledge for clinical informatics subspecialty practice: results of a practice analysis. J Am Med Inform Assoc 26, 586–593.

11. Gadd, C.S., Steen, E.B., Caro, C.M., Greenberg, S., Williamson, J.J., Fridsma, D.B., 2020. Domains, tasks, and knowledge for health informatics practice: results of a practice analysis. J Am Med Inform Assoc 27, 845–852.

Thursday, October 1, 2020

Welcoming the 4th Edition of Information Retrieval: A Biomedical & Health Perspective

I am pleased to announce the publication of the 4th edition of my book, Information Retrieval: A Biomedical & Health Perspective. Published by Springer, the book updates the content, methods, results, and research in the use of search systems for knowledge-based biomedical and health information.

I am gratified to be active in a number of areas of research in biomedical and health informatics, but my original and still most active area is information retrieval (IR), also sometimes called search. The appeal of getting information from a computer by entering a query or question held appeal to me from early times, including when I was dabbling with computers in medical school and residency in the mid-1980s. Upon entering formal training in the field in my postdoctoral fellowship in 1987, this appeal persisted, even as the thrust of research in the field was still focused on the first era of artificial intelligence.

My introduction to the field came through a monograph by Prof. Bruce Croft, which then led me to discover the work of Prof. Gerard Salton. I had the opportunity to meet Salton when he visited Harvard University during my postdoctoral informatics fellowship there. Salton literally invented the IR field and it is unfortunate that he passed away in 1995 before he could see the true impact of his work on IR systems in the world. The approach of Salton and his legions of graduate students he trained in “automated” IR was quite different than the main biomedical focus in the 1980s and 1990s, which was the set-based Boolean retrieval approaches used to search MEDLINE. My earliest work attempted to marry the automated approaches to the controlled vocabularies being developed and collated in the National Library of Medicine (NLM) Unified Medical Language System (UMLS) Metathesaurus.

Another early interest of mine in IR concerned evaluation of systems and users. A perspective of evaluation has guided a great deal of my informatics research, based on the premise that what we do, whether building systems or advocating their use by people, should be studied for its value to human health and healthcare. My foray into IR research led me to recognize the importance of the relevance-based metrics of recall, precision, and their aggregated combinations, but I also felt dissatisfied that they did not evaluate the entire IR experience, especially for users. I was fortunate to be able to attend the very first Text Retrieval Conference (TREC), and then become involved in organizing a number of its tracks in subsequent years.

I never would have imagined in my early days that we would be able to carry around the Internet - and access to the world’s knowledge - in our pockets via mobile devices. I could not fathom that essentially all scientific publishing would become electronic, and that it would include not only articles but the underlying data. I also would never have imagined that searching would be so ubiquitous by all Internet users, or that the name of a search engine would become a verb (Googling).

The world of IR has certainly changed. The basic task of “ad hoc” searching is pretty well a solved problem. There are still, however, challenging problems in IR to solve, such as some of those on which I currently work.

Both the eBook and hardcover editions of the new edition are now available through Springer and Amazon. If you or your institution have access to SpringerLink, the eBook version can be accessed there.

Friday, September 4, 2020

Putting My Evidence Where My Mouth Is

Although my career has mostly been focused on informatics, I have always considered evidence-based medicine (EBM) to be a part of, or at least overlapping with, informatics. Even though I gave up seeing patients almost two decades ago, I still enjoy maintaining a connection to medical practice through my interest in EBM.

It therefore makes an imperative for me to volunteer to participate in a randomized controlled trial (RCT) for a SARS-Co-V-2 vaccine. If I advocate for more use of RCTs to discern what works in medicine, thus requiring others to participate in RCTs, I should put my own proverbial money where my mouth is. As such, I have entered my name into the US government registry of people volunteering for one of the three major COVID-19 vaccine RCTs for vaccine candidates from ModernaTX, AstraZeneca, and BioNTech SE and Pfizer. Although each of the three trials will enroll about 30,000 people, apparently the number of people who have entered their names into the registry is much larger, so not everyone will get called to participate.

Not only do I feel a call to duty to take part, but I am probably a good candidate for one of the trials. Although I am in relatively good health without any of the underlying conditions that increase risk of death and complications from COVID-19, I am in the age group where the risk starts to climb. I am also one who is eager to move on from this pandemic and return to normal life.

If I am called to participate in a trial, it will not be completely risk-free. The main risk, of course, is that I could be among the half of participants who end up in the placebo group. But even if I am given an actual vaccine, there are some other risks. One might be that the vaccine leads to adverse effects, such as Guillian-Barre Syndrome. Another is that vaccines can sometimes cause paradoxical effects, such as antibody-dependent enhancement, where viruses leverage antibodies to aid infection, or cell-based enhancement, which leads to allergic inflammation. And finally, I could end up in an RCT of a vaccine that turns out to be less efficacious than the others being tested.

There are other risks of participation related to the politics of COVID-19, which are being driven by a desire to have a vaccine approved by Election Day. This could be dangerous not only for those who participate in the trials, with both benefits and harms may not become fully apparent with a shortened trial, but also to society at large, in not knowing the true efficacy of the vaccines, and not being able to best compare the different candidates.

Although I am most disturbed by the politics, I am still willing to take the risks of participating if I am called. Bring on the informed consent form! I do hope this pandemic will end and the world can return to some semblance of normal soon.

Thursday, August 20, 2020

Surviving the Pandemic: A Half-Year On

In a few weeks, the COVID-19 pandemic lockdown will have been going on for a half-year for most people in the United States. I still remember its beginning in early March. Nothing in my entire life has impacted my personal and professional activities as much as this.

I can certainly remember my last trip, a short one to one of my favorite places to visit, Salt Lake City, UT. I was invited to give Department of Biomedical Informatics Grand Rounds at the University of Utah on March 5th. The morning I was leaving for Salt Lake City on the 4th, I had decided to cancel my planned trip the following week to Orlando, concerned about being with 40,000 other people at the HIMSS meeting, which I have attended annually for about 20 years. A few days later, HIMSS cancelled the conference.

I also remember the last leg of my flight home, thinking it might be a while before I was on an airplane again. That was prescient, as OHSU made the decision to institute work-from-home the following week. Not only have I not been in a plane since then, but I have no future airplane trips planned. Most of the meetings I normally attend have gone to virtual mode, and I suspect I will not get on an airplane until some time in 2021.

So for almost a half-year now, my daily commute to work consists of walking down the stairs from my bedroom to my home office in my basement. Fortunately I was already well used to working virtually. Most of what I do can be done sitting at my MacBook Pro connected to the Internet.

I have fortunately maintained my health, both through eating healthfully as well as maintaining my exercise regimen. Running has always been my exercise of choice, and it has helped that I have been able to continue doing it through the pandemic. My cross-training gym workout has moved from my former gym to my basement, and I have no idea if or when I might return to a gym.

While the first couple months were dark and depressing, things did lighten up with the arrival of summer. The days became longer and warmer, and the gradual re-opening of the economy in Oregon has allowed us to pursue outdoor activities, especially patronizing restaurants that seat outdoors, and even entertaining small groups - socially distanced - in the airy backyard of our house. Even though I ordinarily enjoy the fall, with the start of the school year, I worry that his year's return of shorter and cooler days will not be as pleasant as usual.

I have enjoyed some other aspects of normalcy, such as spectator sports. The first sport to return live was Korean baseball, televised live by ESPN. Although baseball is not my top sport for being a fan, it seems like a pretty logical one for the pandemic, without a substantial amount of close contact among the players. Of course, those games being on in the evening in South Korea, which is the middle of the night in Portland, meant that I needed to record them and watch them in the Portland evening. Now there has been the return of US baseball and basketball, which has helped. It is still uncertain to me how the football season will unfold.

While I am aghast at those who want to re-open the economy or the schools too fast, or not wear masks, I crave the return to normal life as much as they do. I prefer to follow the science, especially as summarized in the Twitter feeds of Eric Topol and Dereck Lowe, and am encouraged by our growing understanding of COVID-19, its immunity, new approaches to treatment, and ultimately a vaccine. I have even added my name to the government registry to volunteer to participate in a clinical trial. I have not been called yet but will step up if I am.

Thursday, July 16, 2020

Updated Informatics.Health

For many years, I have had a portion of my Web site devoted to an introductory overview of the informatics field entitled, What is Biomedical & Health Informatics? I originally created this site to provide an answer to that question I was asked from time to time. I still maintain and keep it up to date both to still provide an overview of the field as well as demonstrate the technology we use in our virtual courses.

Last year I had an upgrade of sorts, snagging the new domain name, Informatics.Health. With the 2020 updating of my larger course that is offered in the American Medical Informatics Association (AMIA) 10x10 ("ten by ten") program, I have now updated the content of the What Is site.

The main part of the site is the nine lecture segments on the following topics:
  • What is Biomedical and Health Informatics? (1) (24:32)
  • What is Biomedical and Health Informatics? (2) (18:49)
  • A Short History of Biomedical and Health Informatics (22:30)
  • Resources for Field: Organizations, Information, Education (25:29) 
  • Clinical Data (15:08)
  • Examples of the Electronic Health Record (EHR) (24:56)
  • Data Science and Artificial Intelligence (1) (14:15)
  • Data Science and Artificial Intelligence (2) (22:07)
  • Information Retrieval (Search) (23:18)
  • Information Retrieval Content (29:09)
One change this year is that the materials are only in HTML 5, dropping the use of Adobe Flash, which is being phased out at the end of this year. (The tool used to create the lectures is Articulate Studio 360.) The lectures can be viewed on just about any Web platform, and work fine on my iPhone and iPad.

The site also contains links to books, articles, organizations, and educational Web sites.

The materials on the site are freely available and have been used by many educators and others. An article from the American Medical Association (AMA) described their use by medical educators during the COVID-19 pandemic.

Sunday, July 5, 2020

The Informatics Professor Goes Solar

This summer we installed solar panels on our roof at home. The timing was good since we needed our roof replaced, which enabled us to install solar panels right on top of it. Many people tend to think of Portland, Oregon as a cloudy place, but the summers are mostly sunny and, above the 45th parallel, the days are long. Of course, even when it is cloudy, solar rays still shine down on the Earth (and our solar panels). 
A natural question is the economics of solar energy for a home and location like ours. They are surprisingly good. Last year, our electricity use averaged about 600 kilowatt-hours (kWh) per month, which averages to about 20 kWh per day. We have always used more electricity in the winter than the summer, perhaps due to the summers being mild and the days of winter being short. We opted to install a system that would aim to zero out our electric bill. We could have added additional capacity to account for an electric car, but we are not looking to buy a new car at this time.

The system includes a reversible meter, so when the panels exceed our electricity use, the excess goes into the Portland General Electric (PGE) grid. While the excess rolls over from month to month, it does not roll over years. So we will likely build up excess production over the summer that will be offset in the winter. We will see for sure when our PGE bills start rolling in.

Our 24 solar panels generate up to 7.68 kW of DC power and 5.76 kW when converted to AC power. The system includes an app that allows us to track the energy generated by the system. It has some nice reporting features that allow us to compare different days. The app does not track how much energy goes into the grid, although we can read that off our reversible meter. The app also allows us to have a public Web page so anyone can look at the data for our system. While the app has more data to show, the public Web page does allow viewing of daily electricity generation:

As the solar electricity is purportedly cheaper than that delivered by PGE, the system is estimated save about $34,000 over its lifetime. It doesn’t hurt that we will get a 26% federal tax credit this year and additional incentives from the state of Oregon. All in all, we believe it is a sound investment not only in our house, but also in the global energy future.

Our energy usage will also be reduced by the 6.5-inch R35 insulation under the new roof. This will be beneficial both with our electronic air conditioning in the summer and our gas heating in the winter.

Thursday, July 2, 2020

Kudos for the informatics Professor - Winter/Spring 2020 Update

Like many in the informatics field, the Informatics Professor has been very busy the last few months due to increased teaching and research activities taken on in response to the Covid-19 pandemic. As such, I have not had a chance to provide one of my occasional kudos postings of accomplishments until now.

Before Covid-19 struck, I was elected President of the International Academy of Health Sciences Informatics (IAHSI). The IAHSI is an international honorific society of leaders in informatics, and I look forward to assuming the Presidency in November, 2020.

Also before the pandemic, I was very busy with travel and talks:
Shortly after these talks, the Covid-19 pandemic emerged, and my travel came to an abrupt halt while my teaching and research activities accelerated. Due to the need for medical students displaced from clinical sites to have virtual learning activities, I gave several offerings of my introductory informatics course to both OHSU students (3 offerings to a total of 44 students) and non-OHSU students (8 offerings to a total of 178 students). Some educators and others also made use of the my What is Informatics? Web resource, which was featured both in an article as well as a list of resources for medical educators by the American Medical Association (AMA).

Another educational activity of note was OHSU’s hosting of the Informatics Training Conference for those holding biomedical informatics and data science training grants from the National Library of Medicine. The conference was held for the first time ever in a virtual format.

My research activities during this time mostly focused on the TREC-COVID information retrieval challenge, although I was also finishing up some papers (forthcoming soon!) and writing grant proposals for future research activities. We did publish some papers on TREC-COVID in both Journal of the American Medical Informatics Association as well as SIGIR Forum.

As always, I was busy writing both for scientific and other publications. In late 2019, I wrote an article about our informatics program for the publication of our local tech industry, Techlandia.

While the latter half of 2020 will be much prolific for publishing of book chapters and the new forthcoming fourth edition of my information retrieval textbook, I did publish in early 2020 an update of my chapter on clinical informatics in the second edition of the AMA textbook on Health Systems Science (Hersh W, Ehrenfeld J, Clinical Informatics, in Skochelak SE, Hammoud MM, Lomis KD, Borkan JM, Gonzalo JD, Lawson LE, Starr SR (eds.), Health Systems Science, 2nd Edition, 2020, 156-171).

While I hope to back off a bit over the summer, there is much in store for the rest of the year in both research and education.