Thursday, October 1, 2020
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
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
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.
Thursday, July 16, 2020
- 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)
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
Thursday, July 2, 2020
- On Thursday, January 23, I participated in an invited meeting at the National Academy of Medicine in Washington, DC focused on the "evolution of data privacy and the implications for secondary use of health data in support of a learning health system.” My invitation likely stemmed from my informatics research focused on methods to use electronic health record (EHR) data for cohort identification for clinical studies and surveillance for undiagnosed rare diseases.
- On Monday, February 3, I gave a keynote talk at a workshop that was part of the conference, Web Search and Data Mining, in Houston, TX. The workshop was entitled, Health Search and Data Mining, and the title of my talk was, Applying Information Retrieval to the Electronic Health Record for Cohort Discovery and Rare Disease Detection.
- On Thursday, February 13, I gave an invited talk in the UCLA Distinguished Lecture Series for Biomedical Data Science, also on my research area of using EHR data for cohort identification and surveillance for undiagnosed rare diseases.
- On Thursday, March 5, I spoke at Grand Rounds for the Department of Biomedical Informatics at the University of Utah on the topic of competencies in clinical informatics for medical students. They were interested in hearing about the work that we pioneered at OHSU in clinical informatics for the MD curriculum.
Friday, June 5, 2020
It gives me great pleasure to welcome the 2020 graduates of the OHSU Biomedical Informatics Graduate Program to this year’s virtual Commencement ceremony. 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.
This year was already going to be a different Commencement ceremony. I would have attended the main event for all graduates with you all, but then would have not attended the OHSU School of Medicine Graduate Programs portion. That is because I would instead be attending another Commencement event, namely the medical student commencement because this year, as many of you know, my daughter is graduating OHSU with MD and MPH degrees. I am very proud of her and excited that she will be starting her residency in Obstetrics & Gynecology at OHSU later this month.
Of course, now the entire Commencement is a different event for all of us, because of the Covid-19 pandemic and the need for the entire ceremony to be virtual. I was hoping with all the rearranging that I still might get to share this time with you all, but alas, all of the follow-on ceremonies, including graduate programs and medicine, are scheduled immediately after the main session.
So this year you will get this brief message from me. I will miss the pomp and circumstance of graduation, and getting to wear regalia and march in the procession. Hopefully things will be back to normal next year, and perhaps some of you can return to take part then.
In any case, many of you are now stepping from your informatics studies into jobs where the contributions of our field are more critical than ever. Just as the pandemic has exposed problems in our healthcare system, it has also exposed limitations in our information and data systems. It is the mandate for all informatics graduates, and everyone else in the informatics field, to keep improving how we use information and data, not only to overcome Covid-19 but also to improve biomedicine and health generally. From bio- to imaging to clinical and public health informatics, the challenges have never been greater. I am confident that you have the talent, and skills you have acquired in your studies, to meet those challenges.
I am pleased to report that our alumni now number 782 individuals with 872 degrees and certificates dating back to 1998. These include 374 master’s degrees and 31 PhD degrees. Our graduates have achieved success in academia, industry, government, and just about every other place where informaticians work. Your success in your work and life generally 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, we are still here for you and hope you will keep in touch with us as your careers develop and prosper.
Tuesday, May 12, 2020
Sunday, April 26, 2020
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.
Wednesday, April 22, 2020
Thursday, April 16, 2020
Saturday, April 11, 2020
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.
Thursday, April 2, 2020
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.
Monday, March 30, 2020
- How well do tests diagnose active infection with the disease?
- How well do tests diagnose serum antibodies indicating immunity?
- What treatments are available for the disease?
- Are there any preventive treatments for the disease, from drugs to immunizations?
- What is the best way to prevent spread in the general population?
- What is the best way to protect healthcare workers treatment patients with the disease?
Wednesday, March 25, 2020
- A benchmark set of important COVID-related queries (e.g., coronavirus risk factors, COVID-19 ibuprofen)
- A set of manual judgments for CORD-19 articles on these queries
- An ongoing leaderboard for comparison of IR systems
Saturday, March 21, 2020
Sunday, February 23, 2020
a. Information retrieval/search - choose correct sources for specific task, search using advanced features, apply results
b. Evaluate information resources (literature, databases, etc.) for their quality, funding sources, biases
c. Identify tools to assess patient safety (e.g., medication interactions)
d. Utilize knowledge-based tools to answer clinical questions at the point of care (e.g., text resources, calculators)
e. Formulate an answerable clinical question
f. Determine the costs/charges of medications and tests
g. Identify deviations from normal (labs/x-rays/results) and develop a list of causes of the deviation
2. Effectively read from, and write to, the electronic health record for patient care and other clinical activities
a. Graph, display, and trend vital signs and lab values over time
b. Adopt a uniform method of reviewing a patient record
c. Create and maintain an accurate problem list
d. Recognize medical safety issues related to poor chart maintenance
e. Identify a normal range of results for a specific patient
f. Access and compare radiographs over time
g. Identify inaccuracies in the problem list/history/med list/allergies
h. Create useable notes
i. Write orders and prescriptions
j. List common errors with data entry (drop down lists, copy and paste, etc.)
3. Use and guide implementation of clinical decision support (CDS)
a. Recognize different types of CDS
b. Be able to use different types of CDS
c. Work with clinical and informatics colleagues to guide clinical decision support use in clinical settings
4. Provide care using population health management approaches
a. Utilize patient record (data collection and data entry) to assist with disease management
b. Create reports for populations in different healthcare delivery systems
c. Use and apply data in accountable care, care coordination, and the primary care medical home settings
5. Protect patient privacy and security
a. Use security features of information systems
b. Adhere to HIPAA privacy and security regulation
c. Describe and manage ethical issues in privacy and security
6. Use information technology to improve patient safety
a. Perform a root-cause analysis to uncover patient safety problems
b. Familiarity with safety issues
c. Use resources to solve safety issues
7. Engage in quality measurement selection and improvement
a. Recognize the types and limitations of different types of quality measures
b. Determine the pros and cons of a quality measure, how to measure it, and how to use it to change care
8. Use health information exchange (HIE) to identify and access patient information across clinical settings
a. Recognize issues of dispersed patient information across clinical locations
b. Participate in the use of HIE to improve clinical care
9. Engage patients to improve their health and care delivery though personal health records and patient portals
a. Instruct patients in proper use of a personal health record (PHR)
b. Write an e-message to a patient using a patient portal
c. Demonstrate appropriate written communication with all members of the healthcare team
d. Integrate technology into patient education (e.g., decision making tools, diagrams, patient education)
e. Educate patients to discern quality of online medical resources (Web sites, apps, patient support groups, social media, etc.)
f. Maintain patient engagement while using an EHR (eye contact, body language, etc.)
10. Maintain professionalism through use of information technology tools
a. Describe and manage ethics of media use (cloud storage issues, texting, cell phones, social media professionalism)
11. Provide clinical care via telemedicine and refer patients as indicated
a. Be able to function clinically in telemedicine/telehealth environments
12. Apply personalized/precision medicine
a. Recognize growing role of genomics and personalized medicine in care
b. Identify resources enabling access to actionable information related to precision medicine
13. Participate in practice-based clinical and translational research
a. Use EHR alerts and other tools to identify patients and populations eligible for participation in clinical trials
b. Participate in practice-based research to advance medical knowledge
14. Apply machine learning applications in clinical care
a. Discuss the applications of artificial/augmented intelligence in clinical settings
b. Describe the limitations and potential biases of data and algorithms
Tuesday, December 31, 2019
Tuesday, December 3, 2019
- Time in Practice: Three years of practice in Clinical Informatics is required. Practice time must be at least 25% of a Full-Time Equivalent (FTE) to be considered. Practice time need not be continuous, however, all practice time must have occurred in the five-year period preceding June 30 of the application year. Practice must consist of broad-based professional activity with significant Clinical Informatics responsibility. Fellowship activity that is less than 24 months in duration or non-ACGME accredited may be applied toward the practice activity requirement. The actual training must be described for any fellowship activity. Documentation of Clinical Informatics research and teaching activities may also be submitted for review.
- Masters or PhD in Biomedical Informatics: Credit for completion of a 24 month Masters or PhD program in Biomedical Informatics, Health Sciences Informatics, Clinical Informatics, or a related subject from a university/college in the US and Canada, deemed acceptable by the Board (e.g. NLM university-based Biomedical Informatics Training) may be substituted for the Time in Practice option above.
Saturday, November 16, 2019
Both books also deal with another problem in medicine, which is the consolidation of healthcare systems and resulting emphasis on the bottom line, sometimes to the detriment of care and well-being of clinicians. But both books are nice reads, and I won't say more to spoil their stories, other than to note it is interesting to see informatics come of age in fiction.