GABiomed Day 5

The last full day of sessions contained great topics and served as entryways to keep learning more.

Session #1: Controlled Vocabularies and Semantic Standards –Olivier Bodenreider, MD, PhD

  • A great introduction to some core controlled vocabularies and ontologies in use today. Great emphasis on caution with adopting one without knowing its limitations.
  • The hands-on exercises depended heavily on websites to work; unfortunately we had too many people trying to access the same pages at once and not enough bandwidth.
  • We all signed up for a UMLS license but we didn’t do anything with it. Spoke with him later and he thought a workshop session was going to cover it. Oh well.

Session #2: EHRs, APIs, and Apps –Jeremy Warner, MD

  • ALL. THE. THINGS. Plus, fascinating look at the history of medical records and how we got to where we are today.
  • Would’ve liked to learn more about API programming.

Session #3: Natural Language Processing Support for Clinical Tasks –Dina Demner-Fushman, MD, PhD

  • Nice introduction to natural language processing.
  • Wish the hands-on portion was better explained and we actually were able to go in and do some annotation.

Session #4: Organizational Issues in Biomedical Informatics –Kim Unertl, PhD

  • Another amazingly engaging speaker! We had lots of thought-provoking discussions.
  • Organizational issues is a topic we hardly ever talk about and really impacts the way we work so I’m glad it was on the program.

And then evening adventures…

#GABiomed Friday night dinner and a movie

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We had a fun “hayride” to a fancy barn for a sit-down meal. Afterwards a smaller group of us went to the Rollins Planetarium at Young Harris College. We saw “Back to the Moon for Good” which was narrated by Tim Allen. Somehow I missed that there exists prize money for going to the moon through the Google  Lunar XPRIZE.

Side note: I broke down and had cheesecake at lunch AND chocolate lava cake at dinner. They were really good! 😅


GABiomed Day 4

Another packed day of sessions.

Session #1: Security and Privacy –Daniel Fabbri, MD

  • Key phrase: Utility + Privacy = 1
  • Lots of great discussion about the challenges of systems.
  • Interesting idea was proposed: “point-to-point data sharing” to balance privacy with research (reproducibility).

Session #2: Biomedical Data and Information Visualization –Zhiyong Lu, PhD

  • I love data visualization talks. It’s always fun to see how different people present the content and the examples they use to illustrate (haha) their points.
  • Related: BD2K seminars and the symposium I attended last fall

Session #3: Using Telehealth to Increase Multi-Disciplinary Collaboration and Improve Heath Care Outcomes –Karen Rheuban, MD

  • Nice overview of what UVA is doing in telehealth services
  • Would’ve liked a practical action we could take in our current roles

Session #4: Public Health Informatics –Jessica Schwind, PhD

  • Definitely one of the best presentations so far. She was engaging and funny, and her passion for infectious diseases really shone.
  • I actually didn’t mind her Prezi presentation because it was mostly graphics/hardly any text, and very well designed.

Session #5: Mathematical Modeling with Clinical Decision Support –Dmitry Kondrashov, PhD

  • Another great example of science communication at work. He explained modeling in a very accessible way.
  • Reminded me of my college and grad school days. This is the third time I’ve studied/encountered the S-I-R model. The first time was in calculus using this open textbook.

And yes, read Cathy O’Neil’s Weapons of Math Destruction! I’m considering putting in a proposal for MLA’18 to have a book group discussion…

Side note: 2 cups of coffee, no dessert, and a walk! I think I did good today.

GABiomed Day 3

Today we got the afternoon off to rejuvenate and refresh our bodies so our minds can be ready for the rest of the week. My body felt so much better after yoga and after lunch, I went on a group hike with Kathleen Carlson, Maribeth Slebodnik, and Clare Hicks. It was a lot of fun, especially with Maribeth pointing out all the cool plants (and all the poison ivy!) on the trail.

Session #1: Consumer Health Informatics –Rebecca Schnall, PhD, RN

  • First I have to say, I really appreciate and admire Professor Schnall’s dedication to us and her work. She flew in late last night (arrived about 2AM) and flew right back this afternoon.
  • She gave us a researcher’s perspective of working with people living with a chronic disease.
  • We discussed challenges of building a user-friendly application, evaluating consumer health websites, and tailored messaging.

Session #2: mHealth Technology –Rebecca Schnall, PhD, RN

  • This second part built upon the first but it was a great example of science communication. She gave a very accessible research talk about her current projects –in particular VIP-HANA.
  • The group exercise to consider the needs of different stakeholders in app development was enlightening.
  • Too bad we didn’t have time to talk much about how body sensors fit into this landscape of apps and data collection.

Session #3: Ethical Issues Related to Research, Evaluation, Publication, and Implementation in Biomedical Informatics –Randolph Miller, MD

  • One of the best sessions I’ve attended about ethics. It was entertaining and engaging.
  • The scenarios were thought-provoking and generated a lot of discussion.

Side note: I only had cheesecake at dinner!

GABiomed Day 2

Another exciting day of hot topics in biomedical informatics! Lots of great conversations during breaks and meals as well. Click on the tweet to get the threaded view of a session.

Session #1: Genetics, Genomics, and Why We Care –Donald Lindberg, MD

  • Great review of genetics. Reminds me of my college days but the field has grown so fast.
  • It was fun to listen to Dr. Lindberg’s personal stories about major figures in history.
  • Recommended reading: The Double Helix (edit: the Watson one –thanks to Kim Yang for pointing out there are books with same title)

Session #2: Precision Medicine from an Informatics Perspective –Elmer Bernstam, MD

  • I’ve heard similar talks about precision medicine so the first part wasn’t anything new to me
  • Raised questions about issues around patient consent, profiling, cost of testing.
  • We need more interoperability between systems!
  • EHR alerts alone can be a whole other talk. Lots of great post-talk discussion about this.

Session #3: NLM Resources –Kathy Davies, MLS

  • Wow, what a lot of NLM resources I didn’t know about 😳

Session #4: Practical Bioinformatics for the Clinic –Eric Sayers, PhD

  • I’m now a convert of starting with MedGen as a landing page for exploration into the literature, clinical aspects, and genetic aspects.
  • The case study we looked at was really interesting. See this website for their story.

Session #5: Exercises in Knowledge Retrieval –Kathy Davies, MLS and Eric Sayers, PhD

  • I teamed up with Elena Azadbakht to work on case studies, which allowed us to dive deeper into exploring resources presented in Sessions #3 and 4.

Side note: today I was much better about my coffee and sugar consumption during breaks, and took a long walk around the resort before dinner. Next I have to work on choosing which meal to have dessert with! They serve pies and/or puddings during both lunch and dinner. Breakfast is the only time we get fruit!

GABiomed Day 1

What a day! I flew into Atlanta yesterday afternoon and was whisked away to Brasstown Valley Resort and Spa in Young Harris, GA (less than 5 miles from the NC border) to be immersed for a week in a survey course of biomedical informatics with 27 other participants.

Today started with breakfast at 7AM and ended shortly after 9PM with a REDCap workshop. I’ll be tweeting all week under the hashtag #GABiomed and will pull out the first tweet of each session for blog posts so you can read them in order. Overall, all the sessions today were fantastic –the speakers were knowledgeable experts; the presentations were engaging (and used active learning techniques); and I’m learning something new every time. Here are my takeaways:

Session #1: What is Biomedical Informatics? –William Hersh, MD

  • Covered all the terminology I’ve encountered so far in the health sciences surrounding informatics
  • The preferred term seems to be informatician 
  • To ponder later: how does informatics relate to data science and information science?
  • I should pay more attention to AMIA

Session #2: From Engagement to Autonomy –Hugo Campos

  • The patient perspective is not talked about enough in academic/research arenas
  • e-Patient and d-Patient
  • Great stories, initiatives, and innovations coming from empowered and tech savvy patients

Session #3: Imaging Informatics –Michael Ackerman, PhD

  • You have to know something about how digital images are created, stored, and compressed
  • To ponder later: why don’t we have more multimedia medical records or multimedia publications?
  • I love blues and yet humans haven’t evolved to be able to see all the different blues

Session #4: Data Management –Paul Harris, PhD

  • Many of the recommendations in this talk I also pass onto researchers
  • Interesting recommendation to consider DNA collection if appropriate for the study
  • The class exercise to identify variables was insightful

Session #5: REDCap Discussion/Demonstration –Paul Harris, PhD

  • REDCap has built in biomedical ontologies
  • The group exercise to build a survey was good but 7 members to a team is too big
  • Great examples of different ways researchers have used REDCap

On a side note: the food has been great, but I drank 3 cups of coffee and filled up on way too much sugar on breaks. Tomorrow I’ve got to find healthier options and fit some exercise in! Hurricane Irma isn’t affecting this area too badly –just a lot of rain and chilly temps.

DSVIL Write-Up

My write-up for the NCSU Data Science and Visualization Institute for Librarians is published in the NNLM MidContinential Region’s newsletter (recently renamed The MidContinental Messenger)!

Thanks to the A-mazing @ncsulibraries for showing us around during #dsvil. And ‪@NCStateVetMed ‬too

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New Professional Photo


Last week we did staff photos at the library. This one was taken by Bryan Hull. Time to update all my profile pictures everywhere! The one I’ve been using is from February 2012, taken by Marsha Pirone at Kresge Library, Dartmouth College. I don’t look that different, do I?