Posts in category travel

AMIA 2011 Highlight: Dr. Bill Tierney's 10 year story on health care in Africa

Tierney's inspiring closing keynote was truly a highlight of #amia2011. Standing ovations for a great guy and great speaker.
-- Gunther Eysenbach, Oct 26

That's one tweet among a chorus of #amia2011 tweets about Tierney, including:

  • Death by HIPAA: shouldn't sacrifice care on altar of privacy #AMIA2011 keynote by Tierney
  • LIVE: #AMIA2011 Bill Tierney uses Clem McDonald's 1998 JAMA "Canopy Computing" paper; great metaphor for connected health data, no silos!

AMIA 2011 keynote recordings are now available:

"Dr. Tierney’s work has taken him far afield—to Kenya, Africa—to use electronic health records and to gather information from patients, applying the data to critical points in the patient–provider relationship to improve the quality and cost-effectiveness of health care. He led the effort to develop the first ambulatory electronic medical record system in sub-Saharan Africa, which has evolved into a comprehensive, open-source electronic medical record system that has been implemented in more than a dozen developing countries."

The video editing is a little rough, with quite a bit of conference administrivia at the beginning. But by the time he gets to "a Case" at 9:40, I'm sure you'll be hooked. Even if you're not an informatics geek, I'm sure you'll find the "10 year story" (starting at 37:30 into the video) inspiring.

AMIA 2011: Nursing Flowsheets data and the wild west of terminology

Like a number of other CTSA sites, we're Using I2B2 in our HERON research data respository. The original domain of I2B2 was genome/phenome integration and personalized medicine. Genomic stuff is on our long-term radar, but one of our earliest wins has been mining the vast amount of data (~400M observations as of our latest release) recorded by nurses and other practitioners in flowsheets in our EMR.

Height, weight, and BMI are quite common inclusion/exclusion criteria for clinical trials, and those aren't available in the term hierarchy that comes with I2B2 out of the box.

It's been a big challenge because unlike diagnoses with ICD9 codes and procedures with CPT codes, the MedicalTerminologyMarketplace has no widespread norms for flowsheets.

We're presenting some results in Washington D.C. on Wednesday at AMIA 2011:

Stay tuned to KUBMIPresentations for presentation materials.

p.s. I'm new to AMIA. As a long-time Web guy, there's a bit of culture shock: the conference program only seems to be available as a big hunk of PDF or a goofy mobile flash thing, and the "Join the conversation on twitter" box inside gives the hash tag as AMIA2011#, with the hash at the end. Chuckle. And no open-access to the full text of the article. Sigh.

Approaches to data integration for health care research: i2b2, SHRINE, SPARQL and OWL

A couple of us are off to Boston this week for the i2b2 Academic Users' Group First Annual Conference to present a poster and soak up all kinds of good stuff.

i2b2 is the basis of HERON, our health care research data repository, which stores clinical observations into a fairly traditional datamart. I've done database application development of various kinds for decades, but the scale and operational challenges are new to me. I'm particularly happy that the extract/transform/load (ETL) process for our last release ran for 37 hours, lights-out, loading 450 million clinical observations from various sources, primarily, a copy of Epic's Clarity store from the KU Hospital.

While i2b2 includes a modern Ajax web front-end, it makes no use of web-style linked data, let alone OWL or realist ontology, for medical terminology alignment, which is a big part of the challenge in making HERON an effective platform for research and for data integration beyond the KUMC enterprise.

While I'm taking a break from heads-down development mode for this conference, and while I'm in Boston, I hope to take time to look more closely at developments such as:

Our Oracle database on SAS drives handles simple user queries in a few seconds, but in some cases it takes a minute or two or fails altogether. After evaluating fusion-io's solid state storage, we ordered 4 fairly large units. We're still working through the operational details of setting it up, but we hope to see considerable performance improvements for both ETL and end-user queries.

I'm also interested to catch up on some W3C stuff: RDF/SQL mapping (no RIF?! darn.), and the Semantic Web Health Care and Life Sciences (HCLS) Interest Group. It should be interesting to compare SPARQL1.1 federated query with the corresponding i2b2 approach: SHRINE.