i2b2 phenotyping challenges

Plenge, Bickel, Weber, Kohane, McGaw, Liao

Discussed the effortful process required to train a NLP filter for a given phenotype. We

Currently:

Step 1: Experts galore: (clinical, NLP, modeling/statistics, programmers)

Step 2: Build study-specific data mart

Step 3: Extract information

Step 4: Define "Gold Standards" from the extracted knowledge

Step 5: Build filter algorithm and apply to study at hand

Step 6: Not remember very well and loss of institutional memory regarding phenotypes

We reviewed several alternative, more fully automated models.

Auto-immune CVD

Autoimmunity and CVD

Karlson reviewed the i2b2/PGRN project on predicting response to disease modifying drugs in rheumatoid arthritis. This included adding functional status assessment to cTAKES. She articulated the first task is finding the best combination of structured and NLP-derived clinical variables that are predictive of disease activity. As an aside, Elizabeth noted that "Biologicals" have become first line thereapeutics in RA. Quite a change from what is in our EMR from 15 years ago.

Most of the session was a review of the use of the Knowtator tool on the rheumatoid arthritis corpus.

The remainder was focused on a discussion of the selection of the cohort with multiple sclerosis (MS) and a radiologically isolated precursor of MS (i.e. a radiologically made incidental diagnosis).

CVD and Diabetes

Present: Rich Grant, Stan Shaw, Rahul, Murphy, Vivian Gainer, Plenge

As the meeting was gathering, Robert Plenge asked the right question: Given how slow the NLP optimization process is, what can we do to make it faster? He drew an interesting analogy between the era of contigs, BAC's and YAC's that was boutique-like and the industrial whole genome process.

Discussed Richard Grants latest CVD algorithm which heavily uses the text of the clinician's problem lists (not the billing codes). This was implemented as a very large and complex logical predicate, rather than a probabilistic or statistical model.

Temporal queries

Present: Murphy, Weber, Kohane, McGow, Wilson, Mendis, Bickel

Reviewed Griffin's extensive proposal for a user interface. Batted around the implications for the underlying tables (while maintaining backwards compatibility).

Rheumatoid arthritis and PGRN

Discussed the NLP challenge for defining Low/Medium/HIgh Disease Activity Score (DAS).

CVD and Diabetes Mellitus

Shaw, Kohane Gainer, Liao, Churchill, Margarita, Murphy, Savova

Discussed the logistics of loading clinical notes on the 380K patients. Also discussed several control populations.