Use SNOMED in BRAT for Normalization?

[Jessie Tenenbaum]

Hi all-

Newbie here.

I have an NLP project in which we are using cTAKES to annotate clinical notes using SNOMED terms.

I want to evaluate the accuracy of the automated NLP by having clinicians manually annotate the notes for comparison.

BRAT seems like the right tool, and I see there's a way to do normalization (i.e. entity linking) with an existing terminology as of V1.3. I found the instructions for how to do that here- http://brat.nlplab.org/normalization.html#norm-config but I'm not sure what those values would be for SNOMED CT. Has anyone done this? Any hints/suggestions/ideas?

A few additional comments

1. Really what I'm trying to do looks very much like this: http://zuccon.net/publications/airs2015demo_oyster.pdf but I can't find that tool online, and email to the authors bounces back.

2. It's not clear to me if/how the UI scales when one has a list of not a handful of types, but rather thousands of types- has anyone had experience with this? Maybe with GO?

3. I saw the post by Dan Schlegel about https://github.com/digitalneoplasm/OWLToBratNormalization- maybe that's what I need, and create a local instance of SNOMED?

Many thanks for any insights.

Best regards,

Jessie Tenenbaum, PhD

Duke University

[dana...@being-there.com]

Jessie,

I'm trying the same thing.  First I had 400,000 CUI's under the "entity" and it never loaded, but 10,000 CUI's took about 7 minutes, so that wasn't going to work.

Then I got "SimString" installed and I tried using "normalization".  It worked really well!  I would have my ID = "CUI" (which has to be unique) and then I could add an attribute for "preferred term" so I would have something that the annotator could use for string search.  The assigned CUI and preferred term shows up in the ".ann" file, which I can load into a database for display, etc.  I wish the CUI showed up on the user interface, but that seems to be impossible.  Instead I just use the single entity "concept".  Email me if you want more details and my config file, etc.

Best wishes,

Dana Ludwig