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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Update: UMLS, cTAKES, and UIMA for applications in genomics
Date Mon, 24 Feb 2014 19:24:44 GMT
Hi Andy,

We have been using Uima-as here, but with no third-party wrappings.  We have set it up to
run in standalone and lsf cluster environments, but everything is out-of-box with a few custom
bash scripts to set environment settings, etc.


-----Original Message-----
From: andy mcmurry [mailto:mcmurry.andy@gmail.com] 
Sent: Monday, February 24, 2014 2:16 PM
To: dev@ctakes.apache.org
Subject: Update: UMLS, cTAKES, and UIMA for applications in genomics

Hi all:

I'm writing to update about my efforts to make a cTAKES "out of the box" VM with UMLS support.
My specific use cases are for annotating DNA test results, so both publication text and patient
notes are important towards this goal.

Wrote bash scripts to download and install cTAKES on Ubuntu.
Will provide interfaces for REST endpoints for each service (Clojure).

UMLS Services
Wrote Clojure/REST services for invoking the MetamapAPI and looking up concepts/synonym entries
in the UMLS. Will do the same for cTAKES in the upcoming months.

Semantic Representation
Is anyone else using UMLS SemRep <http://semrep.nlm.nih.gov/>?
These annotations provide secondary evidence for the cTAKES medication  and co-reference parsers,
as well as additional annotations for other semantic types.

Genetic variant parser (HGVS)
Reece Hart released a standard HGVS
parser<https://bitbucket.org/invitae/hgvs>which I intend to include in the VM distribution
as an optional UIMA pipeline (callout REST service).

Scalability: UIMA Async Scaleout with Fit ================================= I'm planning on
using Clojuima <https://github.com/jimpil/clojuima> to scale at my company.
Is everyone else using UIMA-AS as well, or planning to?

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