Update: UMLS, cTAKES, and UIMA for applications in genomics

[andy mcmurry <mc...@gmail.com>]

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.

cTAKES VM.
=================
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?

RE: Update: UMLS, cTAKES, and UIMA for applications in genomics

["Finan, Sean" <Se...@childrens.harvard.edu>]

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.

Sean

-----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.

cTAKES VM.
=================
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?