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

2014-02-24 Thread Finan, Sean
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 [m

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

2014-02-24 Thread andy mcmurry
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