Re: upcoming ctakes-temporal bundled models

Do you just mean a brief high-level explanation of how they work? Tim On 06/24/2014 04:04 PM, Pei Chen wrote: > Does anyone happen to have a quick/simple README about the current best > performing models that is being included? > BackwardsTime > Event > DocTimeRel > ContextualModality >

Bacterium Dictionary

Hi there, I was wondering if Ctakes has any Bacterium Dictionary? I need to extract information for bacteria like "Enterococcus Faecium", "Pseudomonas Aeruginosa " , etc and I was wondering if I can do it by using Ctakes annotators? Thanks, Nick Nikandish Product Development Software Engineer

Re: [VOTE] Release Apache cTAKES 3.2.0

The LVG is particularly important, users are most likely to compare cTAKES and MetaMap (or other) performance on the NER task and the LVG clearly helps. Requiring a new user to understand LVG is the hard part, the download isn't a tough requirement but I wonder how many new users would even know to

RE: upcoming ctakes-temporal bundled models

I think it would be nice to have both? - some info about the models - i.e. the training set used, etc. - as well as high level explanation? > -Original Message- > From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] > Sent: Monday, June 30, 2014 10:28 AM > To: dev@ctakes.apa

Re: Bacterium Dictionary

Nick, I am not sure how complete it is, but I believe the UMLS has the semantic type of Bacterium [T007] It's most likely not included in the default cTAKES dictionaries though... Thanks, Pei On Mon, Jun 30, 2014 at 10:31

RE: [VOTE] Release Apache cTAKES 3.2.0

Thanks James. I just did a Jira review for 3.2. There are just 2 remaining items that are pending some clarification from respective dev. Otherwise, it should be up to date now- any items that didn't make it to 3.2 have been updated to 3.2.1 instead now. --Pei > -Original Message- > F

RE: [VOTE] Release Apache cTAKES 3.2.0

Thanks! I haven't downloaded and reviewed the packages themselves yet but I do plan to at least start on that today. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Monday, June 30, 2014 1:47 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Rel

RE: Bacterium Dictionary

Hi Nick, There are ~26,000 T007 Bacterium (falls under Living Being) entries in UMLS 2013aa. They aren't in the cTakes dictionary, but you can build a separate bacteria dictionary using the dictionary creator tool in cTakes sandbox. It can create dictionaries formatted for use with both availa

RE: Bacterium Dictionary

Hi Sean, Thanks for the info. I have written an application for clinical text using Ctakes where one of the annotator retrieves and identifies the bacterium in clinical texts but it uses a small library that I created. Therefore I would like to check those texts against a comprehensive libra

RE: Bacterium Dictionary

Hi Nick, I'm pasting (below) from a howto.txt in the dictionarytool/doc/ directory. You will want to do the following: 1. Download / Install the UMLS dictionary source from NIH (takes a while) 2. Create a file named "bacterium.tui" containing the single line "T007" 3. Decide what ctakes dict

RE: Bacterium Dictionary

Many thanks Sean. This is very useful. I will follow the instruction and create the dictionary. Thanks, Nick -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Monday, June 30, 2014 4:27 PM To: dev@ctakes.apache.org Subject: RE: Bacterium Dictionary Hi

RE: [VOTE] Release Apache cTAKES 3.2.0

This is pretty obvious, but since this is a record of what was voted upon, note that some of the URLs contain an extra ctakes-3.2.0/ For example http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz should be just http://people.apache.org/~chenpei/RCs