RE: false positive [EXTERNAL]

Thanks Sean for the help. The information provided below are really helpful for addressing our challenges. Regards, Abilash Mathew -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 25, 2017 7:17 PM To: dev@ctakes.apache.org Subject:

RE: cTAKES as REST service

Hi Matthew, Big thanks for the response. Actually in our case we are trying to integrate cTAKES with our application and it's our application which will invoke the rest calls and get back the response for further processing. Also I have not worked on Docker before but would love to. So if you

Re: CAS Visual Debugger - [EXTERNAL]

Thanks. On Wed, Oct 25, 2017 at 11:26 AM, James Masanz wrote: > Cool. Thanks > > On Oct 25, 2017 1:24 PM, "Finan, Sean" > wrote: > > > Ok, there is a kludge ... > > > > 1. Start the CVD > > 2. Go to File > load Type System > > 3.

RE: Piper File - [EXTERNAL]

Hi Melvin, This was a bug. I just checked in a fixed pom file. Thanks, Sean -Original Message- From: Melvin Ma [mailto:ma.qian...@gmail.com] Sent: Wednesday, October 25, 2017 12:45 PM To: dev@ctakes.apache.org Subject: Piper File - [EXTERNAL] Sean - I am actually replying your

RE: CAS Visual Debugger - [EXTERNAL]

Cool. Thanks On Oct 25, 2017 1:24 PM, "Finan, Sean" wrote: > Ok, there is a kludge ... > > 1. Start the CVD > 2. Go to File > load Type System > 3. Select your type system > 4. Exit > 5. Go to your home directory > 6. Look at the file named

RE: CAS Visual Debugger - [EXTERNAL]

Ok, there is a kludge ... 1. Start the CVD 2. Go to File > load Type System 3. Select your type system 4. Exit 5. Go to your home directory 6. Look at the file named annotViewer.pref There should be a line starting with " dir.open.xcas=" that points to your type system. 7. Make a copy of

Re: CAS Visual Debugger - [EXTERNAL]

+1 I point it at an engine descriptor .xml file (using the command-line option -desc) that refers to the type system file, but that's a hack... On Wed, Oct 25, 2017 at 1:49 PM, Dligach, Dmitriy wrote: > +1 > > Also, I’d love to be able to point CVD to a directory containing

RE: CAS Visual Debugger - [EXTERNAL]

Dima, I think that there is an -xmi option or something like that, but for individual files. -Original Message- From: Dligach, Dmitriy [mailto:ddlig...@luc.edu] Sent: Wednesday, October 25, 2017 1:50 PM To: dev@ctakes.apache.org Subject: Re: CAS Visual Debugger - [EXTERNAL] +1 Also,

Re: CAS Visual Debugger - [EXTERNAL]

+1 Also, I’d love to be able to point CVD to a directory containing XMI files at startup. Dima On Oct 25, 2017, at 12:41, Miller, Timothy > wrote: I've had the same thought, and come to the same conclusions.

Re: CAS Visual Debugger - [EXTERNAL]

I've had the same thought, and come to the same conclusions. Tim From: Melvin Ma Sent: Wednesday, October 25, 2017 1:33 PM To: dev@ctakes.apache.org Subject: CAS Visual Debugger - [EXTERNAL] This is more of a question. I am fully

CAS Visual Debugger -

This is more of a question. I am fully aware that CAS Visual Debugger is maintained in UIMA project. For me for now, I will frequently need to use CVD to view .xmi file. It would be really nice if I could put the type system xml as an input to CVD startup argument (instead of manully lookup this

RE: Piper File - [EXTERNAL]

Hi Melvin, There shouldn't be any change needed, but let me check ... it could be that I need to specifically include that piper in the .jar ... -Original Message- From: Melvin Ma [mailto:ma.qian...@gmail.com] Sent: Wednesday, October 25, 2017 12:45 PM To: dev@ctakes.apache.org

Piper File -

Sean - I am actually replying your earlier email. I have deleted the email by an accident. So here is a new thread. I searched up all the .piper files in the source and only "DictionarySubPipe.piper" file was not included in the *-res*.jar file downloaded from maven repo. It appears that pom.xml

Re: cTAKES as REST service

Please note that the solution will not use a request/response cycle because my main use case is with EMRs and I am batching up requests so as to not exhaust cTAKES :) Thanks, Matthew Vita www.matthewvita.com On Wed, Oct 25, 2017 at 9:27 AM, Matthew Vita wrote: >

Re: cTAKES as REST service

Gandhi, I am actually working on a series of Docker containers that expose an HTTP endpoint to send clinical text to and then it POSTs the results back to your application's HTTP endpoint in JSON. Please let me know if this approach interests you and we can schedule a Google Hangouts to talk

RE: false positive [EXTERNAL]

Hi again, The blacklists should now accept comma-separated semantic group codes. Thanks, Sean -Original Message- From: Kean Kaufmann [mailto:k...@recordsone.com.INVALID] Sent: Wednesday, October 25, 2017 10:38 AM To: dev@ctakes.apache.org Subject: Re: false positive [EXTERNAL] Sean,

RE: Running Piper File [EXTERNAL] [SUSPICIOUS]

Hi Melvin, This has been changed. Thanks, Sean -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Tuesday, October 24, 2017 6:27 PM To: dev@ctakes.apache.org Subject: RE: Running Piper File [EXTERNAL] [SUSPICIOUS] Hi Melvin, Thanks. There was

RE: false positive [EXTERNAL]

Hi Kean, That is a good idea regarding the comma-separated semantic codes. Give me a moment ... In the Boston Children's group we do use the differentiation between s/s and d/d all the time. It is extremely important to us and combining the two would ruin some of our projects. It is used

Re: false positive [EXTERNAL]

Sean, thanks! Blacklisting is essential, and making it category-specific is a really nice touch. Dispatch from the trenches, FWIW: a) The blacklist can get quite big, e.g. when mining common wordlists. To reduce bloat, might you allow comma-separated lists of semantic groups in the first

RE: cTAKES as REST service [EXTERNAL]

Hi Sean, Thanks for the instant response. Will try to upgrade to Spring 4 and keep you posted about the progress. Regards, Gandhi -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 25, 2017 7:28 PM To: dev@ctakes.apache.org Subject:

RE: cTAKES as REST service [EXTERNAL]

Hi Gandhi, You can always build ctakes in your sandbox with spring 4 and see if it works. This may require some "maven magic"(overrides) on your part. If it does seem to work please create a jira item to upgrade the spring version. Then hopefully before the next release somebody will

RE: false positive [EXTERNAL]

Hi Gandhi, Abilash Mathew, This is a common problem stemming from the nature of the umls and automated dictionary creation. I am still (ever so slowly) improving the dictionary creator code. If anybody can devote some time to help that would be great. Anyway, if you are using ctakes trunk

cTAKES as REST service

Hi All, We have extended the cTAKES web application available under https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo and added our custom annotator. We have tested the same and it works fine with CVD. But we are facing problems while trying to expose this as rest service.

RE: false positive

Hi Abilash, I'm not sure how much it will make sense. But in our custom annotator we wrote on top of cTAKES, we resolved this false positives to an extent by using commonly used English words metadata available from OpenNLP. Regards, Gandhi -Original Message- From:

false positive

Hi all, We are seeing some false positives identified by CTAKES after we tested couple of medical records samples. Can anyone help us on how to ignore these words from tagging incorrectly? Word Finding test Procedure Page Procedure treatment Procedure medicine Drug medication Drug