How to use cTAKES from command line to process only one file instead of all files in a directory?

2016-12-07 Thread Zuo Yiming
Hi guys, Is there any suggestion on using cTAKES to process one specific text file from command line? I was able to follow Tsung-Ting Kuo's post on stackoverflow as shown below to apply cTAKES in a batch mode to process all files in a folder from command line. But the initiation time and processi

RE: How to use cTAKES from command line to process only one file instead of all files in a directory?

2016-12-07 Thread Tomasz Oliwa
Provided you are under Linux, you could just write a bash script that takes your input file as argument, creates a temporary directory with "mktemp -d", "cp" the file into it, and then runs a Java class that calls org.apache.uima.examples.cpe.SimpleRunCPE on this temporary directory. The init a

Re: How to use cTAKES from command line to process only one file instead of all files in a directory?

2016-12-07 Thread Zuo Yiming
Hi Tomasz, Thanks for your suggestion. I'm running cTAKES under a windows server so I guess the mktemp command may not be directly available to me. But I get the idea. What worries me most is the loading time of cTAKES. You mentioned running cTAKES behind a web service. Do you mind talking more a

RE: Allergy Annotator

2016-12-07 Thread Mullane, Sean *HS
I'm reviving this thread with reference to negation detection. I previously posted about this to the User list but this is probably a more appropriate venue. The way the sentences are split on ":" makes the negation annotator miss negation in lists of this form: Hyperlipidemia: Yes Hyperchole

RE: How to use cTAKES from command line to process only one file instead of all files in a directory?

2016-12-07 Thread Tomasz Oliwa
There were some previous posts on this list about a cTAKES web demo, I think you can see it at http://healthnlp.github.io/examples/ Regards, Tomasz From: Zuo Yiming [yiming...@gmail.com] Sent: Wednesday, December 07, 2016 2:29 PM To: dev@ctakes.apache.org

RE: Allergy Annotator

2016-12-07 Thread Finan, Sean
Hi Sean, Even with a change to your sentence detection you may need to change your negation annotator. As a quick change, you can add an annotator to deal specifically with your situation. It can be simpler or more elaborate, but something like this: static private final Pattern NEGATIVE_