Nick,
When you mean no medication is being annotated, I presume you mean the
medication attributes (i.e. dosage, frequency, etc.) are not being
annotated? I think the DrugNER needs a list of section names in the
config; I think it includes SIMPLE_SEGMENT. I am very surprised that
Pei,
I need the name of the medications for the application that I wrote and uses
ctakes.so I cache the medication in DictionaryLookupAnnotator(in
performLookup()) and use them in my program but when I have
SimpleSegementAnnotator it just takes forever. After taking
SimpleSegementAnnotator
I suspect that when you take out simple segment annotated, nothing is getting
processed, and that is why it appears so fast. At least some of the annotators
loop through the list of sections/segments, which is why there is a simple
segment annotator - so that there is at least one
If you just need the medication names, you can remove these:
nodeContextDependentTokenizerAnnotator/node
nodeDependencyParser/node
nodeAssertionAnnotator/node
You might be able to get rid of the LvgAnnotator and still get decent results
since variations of word form should not affect
Hi Nick,
I think that the bottleneck is probably the lookup module itself. So, I just
sent you a secure email/ftp link. It contains a build of the new
dictionary-lookup-fast module. Should you choose to try it, let me know how
things turn out.
Sean
Hi Sean,
Many thanks, I will try it tomorrow. Do you have any special instruction to run
that scrip or I have to use it with cTakes?
Thanks,
Nick
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, September 09, 2014 4:24 PM
To:
Just use it with cTakes. Instead of removing other modules from the pipeline,
replace the dictionary-lookup with dictionary-lookup-fast.
For the
desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
, you would modify:
delegateAnalysisEngine
Sean,
If that is a script for generating a dictionary for use with
dictionary-lookup-fast, I would also be very interested in checking it out.
Thanks,
Bruce
[image: IMAT Solutions] http://imatsolutions.com
Bruce Tietjen
Senior Software Engineer
[image: Mobile:] 801.634.1547
(Trying to avoid passing individual jars via email)
Sent from my iPhone
On Sep 9, 2014, at 5:26 PM, Chen, Pei pei.c...@childrens.harvard.edu
wrote:
Sean-
Aren't the scripts to generate the DB already available in the sandbox area?
Sent from my iPhone
On Sep 9, 2014, at 5:24 PM,
Greetings ctakes-dev:
*UMLS license restrictions have been getting more lax over the years -- *much
of the UMLS can be downloaded directly from the NCBI official FTP site.
In fact, the NIH (and implicitly the NLM) *have already made the standard
terms public for some medical specialities*.
For
10 matches
Mail list logo