ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Tsung-Ting Kuo <ts...@ucsd.edu>
Subject Re: Question about YTEX
Date Wed, 17 Jun 2015 13:39:44 GMT
Hi Vijay,

Would you happen to have chance to take a look and give me some suggestions about the fracture
demo?

Thanks very much!

Best regards,
Tim


> On Jun 12, 2015, at 10:32 AM, Tsung-Ting Kuo <tskuo@ucsd.edu> wrote:
> 
> Hi Vijay,
>  
> I just tried to walk through the fracture demo you mentioned. However, I have two questions:
>  
> (1)   In the step “3. Configure Analysis Engine”, I could not find places in CPE
to assign “analysis_batch” (I am using cTAKES 3.2.2). Where could I set the analysis batch?
>  
> (2)   Therefore, I tried to run without assigning “analysis_batch”, but got an error
message (as attached). How could I solve this exception?
>  
> Thanks very much for your kindness!
>  
> Best regards,
> Tim
>  
> From: vijay garla [mailto:vngarla@gmail.com <mailto:vngarla@gmail.com>] 
> Sent: Friday, June 12, 2015 9:56 AM
> To: dev@ctakes.apache.org <mailto:dev@ctakes.apache.org>; tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
> Cc: Vijay Garla
> Subject: Re: Question about YTEX
>  
> You need to annotate some documents with a Collection Processing Engine that stores results
in the YTEX database.   I suggest walking through the fracture demo sample here: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+YTEX+DBCollectionReader
<https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+YTEX+DBCollectionReader>
>  
> -vj
>  
> On Fri, Jun 12, 2015 at 6:46 PM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>>
wrote:
>> Hi Vijay,
>>  
>> I would like to update my questions:
>>  
>> (1)   Auto-complete of concept IDs. I realized that only concepts in the “v_snomed_fword_lookup”
table are usable (e.g., I use “cough” and the auto-complete works as attached).
>> 
>>  
>> (2)   Clinical document searching. Which table should I use to put the clinical documents
in order to be searchable from the “Semantic Search” function?
>> 
>>  
>> (3)   Fracture demo. I saw there is a “fracture_demo” table in the YTEX database,
how could I use it in the “Semantic Search” function?
>> 
>>  
>> Thanks very much!
>>  
>> Best regards,
>> Tim
>>  
>> From: Tsung-Ting Kuo [mailto:tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>] 
>> Sent: Thursday, June 11, 2015 11:10 AM
>> To: 'Vijay Garla'
>> Cc: dev@ctakes.apache.org <mailto:dev@ctakes.apache.org>
>> 
>> Subject: RE: Question about YTEX
>>  
>> Thanks a lot, I followed the instructions and run “ytexweb.sh” script and successfully
run the web app! However, the search cannot return any results (no matter what keyword I type),
and the auto-complete function seems not work. Our experimental website is over here:
>>  
>> http://textmining.ucsd.edu:8080/semanticSearch.iface <http://textmining.ucsd.edu:8080/semanticSearch.iface>
>>  
>> And I also attached the screenshot and the output of the “ytexweb.sh” script.
Could you kindly help to see if there is any setting / configuration needed to be modified
in order to do the search?
>>  
>> Thanks very much!
>>  
>> Best regards,
>> Tim
>>  
>> From: Vijay Garla [mailto:vijay.garla@yale.edu <mailto:vijay.garla@yale.edu>]

>> Sent: Wednesday, June 10, 2015 11:36 PM
>> To: tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
>> Cc: Vijay Garla; dev@ctakes.apache.org <mailto:dev@ctakes.apache.org>
>> Subject: Re: Question about YTEX
>>  
>> This is part of the Semantic Similarity Web App.  There is a script to start it;
see https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+Semantic+Similarity
<https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+Semantic+Similarity>
- just run the ytexweb.sh script in the bin directory
>>  
>>  
>> On Wed, Jun 10, 2015 at 11:32 PM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>>
wrote:
>>> Thanks very much, this is really helpful! I surely can see the “v_snomed_fword_lookup”
table in my database!
>>>  
>>> So my next question is: would there be any document to tell me how to setup the
Clinical NLP Semantic Search Engine on Tomcat (actually this is the main purpose why I am
seeking for YTEX’s help)? I saw “ctakes-ytex-web-3.2.2-classes.jar” in the “lib”
folder, but I am not sure how to deploy it as a web service.
>>>  
>>> Best regards,
>>> Tim
>>>  
>>>  
>>> From: Vijay Garla [mailto:vijay.garla@yale.edu <mailto:vijay.garla@yale.edu>]

>>> Sent: Wednesday, June 10, 2015 12:10 PM
>>> To: tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
>>> Cc: Vijay Garla; dev@ctakes.apache.org <mailto:dev@ctakes.apache.org>
>>> 
>>> Subject: Re: Question about YTEX
>>>  
>>> You should see a v_snomed_fword_lookup table in your database.
>>>  
>>> YTEX doesn't use all UMLS.  It filters to SNOMED-CT and RXNORM, and specific
Semantic Types
>>>  
>>> The script is uses is here: https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql
<https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dytex_scripts_data_mysql_umls_insert-5Fview.template.sql&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=rw3vAb56jh8xMYlMHfE0hS2hfbV3RFxqvusA5jfoLnc&m=ZKgA04a0yvzxPGVaJuAq7iXhdrZStPNaFJYLNpysn_A&s=A4kHSk5EMA2mDAk0zkZPlkPEDsxFWpazfC8SSMzSYDo&e=>
>>>  
>>> You can create a dictionary with different vocabularies/semantic types very easily
(just change the sql slightly).  
>>>  
>>> For more detail on how this works, see https://code.google.com/p/ytex/wiki/DictionaryLookup_V07
<https://urldefense.proofpoint.com/v2/url?u=https-3A__code.google.com_p_ytex_wiki_DictionaryLookup-5FV07&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=rw3vAb56jh8xMYlMHfE0hS2hfbV3RFxqvusA5jfoLnc&m=ZKgA04a0yvzxPGVaJuAq7iXhdrZStPNaFJYLNpysn_A&s=ZmRyuqnM-9FtXw9jKlfrp29gqd-_kd6rjuGSEVEXGgM&e=>(docs
slightly out of date).
>>>  
>>> I have not tested this with the 'fast' dictionary lookup, but I think the main
speed gain of the fast lookup is due to skipping an extra(neous) database query.
>>>  
>>> HTH,
>>>  
>>> VJ
>>>  
>>> On Wed, Jun 10, 2015 at 8:15 PM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>>
wrote:
>>>> BTW, my YTEX installation just completed, and the results is attached. Does
my YTEX installation create dictionary lookup table with all concepts from the UMLS successfully?
>>>>  
>>>> Thanks very much!
>>>>  
>>>> Best regards,
>>>> Tim
>>>>  
>>>> From: Tsung-Ting Kuo [mailto:tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>]

>>>> Sent: Wednesday, June 10, 2015 9:49 AM
>>>> To: 'Vijay Garla'; dev@ctakes.apache.org <mailto:dev@ctakes.apache.org>
>>>> Subject: RE: Question about YTEX
>>>>  
>>>> Hi Vijay,
>>>>  
>>>> You are absolutely right – after changing the permission of the “resource”
directory, YTEX start installing without problem! In the meanwhile, I have a quick question:
since I have installed the UMLS database and set the “umls.schema” to UMLS database name
(I am using MySQL), how do I know whether YTEX successfully creates a dictionary lookup table
with all concepts from the UMLS or not?
>>>>  
>>>> Thanks again!
>>>>  
>>>> Best regards,
>>>> Tim
>>>>  
>>>> From: Vijay Garla [mailto:vijay.garla@yale.edu <mailto:vijay.garla@yale.edu>]

>>>> Sent: Tuesday, June 9, 2015 11:31 PM
>>>> To: tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>; dev@ctakes.apache.org <mailto:dev@ctakes.apache.org>
>>>> Cc: vijay.garla@yale.edu <mailto:vijay.garla@yale.edu>
>>>> Subject: Re: Question about YTEX
>>>>  
>>>> Hi Tsung-Ting,
>>>>  
>>>> I see the following error:
>>>>  
>>>> templateToConfig.extractTemplates:
>>>>      [echo] unpacking ytex templates from /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar
to /usr/local/apache-ctakes-3.2.2/resources
>>>>     [unzip] Expanding: /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar
into /usr/local/apache-ctakes-3.2.2/resources
>>>>     [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.template.xml
>>>>     [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-msh-csp-aod.template.xml
>>>>     [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.template.xml
>>>>     [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml
>>>>     [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_stem_SNOMED.template.xml
>>>>     [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.template.xml
>>>>  
>>>> I don't know why there was an issue extracting ctakes-ytex-res-3.2.2.jar.
 Can you make sure that  /usr/local/apache-ctakes-3.2.2/resources exists and is writable?
>>>>  
>>>> -vj
>>>>  
>>>> On Wed, Jun 10, 2015 at 12:17 AM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>>
wrote:
>>>>> Hi Vijay Garla,
>>>>>  
>>>>> I am Tsung-Ting Kuo from UCSD, and I am interested in your YTEX project.
I tried to download it and setup based on the following page:
>>>>>  
>>>>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
<https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_YTEX-2BInstallation&d=AwMFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=rw3vAb56jh8xMYlMHfE0hS2hfbV3RFxqvusA5jfoLnc&m=b0QIg7D5IImLEUt69gE-sqJU5GHeSBEMS_oz2Uddul4&s=Jyu357olHH-y9kNgTHIj2B01-i6DhsiGYH2HOwu9yok&e=>
>>>>>  
>>>>> However, in the final step (step 7), I was not able to setup. The attached
“setup.out” seems to show that the “UMLS.hbm.xml” is missing. Could you kindly help
to tell me how to set it up?
>>>>>  
>>>>> Thanks very much!
>>>>>  
>>>>> Best regards,
>>>>> Tsung-Ting
>>>>>  
>>>> 
>>>>  
>>> 
>>>  
>> 
>>  
> 
>  
> <cpe.out>


Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message