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From "John Green" <john.travis.gr...@gmail.com>
Subject Re: Fwd: UMLS integration with cTAKES 3.1​
Date Fri, 25 Jul 2014 17:05:21 GMT
This sounds just like jira ctakes-306. 


JG
—

On Fri, Jul 25, 2014 at 1:04 PM, John Green <hephaestus.studio@gmail.com>
wrote:

> —
> ---------- Forwarded message ----------
> From: "Natalia Connolly" <natalia.v.connolly@gmail.com>
> Date: Fri, Jul 25, 2014 at 12:35 PM
> Subject: UMLS integration with cTAKES 3.1
> To: "user@ctakes.apache.org" <user@ctakes.apache.org>
>> Hello,
>>    I am trying to supplement the basic cTAKES dictionary with the latest
>> UMLS release.  Following the instructions here (
>> https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80#p258), I
>> built a mysql database and imported UMLS data into it as two tables,
>> umls_ms_2013 and umls_snomed_map.     I then modified
>> DictionaryLookupAnnotatorDB.xml as follows:
>> <name>URL</name>
>>    <value>
>>       <string>jdbc:mysql://localhost:3306/umls</string>
>>   </value>
>>    and I also changed LookupDesc_Db.xml to reflect my two table names.
>>    After I added DictionaryLookupAnnotatorDB.xml to my analysis engines in
>> runctakesCPE.sh, I got the following error:
>> org.apache.uima.analysis_engine.AnalysisEngineProcessException CausedBY:
>> org.apache.ctakes.dictionary.lookup.DictionaryException:
>> java.sql.SQLException: Table not found in statement [SELECT tui, text, cui
>> from UMLS_MS_2013 where fword =?]
>>      This is strange because the table does exist and it's not empty:
>> mysql> SELECT tui, text, cui from UMLS_MS_2013 limit 2;
>> +------+--------+----------+
>> | tui  | text   | cui      |
>> +------+--------+----------+
>> | T121 | MSH    | C0000005 |
>> | T121 | MSHFRE | C0000005 |
>> +------+--------+----------+
>> 2 rows in set (0.00 sec)
>>      Can someone please help?
>>      Thank you,
>>      Natalia Connolly
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