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From: "John Green" <john.travis.green@gmail.com>
To: user@ctakes.apache.org, dev@ctakes.apache.org
Subject: Re: Fwd: UMLS integration with cTAKES =?UTF-8?Q?3.1=E2=80=8B?=
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This sounds just like jira ctakes-306.=C2=A0


JG
=E2=80=94

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

> =E2=80=94
> ---------- Forwarded message ----------
> From: =22Natalia Connolly=22 <natalia.v.connolly@gmail.com>
> Date: Fri, Jul 25, 2014 at 12:35 PM
> Subject: UMLS integration with cTAKES 3.1
> To: =22user@ctakes.apache.org=22 <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=3Ff=3D28&t=3D80#p258), I
>> built a mysql database and imported UMLS data into it as two tables,
>> umls=5Fms=5F2013 and umls=5Fsnomed=5Fmap.     I then modified
>> DictionaryLookupAnnotatorDB.xml as follows:
>> <name>URL</name>
>>    <value>
>>       <string>jdbc:mysql://localhost:3306/umls</string>
>>   </value>
>>    and I also changed LookupDesc=5FDb.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=5Fengine.AnalysisEngineProcessException =
CausedBY:
>> org.apache.ctakes.dictionary.lookup.DictionaryException:
>> java.sql.SQLException: Table not found in statement [SELECT tui, text, =
cui
>> from UMLS=5FMS=5F2013 where fword =3D=3F]
>>      This is strange because the table does exist and it's not empty:
>> mysql> SELECT tui, text, cui from UMLS=5FMS=5F2013 limit 2;
>> +------+--------+----------+
>> | tui  | text   | cui      |
>> +------+--------+----------+
>> | T121 | MSH    | C0000005 |
>> | T121 | MSHFRE | C0000005 |
>> +------+--------+----------+
>> 2 rows in set (0.00 sec)
>>      Can someone please help=3F
>>      Thank you,
>>      Natalia Connolly
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