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From Natalia Connolly <natalia.v.conno...@gmail.com>
Subject Re: UMLS integration with cTAKES 3.1​
Date Fri, 25 Jul 2014 18:09:31 GMT
Yes, I did.  The same problem.

Natalia



On Fri, Jul 25, 2014 at 2:06 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
wrote:

>  Did you also try lower case in the table name?
>
> Sent from my iPhone
>
> On Jul 25, 2014, at 2:02 PM, "Natalia Connolly" <
> natalia.v.connolly@gmail.com> wrote:
>
>   Yes:
>
>
>  mysql> use umls;
> Reading table information for completion of table and column names
> You can turn off this feature to get a quicker startup with -A
>
>  Database changed
>  mysql> show tables;
> +-----------------+
> | Tables_in_umls  |
> +-----------------+
> | AMBIGLUI        |
> | AMBIGSUI        |
> | DELETEDCUI      |
> | DELETEDLUI      |
>  …….
>
>  | umls_ms_2013    |
> | umls_snomed_map |
> +-----------------+
> 49 rows in set (0.00 sec)
>
>     Natalia
>
>
>
>
> On Fri, Jul 25, 2014 at 1:59 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu
> > wrote:
>
>>  That is odd.  Nothing seems out of the ordinary…
>>
>> And the database name is umls?
>>
>> jdbc:mysql://localhost:3306/*umls*
>>
>>
>>
>> *From:* Natalia Connolly [mailto:natalia.v.connolly@gmail.com]
>> *Sent:* Friday, July 25, 2014 1:54 PM
>> *To:* user@ctakes.apache.org
>>
>> *Subject:* Re: Fwd: UMLS integration with cTAKES 3.1​
>>
>>
>>
>> Hi Pei,
>>
>>
>>
>>     I can't see any issues with LookupDesc_Db, so I am attaching both it
>> and  DictionaryLookupAnnotatorDB.xml.  I only modified the
>> username/password in the second file to "myusername" and "mypassword" for
>> security purposes.  They were correct before, I checked it many times.
>>
>>
>>
>>     Thank you so much for your help,
>>
>>
>>
>>     Natalia
>>
>>
>>
>>
>>
>> On Fri, Jul 25, 2014 at 1:34 PM, Chen, Pei <
>> Pei.Chen@childrens.harvard.edu> wrote:
>>
>> Natalia,
>> That is strange.  It sounds like it isn't configured to use the right
>> resource.
>> Could you double check the mappings, in particular: in your
>> LookupDesc_Db.xml:
>> externalResourceKey="DbConnection" to ensure it's using the right
>> resource that was added in your DictionaryLookupAnnotatorDB.xml?
>> If it still doesn't work, would you mind attaching the xml config files?
>>
>> --Pei
>>
>> > -----Original Message-----
>> > From: John Green [mailto:john.travis.green@gmail.com]
>> > Sent: Friday, July 25, 2014 1:06 PM
>> > To: user@ctakes.apache.org; dev@ctakes.apache.org
>> > Subject: Re: Fwd: UMLS integration with cTAKES 3.1​
>> >
>> > 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#p25
>> > >> 8), 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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