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From Natalia Connolly <natalia.v.conno...@gmail.com>
Subject Re: Fwd: UMLS integration with cTAKES 3.1​
Date Fri, 25 Jul 2014 18:02:14 GMT
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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