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From Natalia Connolly <natalia.v.conno...@gmail.com>
Subject UMLS integration with cTAKES 3.1
Date Fri, 25 Jul 2014 16:35:18 GMT
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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