This sounds just like jira ctakes-306.
JG — On Fri, Jul 25, 2014 at 1:04 PM, John Green <hephaestus.stu...@gmail.com> wrote: > — > ---------- Forwarded message ---------- > From: "Natalia Connolly" <natalia.v.conno...@gmail.com> > Date: Fri, Jul 25, 2014 at 12:35 PM > Subject: UMLS integration with cTAKES 3.1 > To: "u...@ctakes.apache.org" <u...@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
