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How do I add a new database to the cTAKES pipeline to perform lookup from? How do I specify what columns to look up and how to annotate the text with the returned hits? I have gone through the DictionaryLookupAnnotatorDB.xml and LookupDesc_Db.xml files. However, I could not understand the meanings of the terms like "lookupField", "metaField", "maxPermutationLevel" and "exclusionTags". If I add a new database, I need to configure this xml file properly. Please guide me regarding these problems.

Franck Dernoncourt
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supriyo_basak
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  • You need to use dictionary creator GUI for this - https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI – Gandhi Sep 20 '17 at 14:38
  • Hi @Gandhi . I used the link u mentioned above but i am still getting error. Here is my issue https://issues.apache.org/jira/browse/CTAKES-534 – Deepa MG Jun 18 '19 at 05:38
  • I saw suggestion to install JDK. I have it too.$ java -version openjdk version "11.0.3" 2019-04-16 OpenJDK Runtime Environment (build 11.0.3+7-Ubuntu-1ubuntu218.04.1) OpenJDK 64-Bit Server VM (build 11.0.3+7-Ubuntu-1ubuntu218.04.1, mixed mode, sharing) – Deepa MG Jun 18 '19 at 06:43
  • @DeepaMG Hi Deepa, I guess UMLS needs to be installed separately. Check out this link - https://www.ncbi.nlm.nih.gov/books/NBK9683/ Thats what i followed when i was working on it longtime back – Gandhi Jun 19 '19 at 09:16
  • @Gandhi Thank you!. I followed https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide which include **(Recommended) Add UMLS access rights** isnt this is sufficient to add UMLS? – Deepa MG Jun 19 '19 at 09:31
  • @DeepaMG For custom dictionary creation, you gotta have UMLS installed to generate the required SQL script locally – Gandhi Jun 19 '19 at 10:11

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