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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Hello cTAKES Mailing List
Date Sun, 22 Feb 2015 15:37:48 GMT
Hi Raymond,

If you use the dictionary-fast module there exists an entry "feeling bad" with cui 557911
and cui 231218.  There is also "feel bad" and "feeling bad emotionally"

You will find "horrible present pain" but no other entry with "horrible".   You will not find
any terms with "awful" and probably many other desired words.  If you are really interested
in slang "crappy", "lousy", etc. then they are definitely not present.

What you can do is create a second dictionary.  There are example custom dictionaries in -dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/example/bsv/
You should look at custom_cui_bsv.bsv if you want to specify term unique id codes and term
text alone.  If you want to add tui/group codes then look at custom_cui_tui_bsv.bsv  - you
will probably want to model your dictionary after this so that you can tag your terms with
tuis for "symptoms".

You will want to imitate sections from the corresponding .xml file in that directory.   Make
a copy of cTakesHsql.xml (two dirs up) and add lines: 
      <dictionary>
         <name>CustomCuiRareWord</name>
         <implementationName>org.apache.ctakes.dictionary.lookup2.BsvRareWordDictionary</implementationName>
         <properties>
            <property key="bsvPath" value="org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv"/>
         </properties>
      </dictionary>

And

      <conceptFactory>
         <name>CustomCuiConcept</name>
         <implementationName>org.apache.ctakes.dictionary.lookup2.concept.BsvConceptFactory</implementationName>
         <properties>
            <property key="bsvPath" value="org/apache/ctakes/dictionary/fast/example/custom_cui_tui_bsv.bsv"/>
         </properties>
      </conceptFactory>

And

      <dictionaryConceptPair>
         <name>CustomPair</name>
         <dictionaryName>CustomCuiRareWord</dictionaryName>
         <conceptFactoryName>CustomCuiConcept</conceptFactoryName>
      </dictionaryConceptPair>

Then make sure that you point to your custom cTakesHsql.xml in dictionary-fast/desc/analysis_engine/UmlsLookupAnnotator.xml
(or Overlap depending upon your use):

            <name>DictionaryDescriptorFile</name>
            <description/>
            <fileResourceSpecifier>
               <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/cTakesHsqlYourCopy.xml</fileUrl>
            </fileResourceSpecifier>

You can also skip the UMLS dictionary altogether and just use your custom dictionary.

If you do give this a try then let me know  how it goes.  If you need additional assistance
let me know and I will help the best I can.

Sean


-----Original Message-----
From: Raymond Li [mailto:raywli@bu.edu] 
Sent: Saturday, February 21, 2015 1:26 PM
To: dev@ctakes.apache.org
Subject: Hello cTAKES Mailing List

Hello, my name is is Raymond Li and I am currently working on a team project involving cTAKES.
The goal of our project would be to use cTAKES to analyze posts on social media (such as tweets,
forum posts, public available data) in order to catch in real-time any adverse effects of
prescribed drugs and do a public service of protecting people from harmful drugs.

Aside from this introduction, I do have only one question to ask to proceed with this project:
Is cTAKES capable of understanding slang words as symptoms. An example is if I were to say
"I took Crestor and feeling bad"
is there a way for cTAKES to recognize that Crestor had a negative effect?
My team has not been able to isolate 'bad' as a negative effect as it is not a defined medical
symptom, but it would be nice to figure out if such a solution exists, or if we would need
to develop our own solution and how we could go around doing it.

My team and I would appreciate any comments or assistance regarding our project and this current
issue. Thank you and have a nice day!

--
Sincerely,

Raymond Li
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