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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: Hello cTAKES Mailing List
Date Mon, 23 Feb 2015 20:04:22 GMT
The CHV is a good resource for some things, but before going through the motions of porting
it to a ctakes format, take a look inside.  

 
-----Original Message-----
From: Pei Chen [mailto:chenpei@apache.org] 
Sent: Monday, February 23, 2015 1:52 PM
To: dev@ctakes.apache.org
Subject: Re: Hello cTAKES Mailing List

Raymond,
Probably a combination of UMLS *Consumer Health Vocabulary + Custom Dictionary (as Sean described)
*may work for the use case*:* "OAC CHV connects informal, common words and phrases about health
to technical terms used by health care professionals. It includes jargon, slang, ambiguous,
and misspelled words as used by consumers and health care professionals. Due to its nature,
OAC CHV includes concepts that are not represented by other source vocabularies within the
Metathesaurus."

[1] https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nlm.nih.gov_research_umls_sourcereleasedocs_current_CHV_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1Bkpeno1tqLjX78o0wYm5DmJHCHlK7hrxpeEgPnGtRM&s=-rEmTgTCe0mkSXT34XK56zkiuy_VxIfFvngGJzUwem8&e=


On Sun, Feb 22, 2015 at 10:37 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:

> 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/dicti
> onary/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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