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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: MedicationMention for Acetaminophen
Date Mon, 10 Nov 2014 21:04:09 GMT
Within the output, within MedicationMention there is 
org.apache.ctakes.typesystem.type.refsem.OntologyConcept

Within that, there is an attribute called "code"
If you see code = "C7777777", then you are using a small sample dictionary that is included
in cTAKES only for very basic illustration purposes, and you should try using AggregatePlainTextUMLSProcessor.xml
instead of AggregatePlainTextProcessor.xml

If that is not the problem, please tell us if you have checked cTAKES out from SVN or if you
are have downloaded and are using the binary or source distribution, and which release (such
as 3.1.1).

Regards,
James


-----Original Message-----
From: Mansour Al Akeel [mailto:mansour.alakeel@gmail.com] 
Sent: Saturday, November 08, 2014 2:03 AM
To: user
Subject: MedicationMention for Acetaminophen

I am trying to experiment with the annotations for drugs using
AggregatePlainTextProcessor.xml

I copied some text from the web
http://www.babycenter.com/404_whats-the-difference-between-acetaminophen-and-ibuprofen_12377.bc
to test it.


The following text:

Acetaminophen and ibuprofen are both good medicines, and both provide
the same basic relief from fever and pain, even though they have
different chemical structures and side effects. Ibuprofen is
recommended only for kids 6 months and older.


results in ibuprofen being recognized but not Acetaminophen.

I checked user FAQ http://ctakes.apache.org/user-faqs.html, and found :

Why doesn't my UMLS term get indentified by the system but it exists
in SNOMEDCT/RxNorm?

The Dictionary Lookup that you are using filters out terms that don't
have tui codes registered in the
resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml file.
Edit that file and add "{TUI}" to the value list for
"{semanticGroup}Tuis" property as below: For Example:

< property key="semanticGroupTuis" value="{TUIS}" />

within < lookupConsumer
className="org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedDbConsumerImpl"
>

Unforetunately there was no such property anywhere in the file.

A similar thread
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201406.mbox/%3C162a581621c64333b7ddc4ef9581304a@BL2PR08MB516.namprd08.prod.outlook.com%3E

suggested replacing

 <lookupConsumer
className="org.apache.ctakes.dictionary.lookup.ae.OrangeBookFilterConsumerImpl">

with

<lookupConsumer
className="org.apache.ctakes.dictionary.lookup.ae.NamedEntityLookupConsumerImpl">

in the resources/org/apache/ctakes/dictionary/lookup/LookupDesc.xml

Again, no luck.

Any idea ?

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