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Posted to user@ctakes.apache.org by Mansour Al Akeel <ma...@gmail.com> on 2014/11/08 09:03:19 UTC
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 ?
Re: MedicationMention for Acetaminophen
Posted by Mansour Al Akeel <ma...@gmail.com>.
James,
This was the problem. It's resolved now. Thank you a lot for your help.
On Mon, Nov 10, 2014 at 4:04 PM, Masanz, James J. <Ma...@mayo.edu> wrote:
> 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 ?
RE: MedicationMention for Acetaminophen
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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 ?