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Posted to user@ctakes.apache.org by digital paula <cy...@hotmail.com> on 2013/11/20 21:57:47 UTC
RE: Dictionary and Assertion rules for the Aggregate Plaintext
Processor-Question Answered
forgot to tag something to denote closure in the title :-)
From: cybersation@hotmail.com
To: user@ctakes.apache.org
Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
Date: Wed, 20 Nov 2013 15:56:09 -0500
The information that you had provided is very helpful. Thanks so much James!
From: Masanz.James@mayo.edu
To: user@ctakes.apache.org
Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
Date: Wed, 20 Nov 2013 20:14:55 +0000
I don't have any links handy offhand.
cTAKES uses HSQL. Mostly you can just reference HSQL documentation for learning HSQL, and point to the database in
resources\org\apache\ctakes\dictionary\lookup\umls2011ab
(which will be under whereever you unzipped the ctakes-resources you downloaded from sourceforge)
The only cTAKES-specific thing I can think of that you need to be aware of when updating cTAKES dictionaries is that you need to tokenize the (text part of the) dictionary entries the same way that cTAKES will tokenize the text you will process, so that
when cTAKES compares the text it is processing to the dictionary entries, the tokens match up.
Tokens within the dictionary entries are separated by a space.
For example, should "left-handed" be all together without spaces, or should it be three separate tokens: left - handed
I think the tokenization issue is described in the old forum posts I mentioned earlier.
- James
From: user-return-352-Masanz.James=mayo.edu@ctakes.apache.org [user-return-352-Masanz.James=mayo.edu@ctakes.apache.org] on behalf of digital paula [cybersation@hotmail.com]
Sent: Tuesday, November 19, 2013 11:22 PM
To: user@ctakes.apache.org
Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
Thanks so much James for helping me to get my tiny dictionary to work. If you look up James in it....it states 'a great guy' :-)
I really do appreciate your mentioning of the other options such as the lucene index (as well as links to this) which I don't have any familiarity with, yet. Also, like what you stated on the better alternative on updating the SQL dictionaries. However,
I'm not familiar with that either, is there any reference links or details that you can provide on how to update SQL dictionaries?
Thanks.
Regards,
Paula
From: Masanz.James@mayo.edu
To: user@ctakes.apache.org
Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
Date: Tue, 19 Nov 2013 03:50:10 +0000
Hi Paula,
There is a separate DictionaryLookupAnnotatorCSV.xml descriptor for using the delimited file that you found.
You would have to update the aggregate to refer to DictionaryLookupAnnotatorCSV.xml instead of DictionaryLookupAnnotator.xml in order to use the
delimited files directly.
Or, to create a lucene index to replace the lucene index used by DictionaryLookupAnnotator.xml, there are some posts on the old forum that talk
about creating dictionaries. You could take a look at those.
https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=80&start=20#p1459
https://cabig-kc.nci.nih.gov/Vocab/forums/viewtopic.php?f=28&t=423&p=1465
I think a better alternative would be update the SQL dictionaries – delete all the data and replace with what you want. And remove the check for
the UMLS user ID.
Hope that helps.
-- James
From: user-return-350-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-350-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of digital paula
Sent: Monday, November 18, 2013 8:48 PM
To: user@ctakes.apache.org
Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
Thanks James for the response.
I'd like to update that tiny dictionary and see the changes take effect. I looked in the dictionary-lookup folders and found a dictionary1.csv file with these entires, I added 'elbow 'to it (just typed in and saved file).
ankle|ankle
aspirin|aspirin
cm|cm
cm|cm is a synonym of a UMLS term Cutaneous Mastocytosis which is in SNOMED but cm is not by itself
hyperlipidemia|hyperlipidemia
knee|knee
knee|knee pain
ld|ld
ld|ld SNOMED procedure C0011911
medical|medical nutrition therapy
nutrition|nutrition
nutrition|nutrition therapy
pain|pain
pain|pain, chronic
weight|weight gain
elbow|elbow
I typed in the following text in CVD using the plaintext processor that uses the DictionaryLookupAnnotator.xml descriptor.
"patient has knee pain and gained significant weight gain due to injury. Past history of elbow pain. family history includes hyperlipidemia. ."
There was no annotation for 'elbow' or 'weight' after executing the AggregatePlaintext AE processor. Does something else have to be done to get it to annotate, basically what are the steps to add terms to the tiny dictionary?
Thanks.
Regards,
Paula
> From:
Masanz.James@mayo.edu
> To: user@ctakes.apache.org
> Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
> Date: Mon, 18 Nov 2013 20:17:32 +0000
>
> The "pain" and "aspirin" terms are from a tiny dictionary that has just a handful of terms with made-up codes/CUIs. (For the record, they are in a lucene index instead of an HSQL database.) I think "knee" is also in that tiny dictionary.
>
> As far as I know, the assertion component doesn't work any differently whether you use the UMLS dictionary or the tiny, sample, made-up dictionary.
>
> Which dictionary is used is determined by which Dictionary Lookup analysis engine is included in the aggregate
> DictionaryLookupAnnotator.xml for the tiny one
> DictionaryLookupAnnotatorUMLS.xml for the one that has real UMLS terms and CUIs
>
> -- James
>
>
> From:
user-return-348-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-348-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
> Sent: Monday, November 18, 2013 1:37 PM
> To: user@ctakes.apache.org
> Subject: RE: Dictionary and Assertion rules for the Aggregate Plaintext Processor
>
> Oh, gosh....I meant 'Hello' again.
>
> ________________________________________
> From: cybersation@hotmail.com
> To: user@ctakes.apache.org
> Subject: Dictionary and Assertion rules for the Aggregate Plaintext Processor
> Date: Mon, 18 Nov 2013 14:36:13 -0500
> Hell again cTakes Community,
>
> I think this will be an easy question. Okay I've decided to start simple by first exploring the Aggregate Plaintext Processor without ULMS. Since it's not using ULMS, where is the dictionary and the assertion rules being defined? Can these be modified
easily? For example, I see that 'pain' and 'aspirin' gets annotated in text or if text states 'family history' this will be noted as well. Can someone enlighten me as to how cTakes generates this and if it's easily customizable?
>
> Thanks.
>
> Regards,
> Paula