Yeah, a CPE is one way to go for reading a set of documents and then outputting
specific information. If you go that route, given your desired outcomes, you
would have to write a UIMA Consumer class to extract all the things you
specified and put them somewhere.
Alternatively, many of our projects are moving towards using UIMAFit, which
allows you to do many of the same things without having to deal with xml
configuration files. A good place to start with that approach is the class:
/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java
and its parent class:
/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
It has a main method so you can run it like a normal java program. It will run
the standard ctakes pipeline on a set of files in a hardcoded directory
("data/input") and write out files with the extracted CUIs to another hardcoded
directory ("data/output"). That isn't exactly what you want but I think if you
do need to do some development you can copy that class and extend it for your
own uses, and that is probably the route that requires the smallest amount of
effort.
Tim
On 10/09/2013 06:30 PM, digital girl wrote:
Hi Tim,
Thanks for the prompt response.
For starters, what I'd like to do process several hundred clinical narratives
and extract the key items per narrative (CUI, RxForm, symptoms, relationships,
smoking status, etc) for structured classification in a database. Since I'm
looking at a collection of narratives for processing I see that the CPE tool
would be ideal.
You stated that "for more systematic access and processing we usually will
write java code around an annotator that will use the ctakes API and typesystem
to extract what we need." I'm currently using the user tool I'm guessing that
I will need to graduate to the developer version in order to do what you stated.
I appreciate your feedback.
Regards,
Paula
--------------
Hi Paula,
The typical way we visually inspect this information is in the CVD tool. Then
for more systematic
access and processing we usually will write java code around an annotator that
will use the
ctakes API and typesystem to extract what we need. Looking directly at the xml
is usually
about as useful as you seem to have found it (i.e., not very :) ).
What task are you trying to accomplish? If you just want to see what concepts
are found for
one file at a time that can be done in the CVD. If you are having trouble
finding what you
need there let us know. If you want an output file with all terms that were
listed in any
given input file that would probably require a little bit of programming.
Tim
________________________________
From: [email protected]<mailto:[email protected]>
To: [email protected]<mailto:[email protected]>
Subject: Analyzing and processing cTakes NLP output
Date: Tue, 8 Oct 2013 21:00:17 -0400
Hi Team (or is it just the Team of Samir ;-)
I had processed a 2 1/2 page narrative from the CVD tool and exported to XCAS
file in xml. I would like to extract the key items from the narrative that
cTakes is known for such as identifying diseases/disorders, medications,
signs/symptoms, and so forth. I quickly perused the file via xml browser and
did see the SNOMED and RXNORM codes associated. I decided to printout out the
file to markup the sections and to get an idea of how these codes relate back
to the concepts identified by cTakes. My printer ran out of paper after about
60 pages and when I looked at the top sheet it was 1 out of 2243 pages! A 2
1/2 page narrative resulted in an xml file of over two thousand pages!!!
I examined the first medication mapping. The numeric lines are my comments
and everything else copy/pasted from XCAS file.
1. Identification of RxNorm code is 69749 but it's not associated with a
concept so I copied '163573' and pasted in search in the xml file. See number
2 below for what retrieved.
<uima.cas.FSArray _id="163573" size="1">
<i>163576</i>
</uima.cas.FSArray>
<org.apache.ctakes.typesystem.type.refsem.OntologyConcept _id="163539"
codingScheme="RXNORM" code="69749" oid="69749#RXNORM"/>
2. Retrieved this result with some additional information such as the generic
is false, but not med name mention. I copied "163581" and pasted in search.
See number 3 below for what retrieved.
_indexed="1" _id="163581" _ref_sofa="6" begin="9776" end="9784" id="530"
_ref_ontologyConceptArr="163573" typeID="1" segmentID="SIMPLE_SEGMENT"
discoveryTechnique="1" confidence="1.0" polarity="1" uncertainty="0"
conditional="false" generic="false" subject="patient" historyOf="0"/>
3. Retrieved this result. The RxNorm code associated identifies Coumadin as a
treatment.
<org.apache.ctakes.assertion.medfacts.types.Concept _indexed="1" _id="227307"
_ref_sofa="6" begin="9776" end="9784" conceptType="TREATMENT"
conceptText="Coumadin" externalId="0" originalEntityExternalId="163581"/>
Here are my questions:
1. is there any resources available that explains what the xml output file
contains and the layout? Such as what does confidence of 1.0 and polarity of 1
and uncertainty of 0 refer to?
2. Are there any tools already existing that interpret the NLP output from
cTakes and automatically structure and associate it to the concepts? Such as,
automatically associate the RxNorm to the medication mention as illustrated
above. As you see it took a few steps to associate the RxNorm code to the
actual medication mention from the narrative.
Thanks.
Regards,
Paula
