Hi Gandhi, (Hi Tim, find below the best coref chain I have ever seen),
Unfortunately, it looks like the drug-ner module has not been kept up-to-date.
I just checked the cpe xml files and they contain invalid pointers. Anyway,
you should be able to add the DrugMentionAnnotator by using:
AggregateBuilder (code):
aggregateBuilder.add( AnalysisEngineFactory.createEngineDescription(
DrugMentionAnnotator.class ) );
Piper file:
add org.apache.ctakes.drugner.ae.DrugMentionAnnotator
Unfortunately, the drug attribute types all extend the type Annotation. The
PrettyTextWriter that you are using only marks IdentifiedAnnotation subtypes,
so you will not see the drug attributes without writing some extra code. On
that matter, I recommend that you use HtmlTextWriter for output as it provides
more information in a nicer format - though still not drug ner attributes.
One nice feature is the markup of coreferences. Using your example sentence:
"The patient started study treatment of Thalomid 200mg ( days 1 - 21 ) , and
Epirubicin , 20 mg / m2 ( days 1 , 8 , and 15 ) on 06 / 07 / 02 for the
treatment of hepatocellular carcinoma."
It marks a superscript '1' (coreference chain #1) after "200mg" and "carcinoma"
because Tim's excellent coreference model connected:
"study treatment of Thalomid 200mg" with "the treatment of hepatocellular
carcinoma"!
If you click one of the superscript "4"s it will display the coreference chain
in the margin.
I am still working on that writer in my spare time, so if you have suggestions
please let me know.
As for the missing times, I don't know what you are witnessing. When I run
your sentence I get the times:
"days"
"days 1,8"
"06/07/02" (contains treatment)
The "days" aren't perfect, but the "06/07/02" date and its "contains treatment"
relation are pretty good.
Sean
-----Original Message-----
From: Gandhi Rajan Natarajan [mailto:[email protected]]
Sent: Friday, September 15, 2017 12:40 PM
To: [email protected]
Subject: Enabling drugner pipeline and identifying dates [EXTERNAL]
Hi All,
We are using the pipeline code as mentioned in
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_healthnlp_examples_blob_master_ctakes-2Dtemporal-2Ddemo_src_main_java_org_apache_ctakes_web_client_servlet_Pipeline.java&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yzJCkloh5MR6n2JJ5haAmB4_MQed5JDZnn01SFotO9c&s=CZBlVpS2hKfCLyBRrR_D4KKCAtF2ru6qf6HHtV7HnCs&e=
for the cTAKES web application we are building. But in our case, the
measurements and quantities are identified as events as shown below:
SENTENCE: The patient started study treatment of Thalomid 200mg (days 1-21),
and Epirubicin, 20 mg /m2 (days 1, 8, and 15) on 06/07/02 for the treatment of
hepatocellular carcinoma.
DT NN VBD NN NN IN NN NNS NNS
CC NNP NNS NNS NNS CC IN IN DT NN IN
JJ NN
|=====| |=======| |======| |===|
|========| |=======|
|=======|
Event Procedure Drug Event
Drug Procedure
Disorder
C0087111 C0723668
C0014582 C0087111
C0007097
|======================|
Disorder
C2239176
>From googling what we have found out is that we need to use
>DrugMentionAnnotator to identify measurements and quantities. Are we right? If
>so, how do we enable DrugMentionAnnotator in our code. Could someone provide a
>sample code snippet and help us out on this?
Also the dates are not getting identified in our case as we get the following
error in our console even after using latest temporal resources (model.jar) as
per Sean's suggestion :
"Null value found in Feature(<Time-Class->, <NULL>) from [Feature(<mention1>,
<take>), Feature(<mention1_FirstCovered_0_1_0>, <take>)"
Could someone throw some light on this as well?
Thanks in advance.
Regards,
Gandhi
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