Hi Pei,
Thanks for the prompt response. Okay, I uncommented out StatusAnnotator in
the AggregatePlaintextPipeline config/descriptor and tried again with this text.
"history of diabetes. hx diabetes. prior diabetes. "
Uncertainty and HistoryOf features remained 0.....doesn't look like anything
happened. Note that I'm validating using the CVD debugger tool.
I did read something on that the Status and Assertion have overlapping
functionality so I commented out Assertion and still the same thing. I
looked at the StatusIndicatorFSM.java file, text with history "hx" and
"history" should be annotated so I'm not sure why it's not working.
Am I missing some config?
Regards,
Paula
From: pei.c...@childrens.harvard.edu
To: user@ctakes.apache.org
Subject: RE: Question pertaining to HistoryOf and SegmentID features
Date: Tue, 26 Nov 2013 20:46:12 +0000
Paula,
If you would like to use the old status annotator for history in the interim
while the new assertion module models are added.
One can just uncomment the below from your AggregatePlaintextPipeline
config/descriptor:
<!--
<node>StatusAnnotator</node>
-->
That annotator will set the IdentifiedAnnotation.uncertainty() with one of the
following values:
HISTORY_STATUS = 1;
FAMILY_HISTORY_STATUS = 2;
PROBABLE_STATUS = 3;
--Pei
From: digital paula [mailto:cybersat...@hotmail.com]
Sent: Tuesday, November 26, 2013 10:00 AM
To: user@ctakes.apache.org
Subject: RE: Question pertaining to HistoryOf and SegmentID features
Hi Tim,
I remember you, you helped me out a while back! I can't tell you how much
that BagOfAnnotations.java file has been a Godsend! Thanks again for posting
it last month.
As for historyOf feature, I don't so much mind performance so if you have
something that works for the historyOf with just only a performance issue, I'll
still take it. I do appreciate your prompt response on the historyOf feature
which saved me from stepping
through the code which I've done a few times....the time spent stepping
through is equivalent to watching a feature film and there's a lot going on in
the code that I don't understand yet.
As for sementID's with the rule-based sectionizer/segmenter, I'd like to help
out with testing. It appears that the first step is manual configuration
per your email. Pei, when you have a moment I'd like to start with
explanation of how it works then
we can move forward from there.
Thanks.
Regards,
Paula
Date: Tue, 26 Nov 2013 09:24:20 -0500
From: timothy.mil...@childrens.harvard.edu
To: user@ctakes.apache.org
Subject: Re: Question pertaining to HistoryOf and SegmentID features
Hi Paula,
The historyOf module is currently under development, that explains those files
you're seeing. As of right now we are not satisfied enough with the performance
to release it publicly. It is marked 0 because it is defined as an integer
field I believe, so it
can't be assigned null.
As for the segment IDs in your other question, the default segmenter just makes
the whole document one segment because we don't yet have a module robust enough
to run on notes from any institution. We have been hoping to get one developed
but nothing has materialized
so far. There is a rule-based sectionizer/segmenter in the cTAKES distribution
but it requires some manual configuration and is not very widely tested. If you
are interested in helping test it out that would be great. Pei would be the
best person to explain
to you how it works, we'll see if he's able to chime in.
(Ah, I just checked and saw he already pointed you to it. If you want to try it
we can help you get it working.)
Thanks
Tim
On 11/25/2013 11:13 PM, digital paula wrote:
Matt, sorry but I sent the email by accident and didn't finish my thought.
Since there's this file (historyOf.psv) in the Assertion folder it gives the
impression that Assertion can be configured
to account for historyOf. Though I tried some of the words such as "had
diabetes" or "prior diabetes" and value still 0 for historyOf feature. I think
it is configurable because of the fact the default value for historyOf is 0 as
opposed to <NULL> . Maybe
I should step through the code and see where and when it's assigning 0.
Regards,
Paula
From:
cybersat...@hotmail.com
To: user@ctakes.apache.org
Subject: RE: Question pertaining to HistoryOf and SegmentID features
Date: Mon, 25 Nov 2013 23:09:33 -0500
Hi Matt,
it's me again. Are you sure that historyOf feature can't be configured using
Assertion. I was looking around the Assertion folder and came across a file
called historyOf.psv. What is this?
It contains the following:
has been|historyOf|historyOf
had|historyOf|historyOf
hx of recent|historyOf|historyOf
hx of|historyOf|historyOf
hx|historyOf|historyOf
recent|historyOf|historyOf
s/p|historyOf|historyOf
status post|historyOf|historyOf
post|historyOf|historyOf
previous|historyOf|historyOf
prior|historyOf|historyOf
From:
mco...@mitre.org
To: user@ctakes.apache.org
Subject: Re: Question pertaining to HistoryOf and SegmentID features
Date: Tue, 26 Nov 2013 02:50:59 +0000
The ctakes assertion module does not have an option to set the historyOf
attribute. The assertion module only sets subject, polarity, uncertainty,
conditional, and generic.
Matt
From:
digital paula <cybersat...@hotmail.com>
Reply-To: "user@ctakes.apache.org" <user@ctakes.apache.org>
Date: Monday, 2013-11-25 15:13
To: "user@ctakes.apache.org" <user@ctakes.apache.org>
Subject: RE: Question pertaining to HistoryOf and SegmentID features
