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From Pei Chen <chen...@apache.org>
Subject Re: Question pertaining to HistoryOf and SegmentID features
Date Wed, 27 Nov 2013 03:37:45 GMT
That annotator will set the IdentifiedAnnotation.*uncertainty()* with one
of the following values:

*HISTORY_STATUS* = 1;

*FAMILY_HISTORY_STATUS* = 2;

*PROBABLE_STATUS* = 3;


On Tue, Nov 26, 2013 at 10:32 PM, digital paula <cybersation@hotmail.com>wrote:

> 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.Chen@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:cybersation@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.miller@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: cybersation@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: mcoarr@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 <cybersation@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
>
>
>
>
>

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