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From Pei Chen <chen...@apache.org>
Subject Re: Question pertaining to HistoryOf and SegmentID features
Date Wed, 27 Nov 2013 04:04:05 GMT
Paula,
Could you attach the desc xml and the output xml? Also, are  you using
trunk?
Strange, i'm seeing uncertainty being set to 1/history:
<..DiseaseDisorderMention _indexed="1" _id="299" _ref_sofa="6" begin="11"
end="19" id="5" _ref_ontologyConceptArr="293" typeID="2"
segmentID="SIMPLE_SEGMENT" discoveryTechnique="1" confidence="0.0"
polarity="0" *uncertainty="1"* conditional="false" generic="false"
historyOf="0" _ref_Segment="20"/>

Side note- Not sure if its worth updating the StatusAnnotator to populate
the hisoryOf attribute now (obviously those types were not avail
previously.)


On Tue, Nov 26, 2013 at 10:37 PM, Pei Chen <chenpei@apache.org> wrote:

> 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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