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 <chen...@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 > <cybersat...@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.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 >> >> >> >> >> > >
