James, I was making some changes to the ctakes common type system for CTAKES-224 (Adding a field to save the UMLS term/text in addition to the CUI/Codes). Do you want me to also make originalText an FSArray<BaseToken> instead of String while I have these files open?
--Pei > -----Original Message----- > From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] > Sent: Wednesday, October 02, 2013 10:23 AM > To: dev@ctakes.apache.org > Subject: RE: CTAKES-248- include original covered text of NEs which can't be > recovered post if NE is from a disjoint span > > +1 to have a pointer back to the BaseToken(s) rather than a | String (so we > could get back the spans and other info if needed). > I think the atom will be slightly different, take for example: > Perhaps with an example: > Sentence/LookupWindow: "alcoholic liver disease was acute." > originalText: "disease acute" [New feature to store the Tokens that were > matched due to the permutations?] > UmlsConcept.cui: C0001314 > UmlsConcept.preferredText: "Acute Disease" [New feature to store the > atom/text returned by the UMLS CUI] > > I also ran into a similar case where I wish > IdentifiedAnnotation.segmentID/SentenceID was the actual Segment type > and not a String. > > This is just my 2 cents... open to ideas though. > --Pei > > > > -----Original Message----- > > From: Richard Eckart de Castilho [mailto:richard.eck...@gmail.com] > > Sent: Wednesday, October 02, 2013 3:19 AM > > To: dev@ctakes.apache.org > > Subject: Re: CTAKES-248- include original covered text of NEs which > > can't be recovered post if NE is from a disjoint span > > > > What benefit would it have to store a string with some separation > > character (which may mean that the separation character in the > > elements may need to be escaped), over using a feature of type > > FSArray<Token> pointing to the original segments? > > > > Not sure if that is what Karthik meant when referring to fetching the > > matched atom. > > > > -- Richard > > > > On 02.10.2013, at 01:46, Karthik Sarma <ksa...@ksarma.com> wrote: > > > > > Hmm, couldn't you just fetch the matched atom and use that? Should > > > be the same information (without, I suppose, the original ordering and > split). > > > > > > -- > > > Karthik Sarma > > > UCLA Medical Scientist Training Program Class of 20?? > > > Member, UCLA Medical Imaging & Informatics Lab Member, CA > Delegation > > > to the House of Delegates of the American Medical Association > > > ksa...@ksarma.com > > > gchat: ksa...@gmail.com > > > linkedin: www.linkedin.com/in/ksarma > > > > > > > > > On Tue, Oct 1, 2013 at 12:37 PM, Masanz, James J. > > <masanz.ja...@mayo.edu>wrote: > > > > > >> Yes, this would help address that multiple permutations example. > > >> The new getOriginalText method would return something like > > >> "Acute|Disease". Right now I'm thinking of just using vertical bar > > >> as delimiter, to start with at least, but think it should be > > >> configurable. > > >> > > >> -----Original Message----- > > >> From: dev-return-2067-Masanz.James=mayo....@ctakes.apache.org > > [mailto: > > >> dev-return-2067-Masanz.James=mayo....@ctakes.apache.org] On > > Behalf Of > > >> Chen, Pei > > >> Sent: Tuesday, October 01, 2013 9:38 AM > > >> To: dev@ctakes.apache.org > > >> Subject: CTAKES-248- include original covered text of NEs which > > >> can't be recovered post if NE is from a disjoint span > > >> > > >> This sounds pretty cool. > > >> James, will this address the multiple permutations lookup example: > > >> "Acute alcoholic liver disease." There is a cui: C0001314: Acute > > >> Disease, but if you getCoveredText(), on the UMLSConcept, you would > > >> actually get the same "Acute alcoholic liver disease" instead of > > >> "Acute > > Disease". > > >> So, there is a new field called getOriginalText() that matched the hit? > > >> > > >>> -----Original Message----- > > >>> From: james-mas...@apache.org [mailto:james-mas...@apache.org] > > >>> Sent: Monday, September 30, 2013 5:49 PM > > >>> To: comm...@ctakes.apache.org > > >>> Subject: svn commit: r1527792 - /ctakes/trunk/ctakes-type- > > >>> > > > system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSys > > >>> t > > >>> em.xml > > >>> > > >>> Author: james-masanz > > >>> Date: Mon Sep 30 21:48:01 2013 > > >>> New Revision: 1527792 > > >>> > > >>> URL: http://svn.apache.org/r1527792 > > >>> Log: > > >>> CTAKES-248 - for named entities, since the annotation just has > > >>> the > > >> begin and > > >>> end offset, it is requested to have a way to get the original > > >>> covered > > >> text > > >>> (especially for disjoint spans) so it is possible to know which > > >>> words in > > >> the > > >>> covered text were actually used in the matching to the dictionary > > >>> entry > > >>> > > >>> Modified: > > >>> ctakes/trunk/ctakes-type- > > >>> > > > system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSys > > >>> t > > >>> em.xml > > >>> > > >>> Modified: ctakes/trunk/ctakes-type- > > >>> > > > system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSys > > >>> t > > >>> em.xml > > >>> URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type- > > >>> > > > system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSys > > >>> t em.xml?rev=1527792&r1=1527791&r2=1527792&view=diff > > >>> > > > ========================================================== > > >>> ==================== > > >>> Binary files - no diff available.
