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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: CTAKES-248- include original covered text of NEs which can't be recovered post if NE is from a disjoint span
Date Tue, 22 Oct 2013 18:30:21 GMT
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.Chen@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.eckart@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 <ksarma@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
> > > ksarma@ksarma.com
> > > gchat: ksarma@gmail.com
> > > linkedin: www.linkedin.com/in/ksarma
> > >
> > >
> > > On Tue, Oct 1, 2013 at 12:37 PM, Masanz, James J.
> > <Masanz.James@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.edu@ctakes.apache.org
> > [mailto:
> > >> dev-return-2067-Masanz.James=mayo.edu@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-masanz@apache.org [mailto:james-masanz@apache.org]
> > >>> Sent: Monday, September 30, 2013 5:49 PM
> > >>> To: commits@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.


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