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From "Vogel, James" <JVo...@activehealth.net>
Subject RE: Synonymous terms
Date Wed, 23 Oct 2013 19:17:24 GMT
To quickly get a larger mapping of ICD9 from all the SNOMED-CT codes that cTAKES finds I did
a post processing step using the maps at: http://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html

-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
Sent: Wednesday, October 23, 2013 12:42 PM
To: 'dev@ctakes.apache.org'; 'samir chabou'
Subject: RE: Synonymous terms

Maybe an example is best.

There is a term in  MeSH "Progeria-Like Syndrome"
The CUI for that is C0009207

That term (using those words) does not appear in SNOMED-CT.
But there is at least one SNOMED-CT term (Cockayne syndrome, with code 21086008) associated
with that CUI within the UMLS metathesaurus.
Therefore cTAKES will annotate "Progeria-Like Syndrome" with CUI C0009207and also cTAKES will
list the SNOMED-CT codes that are associated with that CUI, even though none of the SNOMED-CT
terms associated with the CUI C0009207 contain the word "like".

However, the MeSH code (D003057) for "Progeria-Like Syndrome" will not be included within
the CAS.

Hope that helps
-- James

-----Original Message-----
From: dev-return-2138-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2138-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of samir chabou
Sent: Tuesday, October 22, 2013 6:55 PM
To: samir chabou; dev@ctakes.apache.org
Subject: Re: Synonymous terms

sorry i'm having some problem with my e-mail
correct me if i'm wrong. Based in what is said, when i do a lookup i'll get the term (entity,
event for example) that can be from MeSH, ICD9 or NCI but the ontologyConceptArray will contains
the codes synonyms in SNOMED-CT

On Tuesday, October 22, 2013 12:23:06 PM, "Masanz, James J." <Masanz.James@mayo.edu>

Just in case it wasn't clear, when I said it only contains SNOMED-CT codes, I pointing out
that it doesn't have entries for ICD9 or MeSH or NCI Thesaurus, even though those are used
when doing the dictionary lookup.  I wasn't thinking about the codes vs. text part.

-----Original Message-----
From: dev-return-2126-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2126-Masanz.James=mayo.edu@ctakes.apache.org]
On Behalf Of Chen, Pei
Sent: Tuesday, October 22, 2013 11:17 AM
To: dev@ctakes.apache.org; 'samir chabou'
Subject: RE: Synonymous terms

> if I need to get term name do I have to do a lookup on umls ?
FYI: I was proposing adding an additional attribute to store the description/preferredText(term)
[1] since this information is already available in the dictionary lookup.
I think most folks would find this useful in additional to just saving the CUI/Code. Otherwise,
they would have to do another lookup further downstream to get the description of the CUI/Code.

[1] https://issues.apache.org/jira/browse/CTAKES-224

> -----Original Message-----
> From: Masanz, James J. [mailto:Masanz.James@mayo.edu]
> Sent: Tuesday,
 October 22, 2013 10:57 AM
> To: 'dev@ctakes.apache.org'; 'samir chabou'
> Subject: RE: Synonymous terms
> ontologyConceptArray only contains SNOMED-CT codes (except for
> medications, where it contains RxNorm codes or CUIs)
> -----Original Message-----
> From: dev-return-2119-Masanz.James=mayo.edu@ctakes.apache.org
> [mailto:dev-return-2119-Masanz.James=mayo.edu@ctakes.apache.org] On
> Behalf Of samir chabou
> Sent:
 Monday, October 21, 2013 6:59 PM
> To: dev@ctakes.apache.org
> Subject: Fw: Synonymous terms
> On Monday, October 21, 2013 7:58:01 PM, samir chabou
> <samirchb@yahoo.com> wrote:
> Synonymous
> terms
> Given a C0001621 I need to get its synonyms terms for example in MeSH,
> ICD, SNOMED (as shown bellow)…Is that possible ?
> Synonymous
> terms  Adrenal gland diseases                     MeSH  D000307 Diseases of the
> adrenal glands        SNOMED DB-70000
>                         ...
>   Are  the
> synonyms kept in ontologyConceptArray ?  If yes, then in the
> ontologyConceptArray the information displayed is about identifier (code,
> cui, tui, oid …) if I need to get term name do I have to do a lookup on umls ?
> thanks
> Samir

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