You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@ctakes.apache.org by samir chabou <sa...@yahoo.com> on 2013/10/22 01:59:11 UTC
Fw: Synonymous terms
On Monday, October 21, 2013 7:58:01 PM, samir chabou <sa...@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
RE: Synonymous terms
Posted by "Masanz, James J." <Ma...@mayo.edu>.
I think it depends on
- what terminologies you want to get the synonyms from
- if you care that the dictionaries used by cTAKES have been tokenized by cTAKES
If you are happy with the 4 terminologies (SNOMED-CT, NCI thesaurus, MeSH, and ICD-9) that cTAKES uses for things like diseases/disorders, and you don't mind cTAKES' tokenization of the terms, then you could use the tables within the ctakes-resources database.
I think a better option though would be to use an external API or download you own copy of the UMLS metathesaurus, and just get all terms for the given CUI, subsetted by whatever set of terminologies you are interested in.
Note, the UMLS folks are careful to state that just because 2 atoms map to the same UMLS Concept and therefore CUI, they should not be called synonyms.
From: samir chabou [mailto:samirchb@yahoo.com]
Sent: Tuesday, October 22, 2013 6:33 PM
To: Masanz, James J.; 'dev@ctakes.apache.org'
Subject: Re: Synonymous terms
thanks James for the info.,
do you know if there is a way in cTAKES to allow me getting the synonyms for a given CUI ? or should i try to use an external API that could do that ?
On Tuesday, October 22, 2013 10:55:54 AM, "Masanz, James J." <Ma...@mayo.edu> wrote:
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 <sa...@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
Re: Synonymous terms
Posted by samir chabou <sa...@yahoo.com>.
thanks James for the info.,
do you know if there is a way in cTAKES to allow me getting the synonyms for a given CUI ? or should i try to use an external API that could do that ?
On Tuesday, October 22, 2013 10:55:54 AM, "Masanz, James J." <Ma...@mayo.edu> wrote:
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 <sa...@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
RE: Synonymous terms
Posted by "Vogel, James" <JV...@activehealth.net>.
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." <Ma...@mayo.edu> wrote:
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
--Pei
> -----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
> <sa...@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
IMPORTANT WARNING: Information contained in this email is intended for the use of the individual to whom it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is STRICTLY FORBIDDEN. If you have received this communication in error, please notify us immediately by return email and delete this document. Thank you.
Re: Synonymous terms
Posted by samir chabou <sa...@yahoo.com>.
thanks James, definitively these explanations helps
On Wednesday, October 23, 2013 12:42:48 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
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." <Ma...@mayo.edu> wrote:
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
--Pei
> -----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
> <sa...@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
RE: Synonymous terms
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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." <Ma...@mayo.edu> wrote:
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
--Pei
> -----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
> <sa...@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
Re: Synonymous terms
Posted by samir chabou <sa...@yahoo.com>.
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." <Ma...@mayo.edu> wrote:
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
--Pei
> -----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
> <sa...@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
Re: Synonymous terms
Posted by "peistation@gmail.com" <pe...@gmail.com>.
Per UMLS, preferred term /text should be for CUI/TUI/SOURCE combo as defined in the dictionary.
I actually didn't modify the code for this yet, will do that shortly and will see how that turns out.
Sent from my iPhone
On Oct 22, 2013, at 4:25 PM, vijay garla <vn...@gmail.com> wrote:
> I'm curious as to how you decide which is 'the' preferred term; maybe this
> is clear if you are just using SNOMED-CT. However, if you use multiple
> UMLS vocabularies, there can be multiple (or no) preferred terms among the
> MRCONSO entries with the same CUI.
>
> -vj
>
>
> On Tue, Oct 22, 2013 at 12:22 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
>
>> 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
>> --Pei
>>
>>> -----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
>>> <sa...@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
>>
Re: Synonymous terms
Posted by vijay garla <vn...@gmail.com>.
I'm curious as to how you decide which is 'the' preferred term; maybe this
is clear if you are just using SNOMED-CT. However, if you use multiple
UMLS vocabularies, there can be multiple (or no) preferred terms among the
MRCONSO entries with the same CUI.
-vj
On Tue, Oct 22, 2013 at 12:22 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
> 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
> --Pei
>
> > -----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
> > <sa...@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
>
RE: Synonymous terms
Posted by "Masanz, James J." <Ma...@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
--Pei
> -----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
> <sa...@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
RE: Synonymous terms
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
> 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
--Pei
> -----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
> <sa...@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
RE: Synonymous terms
Posted by "Masanz, James J." <Ma...@mayo.edu>.
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 <sa...@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