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From Peter Szolovits <...@mit.edu>
Subject Re: to map UMLS CUI with normalized form
Date Mon, 01 Sep 2014 21:32:02 GMT
A single CUI may have many different preferred names in different vocabularies.  If you have
a mysql version of UMLS installed, you can do something like
CREATE VIEW pname AS 
select cui, lat, ts, lui, stt, sui, ispref, aui, saui, scui, sdui, sab, tty, code, str, srl,
suppress, cvf
from `mrconso` 
where (ts = 'P') 
and (stt = 'PF') 
and (ispref = 'Y') 
and (lat = 'ENG'))

to define the preferred terms for each CUI.  I.e., this gives a subset of MRCONSO containing
only the preferred name of each concept.  As you can see from the table below, some vocabularies
provide many more of these than others.  Then, to find that preferred term for a concept,
you can just do something like:
mysql> select str from pname where cui='C1141949';
+----------------------+
| STR                  |
+----------------------+
| Troponin I increased |
+----------------------+
1 row in set (0.00 sec)

but

mysql> select distinct str from mrconso where cui='C1141949';
+---------------------------------+
| str                             |
+---------------------------------+
| Troponin I zvýšený              |
| troponine I verhoogd            |
| Troponin I increased            |
| Troponine I augmentée           |
| Troponin I erhoeht              |
| Troponin I emelkedett           |
| Troponina I aumentata           |
| トロポニンI増加                |
| トロポニンIゾウカ                     |
| Troponina I aumentada           |
+---------------------------------+
10 rows in set (0.00 sec)

In this case, the source of ambiguity is only from different languages, but it could also
be from the same CUI appearing in different SABs (vocabularies) with different names.

mysql> select sab, count(*) c from pname group by sab order by c desc limit 40;
+---------------+--------+
| SAB           | c      |
+---------------+--------+
| NCBI          | 788995 |
| MSH           | 308591 |
| MEDCIN        | 253291 |
| SNOMEDCT      | 228656 |
| RXNORM        | 220148 |
| ICD10PCS      | 178093 |
| MTH           | 157083 |
| LNC           | 131930 |
| ICD10CM       |  81082 |
| FMA           |  72645 |
| GO            |  57326 |
| OMIM          |  46058 |
| NCI           |  40962 |
| RCD           |  34638 |
| MDR           |  24144 |
| ICPC2ICD10ENG |  23618 |
| MMX           |  22387 |
| CPT           |  20064 |
| MMSL          |  19419 |
| UMD           |  15386 |
| NDDF          |  14635 |
| VANDF         |  12483 |
| SNMI          |  11222 |
| NIC           |  10487 |
| MTHSPL        |   9978 |
| NDFRT         |   9764 |
| ICD10AM       |   9098 |
| CCPSS         |   8226 |
| MTHFDA        |   6545 |
| ICD9CM        |   6521 |
| AOD           |   6513 |
| RCDSY         |   6275 |
| HCPCS         |   5200 |
| HL7V3.0       |   5097 |
| PDQ           |   4941 |
| MDDB          |   4938 |
| MTHICD9       |   4721 |
| CSP           |   3793 |
| GS            |   3770 |
| NOC           |   3645 |
+---------------+--------+
40 rows in set (5.31 sec)

On Sep 1, 2014, at 4:37 PM, Prakash Poudyal <prakashpoudyal@gmail.com> wrote:

> Hi Chen,
> 
> Thanks for mail.  I may be wrong,
> 
> dizziness (normalized form) = C0002940 (CUI value)
> 
> I am searching a system in which if I enter C002940 than dizziness could
> come. Or is there any index, or dictionary for it.
> 
> If you don't understand please write me again.
> 
> Thanks
> 
> Regards
> Prakash
> 
> 
> On Mon, Sep 1, 2014 at 9:13 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
> wrote:
> 
>> Hi Prakash,
>> Could you clarify what you mean by 'normalized form'?  An example?
>> 
>> -Pei
>> 
>> Sent from my iPhone
>> 
>>> On Sep 1, 2014, at 9:16 AM, "Prakash Poudyal" <prakashpoudyal@gmail.com>
>> wrote:
>>> 
>>> Hi!
>>> 
>>> I am working in cTAKES to analysis clinical document. Is it possible for
>> me
>>> to know how the CUI code is provided to the normalized form.
>>> 
>>> Is there any dictionary or webportal that could map  SONMED CT UMLS CUI
>>> code with normalized form.
>>> 
>>> --
>>> 
>>> Regards
>>> Prakash Poudyal
>> 
> 
> 
> 
> -- 
> 
> Regards
> Prakash Poudyal


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