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From Prakash Poudyal <prakashpoud...@gmail.com>
Subject Re: to map UMLS CUI with normalized form
Date Thu, 04 Sep 2014 09:33:49 GMT
Hi Peter,

Thanks for wonderful. Can you tell me how to get this database.


On Mon, Sep 1, 2014 at 10:32 PM, Peter Szolovits <psz@mit.edu> wrote:

> 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
>
>


-- 

Regards
Prakash Poudyal

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