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From Prakash Poudyal <prakashpoud...@gmail.com>
Subject Re: to map UMLS CUI with normalized form
Date Thu, 04 Sep 2014 13:28:36 GMT
Peter, I do have licence already. I am already in

http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html

Can you tell step wise.

Thanks

Prakash




On Thu, Sep 4, 2014 at 12:34 PM, Peter Szolovits <psz@mit.edu> wrote:

> You need to (a) get a (free) license to use UMLS, then (b) download the
> (large) distribution, and (c) install it in a local database.  See
> https://uts.nlm.nih.gov
>
> On Sep 4, 2014, at 5:33 AM, Prakash Poudyal <prakashpoudyal@gmail.com>
> wrote:
>
> > 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
>
>


-- 

Regards
Prakash Poudyal

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