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From andy mcmurry <mcmurry.a...@gmail.com>
Subject Re: ctakes blog
Date Wed, 09 Dec 2015 00:59:44 GMT
Hopefully of use .... a large number of UMLS concepts are publicly
availability to download without UMLS license for sources in MedGen, which
represents 300k+ concepts, including many concepts and relationships in
SNOMED-CT, MESH, NCI Metathausurus (MTH), etc.

You can download UMLS dictionaries for medgen here from NLM (no login)
<ftp://ftp.ncbi.nlm.nih.gov/pub/medgen/>

For custom dictionaries, you can use Bash to download and build many
concepts in UMLS related dictionaries:

https://bitbucket.org/invitae/medgen-mysql

#concepts for each UMLS Semantic Type (STY) referenced by MedGen

+-------------------------------------------+--------+
| STY                                       | cnt    |
+-------------------------------------------+--------+
| Pharmacologic Substance                   | 102511 |
| Finding                                   |  90413 |
| Organic Chemical                          |  81329 |
| Disease or Syndrome                       |  47223 |
| Neoplastic Process                        |  16151 |
| Amino Acid, Peptide, or Protein           |   9383 |
| Congenital Abnormality                    |   6536 |
| Pathologic Function                       |   5655 |
| Steroid                                   |   3919 |
| Sign or Symptom                           |   2909 |
| ...                                       |   ...  |



On Tue, Dec 8, 2015 at 2:19 PM, andy mcmurry <mcmurry.andy@gmail.com> wrote:

> +1 I would be happy to write about the experience of creating the medgen
> (medical genetics) database, especially useful for cancer and cardio
> On Dec 8, 2015 2:04 PM, "David Kincaid" <kincaid.dave@gmail.com> wrote:
>
>> That is a great idea! I'd be happy to help provide some content as someone
>> who has been trying to use cTAKES inside other projects. As I mentioned
>> previously I am working in veterinary medicine which has just enough
>> peculiarities to make cTAKES out of the box a challenge (although it is
>> much better now than it was a couple years ago, so kudos to those of you
>> who have been making it better). I also can't stand Eclipse, happily left
>> Subversion behind years ago and prefer to work in Clojure as much as
>> possible.
>>
>> - Dave
>>
>> On Tue, Dec 8, 2015 at 3:41 PM, Miller, Timothy <
>> Timothy.Miller@childrens.harvard.edu> wrote:
>>
>> > The recent discussion over dictionary building, and someone pointing out
>> > it has come up several times, made me think that maybe we should use the
>> > blog space that apache provides. It could be used for write-ups of
>> > things that are not quite as formal as "documentation" but would benefit
>> > from being written down somewhere that is easier to search and link to
>> > than a mailing list.
>> > Any thoughts?
>> > Tim
>> >
>> >
>>
>


-- 
Andy McMurry, PhD
Chief Technical Officer

http://GetMedal.com

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