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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject RE: Announcement: UMLS MedGen-MySQL dataset now available as open access download
Date Thu, 13 Nov 2014 12:44:10 GMT
Agree with everyone else, this is very exciting.

As far as adopting it as default, I would like to try it first of course, but if all that
means is replacing the toy dictionary that sounds great, then new users will hopefully stop
being confused about why "ctakes doesn't find obvious things." Would we still maintain the
SNOMED resources for those who use them? I think that despite the licensing issues SNOMED
is a widely-used standard and some users probably want to continue using those codes. With
this new resource we would probably not be able to fill in the SNOMED codes even if there
is an equivalent SNOMED concept.

From: Dligach, Dmitriy [Dmitriy.Dligach@childrens.harvard.edu]
Sent: Wednesday, November 12, 2014 9:19 AM
To: cTAKES Developer list
Subject: Re: Announcement: UMLS MedGen-MySQL dataset now available as open access download

Andy, thank you for this resource!

Do you have an estimate of what percentage of UMLS concepts were left out?


On Nov 11, 2014, at 16:02, andy mcmurry <mcmurry.andy@gmail.com> wrote:

> Hello!
> https://bitbucket.org/invitae/medgen-mysql (Apache Licensed ASL2)
> We just released a new library containing a huge chunk of UMLS concepts
> which are available without registering accounts/username/passwords.
> LEGALLY. Yes, really!
> The subset is from NCBI and it contains *thousands of concepts from SNOMED
> and other vocabularies*.
> The code is essentially
> 1. a list of WGET targets to various NCBI FTP site mirrors
> 2. Makefile for building the databases of interest
> Our legal team has approved distribution for Open Access work, ASL2
> I recommend we use this opportunity to make this the default distribution
> for CTAKES UMLS connections, because it obviates the need for so much
> painful credentialing and back and forth agreements with the US National
> Library of Medicine.
> Cheers!
> --Andy
> On Wed, Sep 10, 2014 at 12:13 PM, Masanz, James J. <Masanz.James@mayo.edu>
> wrote:
>> I would love to see the install be as simple as apt-get install to end up
>> with some working dictionary that have more than a handful of entries to
>> get them started.
>> Regards,
>> James Masanz
>> -----Original Message-----
>> From: andy mcmurry [mailto:mcmurry.andy@gmail.com]
>> Sent: Tuesday, September 09, 2014 4:32 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: Recommendation for ctakes default (UMLS) dictionaries
>> Greetings ctakes-dev:
>> *UMLS license restrictions have been getting more lax over the years --
>> *much of the UMLS can be downloaded directly from the NCBI official FTP
>> site.
>> In fact, the NIH (and implicitly the NLM) *have already made the standard
>> terms public for some medical specialities*.
>> For example: Here is the UMLS subset specific to Medical Genetics (MedGen)
>> and Genetic Testing (GTR) complete with SNOMED-CT concept CUI(s) and names,
>> etc :
>> [  ftp://ftp.ncbi.nlm.nih.gov/pub/medgen/README.html  ]
>> My team has developed a JVM based wrapper for MetaMap 2013AB which I
>> intend to open source soon (Clojure).  It includes REST support for
>> invoking MetaMap with any or all of the command line arguments.
>> We do not integrate with UIMA, we are basically a wrapper around the
>> binary installation of MetaMap. The emphasis is on publication text not
>> clinical text, still, some services are common (such as LVG).
>> Strangely, the NLM still requires UMLS licenses to download MetaMap
>> execution binaries. The MetaMap binary install is better but customizing
>> dictionaries (DataFileBuilder) is not as easy to use as CTAKES with YTEXT
>> [ https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation ]
>> *** Hence, there is a real opportunity here to enable Apache cTAKES to
>> have a stronger default dictionary. ** *
>> Imagine if we could
>> *$ apt-get install apache-ctakes *
>> and instantly have a working package for SOME problem domain.
>> In my case (Medical Genetics) the UMLS definitions are already available
>> and the UMLS license problem becomes a non issue, at least for many first
>> time users
>> Your thoughts?
>> AndyMC

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