The old licensed setup would be kept as a packaged option? Much as it is now.... With the unlicensed going out in place of the current "free" dictionary? Am I understanding that right?
JG — Sent from Mailbox On Thu, Nov 13, 2014 at 1:40 PM, andy mcmurry <[email protected]> wrote: > I'll crunch the numbers -- in the meantime I can tell you that phenotypes > vary by semantic type. clinical attributes from SNOMED are abundant, many > concepts in mesh that are mapped to diseases. Tons of "pharmacological > substances" > On Nov 12, 2014 6:19 AM, "Dligach, Dmitriy" < > [email protected]> wrote: >> Andy, thank you for this resource! >> >> Do you have an estimate of what percentage of UMLS concepts were left out? >> >> Dima >> >> >> >> >> On Nov 11, 2014, at 16:02, andy mcmurry <[email protected]> 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 >> > LICENSE. >> > >> > 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. < >> [email protected]> >> > 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:[email protected]] >> >> Sent: Tuesday, September 09, 2014 4:32 PM >> >> To: [email protected] >> >> 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 >> >> >> >>
