Mailing-List: contact dev-help@ctakes.apache.org; run by ezmlm
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Reply-To: dev@ctakes.apache.org
Date: Mon, 16 May 2016 09:35:31 -0600
From: John Travis Green <john.travis.green@gmail.com>
Cc: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Message-ID: <E06FC266-D13B-4674-A127-E948D14F8139@gmail.com>
In-Reply-To: <7D6629E3-BF6F-4823-82EF-8E558914029A@wiredinformatics.com>
References: <A5979460-8E33-464E-BF62-466B73F04679@gmail.com>
 <1463250507883.30200@childrens.harvard.edu>
 <abf3c66cc6d442a38ac81c7a31a74c86@LOFEXMBX207W12V.geisinger.edu>
 <03fbab5006d647038b6153b25f4dc203@CHEXMAIL1A.CHBOSTON.ORG>
 <7D6629E3-BF6F-4823-82EF-8E558914029A@wiredinformatics.com>
Subject: Re: Offline access
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It seems odd they would require repeated checke when you can download the=
 whole thing for input into a db with mmsys.=C2=A0 How is the documentati=
on on building the fast lookup from a local copy of the umls=3F A quick g=
lance at the website didnt reveal much.=C2=A0 ytex reportedly works this =
way but Ive been getting an error with the section annotator that others =
addressed back in early 15 but no resolution was posted to the listserv.=C2=
=A0 Thanks all for your help on this. I have an active irb here in the ar=
my using ctakes but dod security requirements are so strict the entire se=
rver is offline.  Best, John =20


Having a hosted web site which hosts UMLS resources and checks for a lice=
nse before downloading locally(via the NLM/UMLS license validation web se=
rvice) is indeed the norm and a more common way.  (YTEX originally and UM=
LS itself does this when one downloads their resources.)  The responsibil=
ity for any UMLS license adherence afterwards is essentially done by the =
one downloading it since the check is done at that time.  The online/upon=
 initialization license check/bundled solution for cTAKES was really done=
 for convenience to end users and historical reasons.  It just boils down=
 to who wants to build, manage, maintain, host such a site that distribut=
es and ensure the license check before downloading for these specially fo=
rmatted resources.


=E2=80=94Pei


> On May 16, 2016, at 9:12 AM, =46inan, Sean <Sean.=46inan=40childrens.ha=
rvard.edu> wrote:

> =20
> The agreement that the ctakes core group was able to achieve with the N=
LM (distributor of UMLS) was that ctakes would check a user's access righ=
ts upon every use of any database derived from the UMLS.  The reason for =
this was that the NLM did not want one valid UMLS user to download the da=
tabase and then distribute it for use by unaccredited third parties.  We =
have stuck to that agreement.  Upon every initial load of either of the d=
istributed ctakes dictionary modules the user's entered password is check=
ed online with the NLM user registry.

> =20
> I think that a great compromise would be if somebody could create a =22=
remote checkout=22 tool, something that checks-out a virtual license for =
use while you are on the road.  Maybe coordinate with the NLM on getting =
such a thing approved.  As ctakes is open source software you could start=
 toying with such a client first.  To start, delegate to JdbcRareWordDict=
ionary as does the UmlsJdbcRareWordDictionary, and delegate to JdbcConcep=
t=46actory as does the UmlsJdbcConcept=46actory (for the -fast module).  =
Then point to the new trial =22remote checkout=22 classes in your .xml se=
tup file (the default being cTakesHsql.xml).  However, do NOT use these c=
lasses directly or in any production scenario as that would not abide by =
our agreement with the NLM.  Do not even check them into sandbox without =
us getting a new agreement to use such a system with the NLM.  I must emp=
hasize that publicly doing so could cause us to lose our privileges to di=
stribute a default dictionary.  You would still be able to download your =
own UMLS database and create your own dictionary for use with ctakes, but=
 not every user can do that.  And when creating your client code favor co=
mposition over inheritance as the remote checkout client should not have =
IS-A, not that I can enforce anything that you do.

> =20
> I repeat, NEVER use the JdbcRareWordDictionary and/or JdbcConcept=46act=
ory directly unless you are pointing to a database that was not created u=
sing the UMLS as a source.

> =20
> Sean

> =20
> -----Original Message-----

> =46rom: Geise, Brandon D. =5Bmailto:bdgeise=40geisinger.edu=5D

> Sent: Monday, May 16, 2016 8:01 AM

> To: dev=40ctakes.apache.org

> Subject: RE: Offline access

> =20
> I haven't tried it and is a guess based on reading the code, but you mi=
ght be able to change the dictionary implementation name in the xml file =
from UmlsJdbcRareWordDictionary to Concept=46actory, since Umls factory i=
mplements from Concept=46actory.

> =20
> -----Original Message-----

> =46rom: Miller, Timothy =5Bmailto:Timothy.Miller=40childrens.harvard.ed=
u=5D

> Sent: Saturday, May 14, 2016 2:28 PM

> To: dev=40ctakes.apache.org

> Subject: Re: Offline access

> =20
> Well, before we had online verification ctakes required downloading uml=
s, extracting the right subset, and building a database for the dictionar=
y tool. You can still do that - it is often necessary for use cases that =
our default dictionary doesn't have coverage, and while I'm not sure the =
state of documentation there have been several threads on the list about =
it. I think if you do it this way you can skip the UMLS verification step=
 (though I don't remember exactly how that works) because you will have b=
een verified at download time.

> =20
> Can Sean or someone verify that this is true=3F If he builds his own di=
ctionary (with the same subsets) can he skip the online verification=3F

> Thanks

> Tim

> =20
> =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F

> =46rom: John Travis Green <john.travis.green=40gmail.com>

> Sent: Saturday, May 14, 2016 10:12 AM

> To: dev=40ctakes.apache.org

> Subject: Offline access

> =20
> I have a dod use case that requires offline umls verification. Anyone a=
ccomplish this yet=3F I recall some chatter awhile back but initial flirt=
ations with google were unsuccessful. thanks=21John

> =20
> =20
> =20
> =20
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> =20
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