Hi Akram It's not a matter of instructions. It's not been made easy because obviously we won't want people to do it. It's a matter of writing code that serves as an intermediary between ctakes and the UMLS authentication service or a simulated version thereof. As an example, I have a use case where the instance of ctakes is buried deep in a PHI protected environment where we have forbidden web services to connect direct;y with the outside world. So I've written a proxy mechanism that stands half in the protected perimeter and half out. But we're still authenticating.
Perhaps you can figure out a strategy for authenticating and creating a time-limited token that can be taken offline. The hook to do something like that is in the System property -Dctakes.umlsaddr Peter Peter On Mon, May 25, 2020 at 10:56 AM Akram <as...@yahoo.com.invalid> wrote: > Thanks Sean & Peter > I totally appreciate what NLM and cTAKES are doing. > you said "It is possible to use ctakes and the UMLS dictionary completely > offline" > How can I use them offline?Is there any document that shows how?If not, > then could you please help me with instructions. > Best Regards > > On Monday, 25 May 2020, 11:26:04 pm AEST, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > Peter is absolutely correct. > > It is possible to use ctakes and the UMLS dictionary completely offline, > but it isn't recommended for regular use. If you have any way to connect > to the internet please use the standard methods. > > Many years ago the initial creators of ctakes negotiated with the NLM to > enable the unique manner in which ctakes uses the UMLS. At the time it had > never been done and the UMLS could not be redistributed by outside > agencies. A legal (and amicable) partnership between the NLM and ctakes is > absolutely necessary, and upholding our side of the agreement is how we > make that happen. > > NLM maintains the umls and without proof of importance this maintenance > would cease. > > NLM grants are one mechanism by which ctakes development gets funding, so > it really is important that they know who is using the UMLS and how > frequently. There is no detriment to providing them this information. You > will never be charged for use, no matter how heavy it may be. > > The NLM sends annual requests for users to complete a survey. It is > extremely important that you complete the survey and indicate that you use > the UMLS for NLP and ctakes. The NLM and other agencies fund projects in > part upon user-base. The larger the user base of ctakes, the greater the > chance of funding for its development. Any funding in development turns > into more accurate annotation engines, more capabilities and simpler usage > for everybody. > > Of course, private funding would also help ... > > Sean > > > ________________________________________ > From: Peter Abramowitsch <pabramowit...@gmail.com> > Sent: Sunday, May 24, 2020 2:49 AM > To: dev@ctakes.apache.org; Akram > Subject: Re: using UMLS Metathesaurus in cTAKES offline [EXTERNAL] > > * External Email - Caution * > > > Having the data is not synonymous with umls authentication. Out of the box, > you do need internet connectivity for the authentication to take place. > It will happen once during startup. That will be sufficient for as long as > the instance is running. > > The authentication is really meant to be umls' way to measure usage as much > as it is a permission scheme. > > There is a mechanism for the authentication to be proxied through a > different url which can be built onto to create something like you're > thinking of. I've used that, but for a different purpose. > > But in these days of ever diminishing government, it's valuable for the nlm > to have those authentication hits. > > Peter > > On Sat, May 23, 2020, 6:30 PM Akram <as...@yahoo.com.invalid> wrote: > > > I want to use cTAKES offline > > > > I am using command line > > > > run\runClinicalPipeline -i E:\cTAKES\files\MedReps\Input --xmiOut > > E:\cTAKES\files\MedReps\Output --user myuser --pass mypassword > > > > This is my piper file > > > > load DefaultTokenizerPipeline.piper > > > > add DefaultJCasTermAnnotator > > > > load AttributeCleartkSubPipe.piper > > > > writeXmis > > > > > > I thought UMLS will be accessed once and download all needed files so the > > next time it does not need the internet to access **UMLS** > > > > but I was wrong. > > > > When I work offline cTAKES does not work in attempt to access UMLS and > > gives error. > > > > I found that UMLS offers to download its data, so I did > > > > I downloaded **umls-2020AA-full.zip** > > > > I extracted Metathesaurus using MetamorphoSys and added it to > > > > E:\cTAKES\resources\org\apache\ctakes\dictionary\lookup\umls2020aa > > > > It is a huge folder 30GB+ full of .RRF files but did not work > > > > Not sure where the problem is > > > > do I have to change pipers? > > > > do I have to change the command? > > > > do I have to change files in the folder umls2020aa? > > > > > > How to fix these problems to use cTAKES offline? > > > > >
