Hi Peter, As you said, even if I don't use the UMLS dictionaries, I should be able to run the pipeline, right? But the class ClinicalPipelineFactory in the ctakes-clinical-pipeline module, which initializes multiple pipelines for these various use cases, only defines a getDefaultPipeline() and getFastPipeline() which have some annotating components in them. The getDefaultPipeline() method defines a UmlsDictionaryLookupAnnotator in its workflow. Even the fast pipeline defines a DefaultJCasTermAnnotator in its workflow. When I try to run the sample main() method with either of these pipelines, they throw an error requiring the UMLS credentials. I mean, the ClinicalPipelineWithUmls class is already present for handling the UMLS path. Why do the rest of the pipelines also require UMLS authentication? Please suggest a pipeline which I might run and get some annotations identified from the text without UMLS.
Thanks and Regards, Abhishek On Sat, Aug 11, 2018 at 1:36 PM Peter Abramowitsch <[email protected]> wrote: > Hi, yes there are a lot of details and use cases that are not documented, > but there are quite a few bits of information if you take the time. > > To give some quick "answers" to your questions... (I put that in quotes > because these are interpretations and not legal opinions) > > You do not need a UMLS license if you don't include the UMLS lookup > mechanism. In this case only the Apache license probably applies > http://www.apache.org/licenses/ > > But if you do use UMLS, start by reading > https://www.nlm.nih.gov/databases/umls.html > https://uts.nlm.nih.gov/license.html > https://uts.nlm.nih.gov//help/license/validateumlsuserhelp.html > > There are options for situations where you would centralize a ctakes > service. Some of the provisions have to do with the fact that > that SNOMED vocabulary details are included in the UMLS output, and the > SNOMED organizations have specific licensing requirements that you can see > on their site. > > I am nearly positive that you cannot use the UMLS mechanism in a for-profit > setting without an explicit license from SNOMED. Also, regardless of > whether the service as you deliver it is centralized, as I understand the > language and diagrams on these sites, each and every end user needs to > have, and actively validate a current UMLS license. > > I've been involved in something similar to what you describe, but in a > non-commercial setting, and it does validate every end user. > > Peter > > > > > > > On Sat, Aug 11, 2018 at 7:45 AM Abhishek De <[email protected]> > wrote: > > > Hi all, > > > > I am Abhishek De, a newcomer to the CTAKES community. I had worked with > > CTAKES over 4 years ago, but now I am trying to incorporate it into my > Java > > application as a senior developer, so I need to know a lot of things > about > > it. For starters, I can see that even the pipeline without UMLS needs > UMLS > > credentials in order to run. So I have the following questions: > > > > 1. Is there a certain fee which is required in order to apply for a UMLS > > license? > > > > 2. My organization is building this pharmacovigilance app which will > > internally use CTAKES for its client. Is it okay for only my parent > > organization to have the UMLS license or do the client needs to have it > > too? If I expose the application as a service, with the servers residing > in > > our organization's premises, would the client still need to have a > licnse? > > > > 3. As there is precious little documentation on CTAKES, and many links > > there are now dead including the ones giving instructions on how to > install > > dictionaries for RxNorm or SNOMED-CT, could anyone please help me in this > > regard? > > > > 4. Also, I would like to know if there are any small dictionaries which > > could be used free of charge or licensing, for my PoC. > > > > Thanks and Regards, > > Abhishek De > > >
