I would suggest looking into the piper system - the scripts piperCreator
and piperRunner so you can construct/run pipelines with the bits you want.
Also look for the piper samples scattered throughout the resources area.
But assembling pipelines using Java is simple too.   You just need to learn
the flow and the upstream dependencies of the parsers and annotators.

Peter

On Sat, Aug 11, 2018 at 3:28 PM Abhishek De <abhishekde1...@gmail.com>
wrote:

> 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 <
> pabramowit...@gmail.com>
> 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 <abhishekde1...@gmail.com>
> > 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
> > >
> >
>

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