Hi Abhishek, not meaning to offend, but I think you need to spend more time on the wiki site, a lot of what you are asking about is documented there
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide#cTAKES4.0UserInstallGuide-cTAKESPipelineFabricatorGUI(CreatingPiperFiles) If you have the binary release, you'll find the launch scripts in ./bin, if you have source you'll find it all in ./ctakes-distribution/src/main/bin The piper files are sprinkled throughout based on the modules that use them and are grouped under a common resource folder in the binary release ./ctakes/trunk/ctakes-assertion-res/target/classes/org/apache/ctakes/assertion/pipeline/TsAttributeCleartkSubPipe.piper ./ctakes/trunk/ctakes-assertion-res/target/classes/org/apache/ctakes/assertion/pipeline/AssertionSubPipe.piper ./ctakes/trunk/ctakes-assertion-res/target/classes/org/apache/ctakes/assertion/pipeline/AttributeCleartkSubPipe.piper ./ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/TsAttributeCleartkSubPipe.piper 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./ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/pipeline/DictionarySubPipe.piper ./ctakes/trunk/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/pipeline/TsDictionarySubPipe.piper ./ctakes/trunk/ctakes-chunker-res/target/classes/org/apache/ctakes/chunker/pipeline/ChunkerSubPipe.piper ./ctakes/trunk/ctakes-chunker-res/target/classes/org/apache/ctakes/chunker/pipeline/TsChunkerSubPipe.piper ./ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/ChunkerSubPipe.piper ./ctakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/pipeline/TsChunkerSubPipe.piper On Sun, Aug 12, 2018 at 6:04 AM Abhishek De <abhishekde1...@gmail.com> wrote: > Hi Peter, > > I found the PiperCreator class in the ctakes-gui module which is opening up > the Pipeline Fabricator GUI with a lot of pipe bits which are seeming to be > overwhelming!! If I could get the piper samples which you are talking > about, I could have got a taste of how this thing works. But the resources > for this module does not contain those, nor does the ctakes-resources > separate download which contains the dictionaries. Also, you said "script" > and not "class". That makes me think you are speaking of something else > entirely, since there is no class named PiperRunner. So could you please > point me where to download these scripts and the resources? > > Thanks and Regards, > Abhishek > > On Sat, Aug 11, 2018 at 7:10 PM Peter Abramowitsch < > pabramowit...@gmail.com> > wrote: > > > 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 > > > > > > > > > > > > > > >
