Sean, I may just be missing something obvious, but having signed up for the confluence wiki I don't see any Edit button on the cTAKES pages even though it does look like everyone has permission to edit.
On Fri, Feb 22, 2019 at 11:01 AM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Jeff, > > >Do you accept documentation > contributions? > > Of course!! We are completely open source, documentation included. I > think that you should be able to edit the wiki after signing up on > confluence: > https://cwiki.apache.org/confluence/signup.action > > Cheers, > Sean > > ________________________________________ > From: Jeffrey Miller <jeff...@gmail.com> > Sent: Friday, February 22, 2019 10:57 AM > To: dev@ctakes.apache.org > Subject: Re: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL] > > Thank you Sean, that clears it up for me. Do you accept documentation > contributions? I might be able to document a few of the things I have > learned along the way setting up ctakes. > > On Tue, Feb 19, 2019 at 12:14 PM Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi Jeff, > > > > The short answer: No, LVG is not in the pipeline created by the > > DefaultFastPipeline.piper > > > > Longer answer: > > In older versions of dictionary lookup the Lexical Variant Generator > > module (LVG) was recommended to capture lexical variants of terms. > > However, the dictionary resource already contains variants so the LVG > > module should not make much of a difference. When the fast lookup was new > > several years ago I ran a test with and without LVG on two datasets and > the > > difference was along the lines of +1-2% recall, -1% precision. > > > > I think that ClinicalPipelineFactory.getFastPipeline() was a copy-paste > of > > the previous .getClinicalPipeline() but with the dictionary module > > replaced. So, LVG is still in that method -created pipeline. > > > > When I (more recently) wrote that piper file that you reference I left > out > > LVG as the added burden didn't seem to warrant its presence. When I say > > burden I don't just mean speed decrease and memory footprint. There have > > been a lot of configuration problems with LVG on various systems which > led > > to difficulty using ctakes. > > > > The diagram that you reference places LVG after the dictionary lookup, > and > > after the part of speech tagger, while the page on lvg > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2B-2D-2BLVG&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Odd-RqfBFrKxLVWy-Nf_-gmZ-UKh9phdcGO0ifqffis&s=ly656xPq-DlDPCj5eTsrlErYHA6FU7gC8h_nofoZRTo&e= > lists > > those as the two modules that may benefit from its presence. That > diagram > > is very old and should definitely be updated. Both the diagram and the > > page on lvg include information that precedes (does not account for) the > > existence of the fast dictionary lookup. > > > > Sean > > > > > > ________________________________________ > > From: Jeffrey Miller <jeff...@gmail.com> > > Sent: Tuesday, February 19, 2019 10:53 AM > > To: dev@ctakes.apache.org > > Subject: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL] > > > > Hi, > > > > I was wondering if the LVG Annotator is included > DefaultFastPipeline.piper > > < > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dclinical-2Dpipeline-2Dres_src_main_resources_org_apache_ctakes_clinical_pipeline_DefaultFastPipeline.piper&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=3Sgs1Jc-C37kcy1efCEhU_3RV4aFipAt1lbTO0Wu_Ns&e= > > >. > > I have tried to trace through all the includes, but I cannot find it. > > However, when I look at the code for the > > ClinicalPipelineFactory.getFastPipeline() it seems to be included. > > < > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_apache_ctakes_blob_513bb49ebb98c4ac63f690c7b88a82aff18947b8_ctakes-2Dclinical-2Dpipeline_src_main_java_org_apache_ctakes_clinicalpipeline_ClinicalPipelineFactory.java-23L98&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=kmZDExXBOyXg84kix__UvgD3LniSHa8MgL8K5fK3XC4&e= > > > > > From > > documentation in this flow diagram > > < > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_download_attachments_68718172_ctakes-2D3.1-2Ddependencies.png-3Fversion-3D1-26modificationDate-3D1488992146000-26api-3Dv2&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=4yYVqkyLiodAWATji1EjSwoMh-YpU7qTz2J8tZvRT6I&e= > > > > > from > > the components documentation page > > < > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2BComponent-2BUse-2BGuide&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=TrXJiUUghmeYrvrV21K68pCfJk5KnG-xwBfzwVbxoRo&s=m-9MenhmNTr2vdVAhCvKgBt48OUiQB8R2TkR7fEYtsY&e= > > >, > > it seems to be a recommended component for the dictionary annotator. > > > > Thanks for your help, > > Jeff > > >
