cTAKES 3.2 Analysis Batch Issue

batch field is missing? Side question: Any update on when cTAKES 3.2 will be officially released? I see we're passed the expected release and was curious on how long it will be until it will officially come out. Thanks a lot, -- Clayton Turner

Re: cTAKES 3.2 Analysis Batch Issue

red (it will > default to the current date). Can you attach the log file? > > -vj > > [image: Inline image 1] > > > On Wed, Jul 2, 2014 at 12:22 PM, Clayton Turner > wrote: > >> Hi, I'm a relatively new user of cTAKES. >> >> I recently cloned cT

Re: cTAKES 3.2 Analysis Batch Issue

Any update on this issue? I have this problem even if I don't use the ytex version of the aggregate text processor (UMLS-independent as well). On Thu, Jul 3, 2014 at 2:33 PM, Clayton Turner wrote: > Yes, I am running the fracture_demo.xml cpe. > > There is no option for the

Re: cTAKES 3.2 Analysis Batch Issue

screenshot is not coming through via the newsgroup emails. can you > attach the log file? > > vj > > > On Mon, Jul 7, 2014 at 5:38 PM, Clayton Turner > wrote: > > > Any update on this issue? I have this problem even if I don't use the > ytex > > version

cTAKES CPE MySQL Exception

at a loss with this error, especially since it takes so long to actually spit the error out at me. Thanks in advance everyone, Clayton -- -- Clayton Turner email: caturn...@g.cofc.edu phone: (843)-424-3784 web: claytonturner.blogspot.com

ytex examples

I've been following the usage component guide for ctakes 3.2 and ytex, but I'm having an issue. I get to the point where I want to export my data as a bag of words (or cuis), but the documentation on the wiki seems to be really out of date when it comes to the exporting for data mining step. The

Re: ytex examples

look here for examples: > > https://code.google.com/p/ytex/source/browse/#svn%2Ftrunk%2Fworkspace%2Fexamples%2Ffracture > > If you are using R/Matlab/Python it is easy to generate a sparse matrix > directly via database queries, I can give you a few examples > > Best, > > VJ >

Re: ytex examples

#x27;re in a jar that I'm somehow not including?) On Thu, Jul 24, 2014 at 2:24 PM, Clayton Turner wrote: > Hi, > > Alright, I planned on using weka, but it might not be a bad idea to just > jump in with either R or Python. > > I'll check out that link. > > Thanks

Re: ytex examples

Hi again: This issue is still persisting. I can only find the SparseDataExporterImpl class outside of the ctakes snapshot and, even using that version, I cannot get the exporter to work, regardless of the parameters I pass to it. On Thu, Jul 24, 2014 at 3:18 PM, Clayton Turner wrote: >

Exporting YTEX Pipeline

Hi, I'm trying to export the data I get from running the pipeline through the Collection Processing Engine. I set up the pipeline where I have a directory where all the XML is output to, but I am having issues at this point. I've tried using the built in Exporter from the Data Mining section on t

Re: Exporting YTEX Pipeline

-prop > desc\ctakes-ytex\fracture\cui.xml -type weka > > Tell me if you run into any issues. > > I will add this to the ctakes confluence doc. > > Best, > > VJ > > > On Wed, Jul 30, 2014 at 5:11 PM, Clayton Turner > wrote: > > > Hi, I'm tr

v_snomed_fword_lookup view

2) Reinstalled a second time after redownloading umls through metamorphosys, ensuring that snomed vocabularies were included (also checked file sizes and noticed a big difference so I know those vocabularies ARE included Anyone got any ideas as to what the issue could be? Thank you, Clayton Turner

Re: v_snomed_fword_lookup view

like to eventually work together on reusing the same code for > ytex? I have no idea what ytex does, but I know the ins and outs of the > cdl-fast module. > > Sean > > > -Original Message- > > From: clayclay...@gmail.com [mailto:clayclay...@gmai

Re: v_snomed_fword_lookup view

sSnomed.xml Now, I don't even have a "lookup2" folder and, subsequently the Tui folder and cTakesSnomed.xml file. This seems to be the problem, but I'm not sure where these files are supposed to be grabbed from. On Mon, Aug 11, 2014 at 11:47 AM, Clayton Turner wrote: >

Re: v_snomed_fword_lookup view

I'm going to do a clean install through the repo rather than the binaries and see if that fixes my issue because I think I just read a past post saying the lookup2 folders exist there. On Mon, Aug 11, 2014 at 11:52 AM, Clayton Turner wrote: > When navigating to ctakes-dictionary-loo

Re: v_snomed_fword_lookup view

I still get the same error with the ctakes3.2 branch. Any suggestions? On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner wrote: > I'm going to do a clean install through the repo rather than the binaries > and see if that fixes my issue because I think I just read a past post &

Re: v_snomed_fword_lookup view

> > > ${ctakes.version} > > > > > > > > > > > > these two dependencies to the file. > > > > > > > > > After this, I also added the dependency > > > > > > org.apache.ctakes > > > ctak

Re: v_snomed_fword_lookup view

doilies, etc. > > I'm sure that none of the above helps you, but I felt obliged to provide > some kind of answer to your question. > > Sean > > > -----Original Message- > > From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On Behalf Of > > Clayto

Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup

27;T047', 'T048', 'T049', 'T050', > > > 'T190', 'T191', 'T033', > > >'T184', > > >'T017', 'T029', 'T023', 'T030', 'T031', 'T022',

Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup

Ah, I just switched to the ytex branch and all is good now. The SNOMED_US issue has been plaguing me for weeks now so thanks a million for that. On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner wrote: > Awesome. This is just what I needed for the longest time. > > I'm having

Re: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup

gt; Clayton - this indeed did fix the @db.schema@ for you? Im gonna try and > reproduce (havent had time yet) then ill close the Jira ticket out. > > > JG > — > Sent from Mailbox for iPhone > > On Thu, Aug 21, 2014 at 1:24 PM, Clayton Turner > wrote: > > > Ah, I jus

v_document_cui_sent not being populated

Hey everyone: I'm using the ytex branch of ctakes and am trying to pull down polarities of concepts and other related information after running the ytex pipeline AE on my data. the v_document_cui_sent table contains 0 rows of data, but v_document and v_document_ontoanno both contain data. I woul

YTEX Exporting with Large Dataset

x27;m getting a null pointer exception when using the big dataset, but no error occurs if I use my old, smaller dataset​ even though the export files are nearly identical. Are there file size limits that I am potentially hitting or is my error likely something else? Thanks, Clayton Turner

Re: YTEX Exporting with Large Dataset

Ah, so apparently YTEX does not like me using a join inside the InstanceClassQuery. This is inconvenient, but I can work around it. Clayton Turner Graduate Research Assistant at The College of Charleston Web Developer at Innovative Resource Management Email: caturn...@g.cofc.edu Phone: (843)-424

Re: YTEX Exporting with Large Dataset

So, YTEX does not like having a join inside the InstanceClassQuery. This is inconvenient, but I can work around it. On Wed, Oct 29, 2014 at 2:16 PM, Clayton Turner wrote: > ​Hi everyone: > > So I'm doing some work with the ctakes-ytex branch of ctakes. So, in the > past, I&#x

Re: YTEX Exporting with Large Dataset

Oops! Let me clarify in case someone else hits this or thinks I'm just messing up really badly. I had null values in my dataset and forgot to do a simple "is not null" - that explains a 'null pointer exception' alright. On Wed, Oct 29, 2014 at 2:39 PM, Clayton Turner

Pausing the CPE

ng side-by-side with it which requires more heap space for the JVM. So my question is, does hitting the pause button on the CPE disrupt the pipeline? Aka, can I resume the pipeline after pausing it without losing any information? Clayton Turner