Re: Preparing for an Apache cTAKES 3.2 Release?

There is some documentation in the dictionary2 module under /doc/DictionaryLookupHelp.{txt | docx} that gives some some details of the different lookup implementation options within that module that I found helpful. On Jun 9, 2014, at 5:17 PM, Masanz, James J. wrote: > > Will ctakes-dictiona

Re: Preparing for an Apache cTAKES 3.2 Release?

n for those who are curious). > > --Pei > >> -Original Message- >> From: britt fitch [mailto:britt.fi...@gmail.com] >> Sent: Monday, June 09, 2014 5:42 PM >> To: dev@ctakes.apache.org >> Subject: Re: Preparing for an Apache cTAKES 3.2 Release? >>

Re: question about sentence segmentation

My preference is to treat the list row number as outside of the sentence of interest. Or if it is necessary to be included in a sentence, have it be a sentence on its own. That won't be as straightforward as splitting on a period in cases like "2. Magnesium oxide 400 mg p.o. daily." In cases where

Re: question about sentence segmentation

ce). >> This behavior is probably strongly dependent on the annotations we give the >> sentence detector so as I'm prepping new training data I should have a >> default in mind. >> >> Does anyone have any objections to changing the sentence detector behavior >> to break list headers

Re: question about sentence segmentation

llowed by a period or a > newline it is considered a sentence break and otherwise it is part of the > sentence. > > e.g. > > 1. 20 mg flomax > > is two sentences, while: > > 1 - 20 mg flomax > > is one sentence. > > For headings: > > Allergies: Pt i

Re: LabMentions

We have been actively working on a lab annotator at Wired Informatics that we are planning to contribute back to the community once its fully tested. We will post to the dev list when we have a date that that becomes available. Cheers, Britt On Aug 4, 2014, at 5:19 PM, Harpreet Khanduja w

Re: cTAKES min requirements

No objections here. On Aug 25, 2014, at 12:16 PM, Pei Chen wrote: > Since we default the runtime java heap sizes to 3g in 3.2.0, should we > update our documentation to officially only support 64bit? I can only > see models/pipelines being loaded into mem grow in size. I know it > may seem t

Re: [DISCUSS] cTAKES BigTop/Hadoop integration

This is a really exciting. I can’t wait! Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com On Sep 22, 2014, at 11:23 AM, Murali Nagendranath wrote: > +1 > > On Mon, Sep 22,

Re: cTakes output predictability

Before making changes to the data structure I think it would be good to understand the use case. Bruce, can can you give a high level description of the issue you are trying to solve? Cheers, Britt On Mon, Oct 6, 2014 at 7:38 PM, jay vyas wrote: > Im not a ctakes expert by any means, but in

Re: cTakes output predictability

The option Sean mentioned of writing your own custom consumer (without the UIMA id that is causing your issues) should meet these needs I believe. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi

Re: cTakes output predictability

I think changing the code raises at least some concerns of affecting others, while adding a custom consumer raises zero. Given how easy it is to write a custom consumer, that is my vote. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http

Re: cTakes Document Preprocessor Component Error

Hi Samir, it looks like you might have the wrong SVN client option specified. If I recall correctly, in Windows it defaults to ‘JavaHL’ and you want to go to: ‘Preferences' > ‘Team' > 'SVN' > 'SVN Client’ and select the ‘SVNKit’ option from the drop down.

Re: [DISCUSS] new cTAKES web site

I prefer option 1. Largely because of the prominence of ‘downloads’ and ‘examples’. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Dec 31, 2014, at 2:53 PM, Chen, Pei wrote: > > Hi folks, &

Re: cTakes 3.2 Installation Guide doubt

Hi Mohammad, the resources should go in the corresponding “-res” project. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jan 6, 2015, at 11:03 PM, Mohammad Alodadi wrote: > >

Re: cTakes setup

Hi Mitch, Are you on a 32 bit machine or a 64 bit machine? If its 32 you might want to upgrade that as well. You can also try lowering the Xmx to 2500M but it’ll be tight. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com

Re: Medical de-identification

ck to the dev list while getting it running in ctakes. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Mar 20, 2015, at 7:57 PM, andy mcmurry wrote: > > Britt et al: here is a

Re: Medical de-identification

room numbers in documents and identifying a persons title in documents. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Mar 24, 2015, at 12:09 AM, Rohit Shinde > wrote: > > Thanks Britt! I am

Re: Smoking Status Pipeline

org.apache.ctakes.smokingstatus.type.NonSmokerNamedEntityAnnotation; org.apache.ctakes.smokingstatus.type.SmokerNamedEntityAnnotation; In partiuclar: SmokingDocumentClassification.getClassification(). Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com

Re: Error processing text documents in CPE

You can find details on unsubscribing here: https://ctakes.apache.org/mailing-lists.html <https://ctakes.apache.org/mailing-lists.html> Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Apr 9, 20

Re: Error processing text documents in CPE

bf1.yahoo.com%3E> I don't recall if this has already been fixed in trunk or not. If not, would you mind opening a Jira ticket for it and we can be sure to fix it in the next release? Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.c

Re: build tool suggestion

There is a Sonar plugin for Jenkins that's pretty rad. Sent from my iPhone > On May 6, 2015, at 10:57 AM, Masanz, James J. wrote: > > > Sorry, I wasn't clear, when I said "at build time", I meant the Jenkins > automated build. > > > -Original Message- > From: Finan, Sean [mailto:s

Re: Authentication fails for uts.nlm.nih.gov

c35...@chexmbx4a.chboston.org%3E> Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On May 13, 2015, at 1:13 AM, Sangram Patil wrote: > > Hi, > > For https://uts.nlm.nih.gov/ I have got lice

Re: The fast dictionary pipeline vs. the regular one

, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jun 21, 2015, at 2:45 PM, Miller, Timothy > wrote: > > Sean wrote the fast version and may be able to answer your specific > qu

dictionary-look-fast fails to handle alternative CUIs

these edits and check them in whether that means updating the CuiCodeUtil class or creating an entirely new BSVConceptFactory if thats what makes the most sense. Thoughts? Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com bri

Re: dictionary-look-fast fails to handle alternative CUIs

NLM + 300 In that case, do we need to store it as a Pair at all or is just storing the prefix in a String[] sufficient? I’m happy to start working on this unless you have a preference for splitting it out into multiple tasks. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Bo

Re: dictionary-look-fast fails to handle alternative CUIs

I don’t think that is too much of a constraint, at least initially, to have all CUI values a consistent length for a given prefix. Thanks Sean, let me know if there is any part of this you’d like a hand with. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA

Re: dictionary-look-fast fails to handle alternative CUIs

Absolutely. I’ll create it now. Thanks! Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jul 9, 2015, at 3:12 PM, Finan, Sean > wrote: > > Hi Britt, > > I’ve got some code and

Re: dictionary-look-fast fails to handle alternative CUIs

Linking ticket here for completeness https://issues.apache.org/jira/browse/CTAKES-368 <https://issues.apache.org/jira/browse/CTAKES-368> Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jul 9, 2

Re: dictionary-look-fast fails to handle alternative CUIs

Thanks, just finished testing and closed the ticket. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jul 9, 2015, at 3:44 PM, Finan, Sean > wrote: > > Checked in, please give it a test a

Re: dictionary-look-fast fails to handle alternative CUIs

. I’ll definitely report back if I notice any performance change given the new logic though. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jul 10, 2015, at 5:31 PM, Finan, Sean > wrote: > > G

periods and the interaction with PTB & Fast Dict Lookup.

the same components? Let me know if I read into one of these points wrong. Since these items would likely cause large changes I am looking to get some feedback before moving forward. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com

Re: periods and the interaction with PTB & Fast Dict Lookup.

particular gene or disorder grouping. The term I mentioned was just meant to be an example. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jul 15, 2015, at 8:57 AM, Finan, Sean > wrote: > &

Re: periods and the interaction with PTB & Fast Dict Lookup.

Hi Sean, do you want a ticket for the PTB update? Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Jul 15, 2015, at 9:07 AM, britt fitch > wrote: > > Thanks Sean. > >

Re: multiple issues with Ctakes 3.2.2

have” or “no evidence of” or the like to confirm. Was an image pasted after "The SignSymptomMention for numbness” it renders as a ?-box for me Hope that helps. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com bri

Re: Boston cTAKES Hackathon?

I am interested in participating! Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Sep 16, 2015, at 4:23 PM, Pei Chen wrote: > > Hi, > I hope everyone had a great summer. I just wanted to r

Re: Creating a new annotator

Did you declare the new Age type in TypeSystem.xml? You may want to extend one of the existing types like EntityMention or IdentifiedAnnotation. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com

Re: cTAKES dictionary lookup behavior question

apy” “pathology” > “pathology department” , “pathology procedure” “exercise” > “exercise pain management” Those are just some quick examples. It depends heavily on what the ontology contains though. Cheers, Britt Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 0

Re: ctakes blog

I like the blog approach. I think it will help direct the creation of various guide-type documentation going forward. Britt Fitch Wired Informatics 265 Franklin St Ste 1702 Boston, MA 02110 http://wiredinformatics.com britt.fi...@wiredinformatics.com > On Dec 8, 2015, at 4:41 PM, Mil

Re: [VOTE] Release Apache cTAKES 3.1 (rc3)

+1 here as well. On Tue, Sep 3, 2013 at 11:47 AM, Pei Chen wrote: > James, > +1 > [x] +1 Release the packages as Apache cTAKES 3.1.0 > > Below is what I verified so far (plan to go through the documentation in > parallel): > > Tested: > 1- Downloaded src and bin tz > 2- Verified Signatures > 3-

Re: cTAKES user interface

+1 to Andy's suggestion. Ease of initiation + community engagement = positive growth. On Tue, Oct 29, 2013 at 6:09 PM, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > I think this is also an area where Maven integration was a small step > backwards (I greatly appreciate the step

Re: [VOTE] Release Apache cTAKES 3.1.1

+1 On Mon, Dec 2, 2013 at 1:16 PM, Karthik Sarma wrote: > +1 > > > > > > -- > Karthik Sarma > UCLA Medical Scientist Training Program Class of 20?? > Member, UCLA Medical Imaging & Informatics Lab > Member, CA Delegation to the House of Delegates of the American Medical > Association > ksa...@k