Re: Current thinking on new UMLS authentication [EXTERNAL]

Here is a copy of the email we received with a similar message: Dear UMLS Licensee, You are receiving this email from the U.S. National Library of Medicine because you have used a username and password to authenticate with an API that relies on UMLS Terminology Services (UTS) authentication ( h

Re: Current thinking on new UMLS authentication [EXTERNAL]

Here is another similar, but different version of the letter: On Fri, Sep 18, 2020 at 12:34 PM Peter Abramowitsch wrote: > Ok. Here you go. > It seems only for users that are also registered content providers, so > perhaps that's why some (all?) of you may not have received it. > > > --

Re: ctakes our existing web application

mage: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Feb 26, 2016 at 1:57 PM, Ben Yu wrote: > Oh beautiful! Thank you Chris. Exactly the direction I was going to. I'll > dive in

Re: Unable to start cTAKES in Ubuntu

I would suggest trying it with minimum memory set to at least 2048M (-Xms2048M). cTakes does take a huge amount of memory to run. [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Sa

Re: UMLS Authentication failing despite correct username and password

Would it be possible to loosen up the checking a little to avoid this kind of problem in the future, such as pass if the the result contain "true"? [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634

Re: UMLS Authentication failing despite correct username and password

enseCode=NLM-6515182895 Replace with your NIH userID Replace with your password You should get a response that looks like: true [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com

Re: What is the correct way to enable cTakes to recognize and annotate mentions of medical devices?

f_ontologyConceptArr to find out the TUI associated with the annotation. > > > Regards, > James > > -Original Message- > From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com] > Sent: Thursday, April 30, 2015 3:39 PM > To: dev@ctakes.apache.org > Subject

What is the correct way to enable cTakes to recognize and annotate mentions of medical devices?

Hi, I am using the cTakes 3.2.0 code base and I have been trying to figure out what would be the proper way to get cTakes to recognize and annotate mentions of medical devices. I am using the AggregatePlaintextUMLSProcessor.xml because one of the main requirements for the annotation is that it nee

Re: cTakes Annotation Comparison

: FastUMLSProcessing: 12,811 UMLSProcessing:46,571 [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Dec 19, 2014 at 3:04 PM, Bruce Tietjen < bruce.tiet...@perfectsearchcorp.c

Re: cTakes Annotation Comparison

ttp://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Dec 19, 2014 at 1:49 PM, Bruce Tietjen < bruce.tiet...@perfectsearchcorp.com> wrote: > > I'll do that -- there is always a possibility of bugs

Re: cTakes Annotation Comparison

I'll do that -- there is always a possibility of bugs in the analysis tool. [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Dec 19, 2014 at 1:39 PM, Finan, Sea

Re: cTakes Annotation Comparison

ached the modified ones I used (but they may not get through the mailing list). [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Dec 19, 2014 at 1:27 PM, Finan, Sea

Re: cTakes Annotation Comparison

Correction -- So far, I did steps 1 and 2 of Sean's email. [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Dec 19, 2014 at 1:22 PM, Bruce Tietjen &

Re: cTakes Annotation Comparison

spans, this run only matched 220 (default configuration matched 224) Bruce [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Dec 19, 2014 at 12:16 PM, Chen, Pei wrote: &g

Re: cTakes Annotation Comparison

Rather than spam the mailing list with the list of filenames for the files in the set we used, I would be happy to send it to anyone interested privately. [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruc

Re: cTakes Annotation Comparison

only have Disease_Disorder annotations. [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Fri, Dec 19, 2014 at 9:54 AM, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote:

Re: cTakes Annotation Comparison

: Human adjudicated annotations: 4591 (excluding CUI-less) Annotations found matching the human adjudicated standard UMLSProcessor 2245 FastUMLSProcessor 215 [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile

cTakes Annotation Comparison

With the recent release of cTakes 3.2.1, we were very interested in checking for any differences in annotations between using the AggregatePlaintextUMLSProcessor pipeline and the AggregatePlanetextFastUMLSProcessor pipeline within this release of cTakes with its associated set of UMLS resources. W

Re: Differences in MedicationMention annotations on subsequent processing runs

.java:127) at org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:123) ... 31 more [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Thu,

Re: Differences in MedicationMention annotations on subsequent processing runs

image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Wed, Oct 8, 2014 at 10:02 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Bruce, > > With Pei's help I ju

Re: Differences in MedicationMention annotations on subsequent processing runs

If I understand correctly, I would need new dictionary resources to run the rare word lookup method. Where can I find the necessary dictionary(ies) or how do I build them? [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.63

Differences in MedicationMention annotations on subsequent processing runs

hat would be the expected behavior? [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@im

Re: cTakes output predictability

trun: Note that in the first instance, there were two MedicationMentions, but in the second, there is only one. Yes, everyone could write their own custom compare code, but wouldn't it be more valuable to the community to make that task easier? Thanks, Bruce Tietjen [i

cTakes output predictability

community would be interested in and find helpful? Thanks, Bruce Tietjen Perfect Search Corp.

Re: Ctakes to process 5000K recoreds

Sean, If that is a script for generating a dictionary for use with dictionary-lookup-fast, I would also be very interested in checking it out. Thanks, Bruce [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruc

Re: Procedure

p, the word 'pulsatile' has already been dropped and so it will not match the full word matching for this entry. [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Thu,

Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2)

The candidate and convenience binary links listed appear to be broken. Can someone supply a corrected link? [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [image: Mobile:] 801.634.1547 bruce.tiet...@imatsolutions.com On Wed, Jul 9, 2014 at 9

Converting UMLS codes to SNOMED codes using the YTEX pipeline

then noticed that the LookupConsumer identified there specifically uses the UMLS codingscheme. Or is there a reason why the ytex pipeline should not produce SNOMED codes? Thanks, Bruce Tietjen [image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [im

Infinite recursion in DrugMentionAnnotator.java

beginChunk = drugChangeStatus.getEnd(); } Changing the logic inside getAdjustedWindowSpan() might be a more correct and complete fix, but requires a much more detailed knowledge of the code. Your evaluation of the correctness of this code modification would be appreciated. Bruce Tietjen Perfect Search Corp.