Re: Fw: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch

This is missing critical items which constitute an apache release [1]. If it has already been dist'd, I would suggest retroactively correcting the missing steps as outlined in the release process. [1] http://www.apache.org/legal/release-policy.html#policy On Sat, Jan 23, 2021 at 10:39 AM Finan,

Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch

- Link to public KEYS to verify the sigs? - Link to the VOTE results? - Anyone get a chance to download/test/verify the release candidate artifact in staging before dist'ing? Not sure if the release guide procedures changed, but it's fairly typical

Re: Demos menu option on cTAKES homepage

Hi James, The demos were being upgraded to use 4.0.0 last night. They should be up and running now. Let me know if you encounter any issues. --Pei On Tue, Apr 25, 2017 at 10:59 PM, James Masanz wrote: > Pei and others with access to update

[CANCEL] [VOTE] Re: Release Apache cTAKES 4.0.0 (rc2)

o be put onto >>> maven central for ctakes to work as a maven dependency) >>> Sean fixed some issues today (I saw commit notices today) which I'd >>> like to see included in 4.0 before it's released >>> >>> -- James >>> >>> >>

Re: Release Apache cTAKES 4.0.0 (rc2)

thyme.healthnlp.org > http://cancer.healthnlp.org > http://share.healthnlp.org > http://center.healthnlp.org > > > -Original Message- > From: Pei Chen [mailto:pei.c...@wiredinformatics.com] > Sent: Saturday, April 15, 2017 9:13 AM > To: dev@ctakes.apache.org > Subject:

Re: Release Apache cTAKES 4.0.0 (rc2)

es to work as a maven dependency) > Sean fixed some issues today (I saw commit notices today) which I'd > like to see included in 4.0 before it's released > > -- James > > > On Wed, Apr 12, 2017 at 5:31 PM, Pei Chen <chen...@apache.org> wrote: > >> This is a

Release Apache cTAKES 4.0.0 (rc2)

This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 4.0.0. For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621=12340211 The release was made using the cTAKES release

Re: Labs annotator?

Kean, This would be really useful. If you would like make a contribution, could you please open a Jira and attach the patch or code? When you submit a patch via jira/attachment, it has legal verberage about donating the code, etc. --Pei On Wed, Mar 29, 2017 at 9:30 AM, Finan, Sean

Re: (Re)introduce myself - James Masanz

Welcome back James! Good to hear from you again. Out of respect for the others in the community who already volunteered to be RM, I do not see an need for BCH to override existing volunteers. Unless they unable or unwilling. Would you/others agree? Sent from my iPhone > On Jan 27, 2017, at

Re: Infrastructures questions.

le:// instead of ResourceAsStream forcing resources to be unpacked. This doesn't jive well during the package phase of the maven build cycle where it references your .m2 repo. mvn test works fine because it will reference the explicit local unpacked lvg resources. Pei Chen Wired Informatics &

Re: Infrastructures questions.

What release are you referring to? On Tue, Dec 13, 2016 at 11:08 AM, Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > By the way, did we ever vote on the release? > http://www.apache.org/dev/release.html#approving-a-release > > > -Original Message- > Fro

Re: cTAKES - 3.2.3 release

and maybe I shouldn’t express an opinion. > Apologies in advance if this is inappropriate. However as someone who has > gone through the pain of trying to install, learn, and use ctakes; I strongly > agree with Sean. I don’t inject myself into the situation lightly or to > “ven

Re: cTAKES - 3.2.3 release

Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release. I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now. In the past, the

Re: Migration of ctakes-vm

Hi Freddy, I left some comments directly on the Jira earlier... I don't believe that VM was actually used. It may be easier to just decom it and we can re open a request a new one later on in the future. --Pei On Mon, Nov 28, 2016 at 12:43 AM, Freddy Barboza Oviedo wrote: >

Re: [DISCUSS] Hadi Amiri as Apache cTAKES committer

[-dev@, + private@] Moved to the private list as this is typically better suited for personnel matters, voting in committers, pmc, security-related issues. Sounds like a good addition to grow the group, but what has Hadi contributed to Apache so far? Wait until there have been some contributions

Re: Karma for Jira

Done. Also dded the new committers- Lewis, Peter, and Azad as well. —Pei > On Jun 10, 2016, at 2:11 AM, Richard Eckart de Castilho > wrote: > > Hi all, > > could somebody please add me to the cTAKES project in Jira > such that I can assign issues to myself? > > Best, > > --

Re: headword field in identifiedannotations

I don't see any issues with adding the additional optional attribute... I think we already did the same for other items like relations for similar reasons. The only catch is probably that the dependency will need the dictionary lookup to be run first (assuming that the logic will be added to the

Welcome Lewis John McGibbney as a cTAKES committer

The Apache cTAKES PMC is pleased to introduce Lewis John McGibbney as a new committer. We are very happy with the sustained growth of the project and look forward to continued contributions from the community and adding to the ranks of the cTAKES committers. --Pei

Re: cTAKES dirty on checkout

+1 I think there was already a Jira to remove the Eclipse specific settings; or at least make it automatically derived from the pom.xml’s. —Pei > On May 13, 2016, at 11:48 AM, Richard Eckart de Castilho > wrote: > > Hi all, > > when checking out the sources of cTAKES from

Re: ctakes uimafit analysis engine resource initialization errors

Also, check that the liblinear dependency is in your pom.xml (it should already be included in ctakes-assertion/pom.xml). org.cleartk cleartk-ml-liblinear On Tue, Mar 1, 2016 at 7:53 AM, Miller, Timothy

Re: ctakes gui

Hi Ben, I think the ctakes-gui in the sandbox area is really outdated and hasn't been maintained in a long time (hence in sandbox). But there was a old thread [1] that you may find useful. [1]

Re: ctakes resource exception

resources-3.2.1.1-bin.zip/download> Fast Version <http://sourceforge.net/projects/ctakesresources/files/ctakessnorx-3.2.1.1.zip/download> Pei Chen Wired Informatics <http://www.wiredinformatics.com> 265 Franklin St Ste 1702 Boston, MA 02110 tel: (617) 433-7544 pei.c...@wiredinforma

Re: Mac/download link broken

ject:RE: Contributing to documentation > > > > Hi Jessica, > Thank you very much for offering to contribute to the documentation! > Indeed this is our weak link and any help there will be greatly > appreciated. > A warm welcome to the community! > --Guergana >

Re: Mac/download link broken

tly delete this e-mail and any > attachments without reading, forwarding or saving them. Thank you. > > > > > > From:Pei Chen <pei.c...@wiredinformatics.com> > To:dev@ctakes.apache.org > Date:02/11/2016 01:05 PM > Subject:Re: Ma

Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

h the patch. All new files are >> missing (and also the svn-ignore settings). >> >> Can you take a look? >> >> Best, >> >> Peter >> >> Am 28.01.2016 um 14:43 schrieb Pei Chen: >>> patch applied. >>> Thanks, >>> Pei

Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

patch applied. Thanks, Pei On Thu, Jan 28, 2016 at 4:14 AM, Peter Klügl <peter.klu...@averbis.com> wrote: > Hi Pei, > > can you commit the recent patch for us? > > CTAKES-384-20160120.patch > > Best, > > Peter > > Am 20.01.2016 um 19:35 schrieb Pei Chen:

Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

>>>> Cheers, >>>> Azad >>>> >>>> On 24 Nov 2015 09:55, "Peter Klügl" <peter.klu...@averbis.com> wrote: >>>>> Hi, >>>>> >>>>> I just wanted to mention that I haven't forgot about it. Unfortuna

Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

;>>> Hi, >>>> >>>> I just wanted to mention that I haven't forgot about it. Unfortunately, >>>> there is just no spare time right now. I hope I will be able to provide >>>> the patches in December. >>>> >>>> Best, &

Re: Need help to identify procedures in xml file using AggregatePlaintextFastUMLSProcessor

Hi Reena, If you search for "ProcedureMention" in the attached output xml, you should be able to find the Procedures (plus the FSArray of the associated Concepts) that were extracted... Or am I missing something... --Pei On Mon, Dec 7, 2015 at 12:40 AM, Reena Duggal

Re: ctakes with icd10; 2015 versions available on sourceforge!

Brandon, That sounds great! Please open a Jira ticket for any contributions (anyone should be able to create a Jira account). There are some legal items built into the ASF Jira attachments for accepting contributions/donations. It will also credit the contributors with the merit appropriately.

Re: Create next cTAKES release (3.2.3)?

.apache.org/jira/browse/CTAKES-172 > > > Another Major improvement is an lvg update. Do we have time to play with > this or should we bump it? https://issues.apache.org/jira/browse/CTAKES-388 > Related to https://issues.apache.org/jira/browse/CTAKES-122 > > > Pei or Jay,

Re: user Digest 16 Nov 2015 19:44:10 -0000 Issue 343

[+dev, -user] Hi Lewis, I've applied the patches. Would you mind looking into using and see if it works for your tests/use cases?: org.apache.ctakes.core.resource.FileLocator.getAsStream()? It has a built in fall back mechanism. On Mon, Nov 16, 2015 at 3:25 PM, Lewis John Mcgibbney

Re: cTAKES corpus

Hi Jose, There were some previous discussions[1] on how to get the annotated training data. Essentially, there currently isn't a centralized or easy way of getting w/o having to sign individual Data Use Agreements from source institutions. There is a clear need to simplify this and I believe

Email address update

Hi, Just wanted to give a heads up- My usual childrens/harvard email address will no longer be valid after this week. I will continue to use my chenpei@a.o one as I will be moving on to focus on our startup, Wired Informatics. --Pei

Re: cTakes 3.2.2 CPE error

Hi Eric, could you copy and paste the java command that was used? It some look something like: "java -cp ..." --Pei On Sat, Oct 31, 2015 at 1:58 PM, Eric Benzschawel wrote: > To whom it may concern, > I'm Eric Benzschawel, a masters student at Brandeis University. I'm >

Re: cTAKES scale out using UIMA DUCC

Yi-Wen, ctakes-clinical-pipeline/desc/**/ for the descriptors? Hope that helps.. On Wed, Oct 28, 2015 at 5:55 PM, Yi-Wen Liu wrote: > Hi, > > I am trying to run cTAKES on UIMA DUCC, and I am working on some > configuration files. > In UIMA DUCC job files, I have to specify the

Re: Can one pass UMLS username and password as API arguments?

Pete, System.setProperty()? Were you suggest we add an overloaded method?: ClinicalPipelineFactory.getFastPipeline(String user, String pw) {} It's not a bad suggestion- if you require it, feel free to create a Jira or even better a patch... --Pei On Mon, Oct 26, 2015 at 1:27 PM, Peter Szolovits

Re: Can one pass UMLS username and password as API arguments?

Yes, I wasn’t sure if your application had a security restriction to store paw’s into the env var for any code to read. Anyhow, anyone should be able to create an Jira account at: https://issues.apache.org/jira/browse/CTAKES Pei Chen Wired Informatics <http://www.wiredinformatics.com&g

Re: cTakes - help please

Chris, Could you confirm if the paths were modified? if so, is it accurate? In particular, per error message: des -> desc? Malformed URL c:/apache-ctakes-3.2.2/*des*/ctakes-chunker/desc If not, would you mind including the descriptor xml's? --Pei On Mon, Oct 19, 2015 at 5:38 PM, Tonner, Chris

Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

verified.] [1] http://www.apache.org/licenses/#clas Thanks, Pei Pei Chen Wired Informatics <http://www.wiredinformatics.com> 265 Franklin St Ste 1702 Boston, MA 02110 tel: (617) 433-7544 pei.c...@wiredinformatics.com On Sun, Oct 11, 2015 at 3:51 PM, Azad Dehghan <azad.dehg...@gmail.c

Re: Boston cTAKES Hackathon?

http://www.meetup.com/cTAKES/events/225926425/ has been set up... On Fri, Sep 18, 2015 at 11:46 AM, Pei Chen <chen...@apache.org> wrote: > Yes, we can plan for lightning talks and we can potential find some > Docker experts in the area to help. > I'm thinking over the next few w

Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

Hi Azad, This is awesome news. Thanks for adding in the code that was referenced by the paper. I'll create a Jira to track we need to port it over to UIMA/Ruta. In the meantime, the link is at: http://sourceforge.net/p/clinical-deid/code/ci/master/tree/ for those who may be interested in

Re: Boston cTAKES Hackathon?

>> off? >> I know Harvard is using ctakes for some stuff. >> >> >> > On Sep 16, 2015, at 4:23 PM, Pei Chen <chen...@apache.org> wrote: >> > >> > Hi, >> > I hope everyone had a great summer. I just wanted to resurrect the >> > Docke

Re: CTAKES-377 : Upgrade to Java 8

+1 upgrading to Java 8; been using it unofficially locally. On Wed, Sep 16, 2015 at 1:37 PM, Finan, Sean wrote: > Can anybody out there think of a reason why we shouldn't upgrade to Java 8? > Please comment on Jira. > >

Boston cTAKES Hackathon?

Hi, I hope everyone had a great summer. I just wanted to resurrect the Docker integration idea. Anyone interested in joining a small hackathon with the single goal of deploying cTAKES in a docker container. One of the evenings 6pm? --Pei

[DRAFT] [REPORT] Apache cTAKES Sep 2015

Feel free to edit/add. Report from the Apache cTAKES committee [Pei Chen] ## Description: Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is an open-source natural language processing system for information extraction from electronic medical record clinical

Re: Bug in resource import in LvgAnnotator?

Hi Jakob, Yes, there is currently a limitation in the LVG component to have their jar unpacked and added to the classpath. I think there is an outstanding Jira to enable it read it from a jar like the rest of the jars. (There are some limitations such as hsql/lucene not being able to read

Re: Error while running DrugMentionAnnotator.xml

Chandra, How are you wiring up the DrugMentionAnnotator? The default AggregatePlaintextFastUMLSProcessor.xml should already have the Drug NER included. http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml In general,

Re: Role of white-box logic/models in cTAKES

Peter, Good to hear from you again! Yes, I believe there are some regex and rules based annotators that are in used (and probably the future for as long as it out performs other methods for certain tasks.) I don't think there is specific position form the community on this approach. (ASF's

Re: cTAKES GUI for I2B2

Sekhar, That application was done as a prototype/POC many years ago and hasn't been actively maintained (hence in sandbox). It seems from your screenshot that you have it up and running though. Would you mind attaching the log files as well? --Pei On Wed, Aug 5, 2015 at 4:41 AM, Hari, Sekhar

Fwd: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

[+dev] Hi Azad, This is great news! Looking forward to it. --Pei On Thu, Jul 30, 2015 at 8:16 AM, Azad Dehghan azad.dehg...@gmail.com wrote: Hi Pei, Just to keep you in the loop: I am currently tailoring a version of the de-id tool for The Christie NHS Foundation Trust (UK)--this is due to

Re: xml org.apache.ctakes.core.analysis_engine.TokenizerAnnotator not found

Justin, Is this still an issue for you? I believe there was a known issue and someone submitted a patch: https://issues.apache.org/jira/browse/CTAKES-370?jql=component%20%3D%20ctakes-smoking-status%20AND%20project%20%3D%20CTAKES%20AND%20resolution%20%3D%20Unresolved%20ORDER%20BY%20priority%20DESC

Re: How to use cTakes as a UIMA component

Ralph, Could you describe a bit on you were using the UIMA framework? i.e. PEAR files, XML descriptors, and/or uimaFIT to programmatically wire the components together? I think the easiest would be to have your application pull the necessary ctakes components from maven central and use the

Re: Mvn package error

Zhiwen, I think this unit test needs to be updated/fixed. Even though it runs fine in mvn compile test. In the interim- package needs to -DskipTests=true. The longer story is that once modules are packaged (i.e. lvg, dictionary) mvn loads them from the jars instead of unpacked resources. So

Apache cTAKES hosted demos and examples

There seems to be a significant interest in having a hosted demo and examples, so I started this index page along with initial code examples: Index page: http://healthnlp.github.io/examples/ Live demo: http://52.24.118.198:8080/index.jsp --Pei

Re: PAD Term Spotter

Hi Christopher, The PAD Term Spotter hasn't been supported for over a year now [1]. It was mostly written with specialized rules and no one had been maintaining it. I am not sure if there are any generic diseases annotators; if you would be willing to contribute the changes, we can incorporate

Re: [DRAFT] [REPORT] Apache cTAKES Jun 2015

appreciate if I can get small help also. Thanks Regards, Soumya Shree -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Friday, June 05, 2015 2:32 AM To: dev@ctakes.apache.org Subject: [DRAFT] [REPORT] Apache cTAKES Jun 2015 [DRAFT- Feel free to add/edit

[DRAFT] [REPORT] Apache cTAKES Jun 2015

[DRAFT- Feel free to add/edit] --- Report from the Apache cTAKES project [Pei Chen] ## Description: Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is an open-source natural language processing system for information extraction from electronic medical

[ANNOUNCE] Apache cTAKES 3.2.2 released

The Apache cTAKES team is pleased to announce the availability of the 3.2.2 release. For the complete release notes, please visit http://s.apache.org/ctakes-3.2.2-release-notes Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is an open-source natural language processing

[RESULT] [VOTE] Release Apache cTAKES 3.2.2 (rc2)

More than 72 hours has passed. The vote for Apache cTAKES 3.2.2 (rc2) *passes* [1] with 5 +1 votes (4 binding) +1 (binding) Pei Chen Tim Miller Kim Ebert Jay Vyas Michal Iglewski There were no -1 or +0 votes cast. I will be publishing the release, then will announce the release as soon

Re: [VOTE] Release Apache cTAKES 3.2.2 (rc2)

On 05/13/2015 08:37 AM, Pei Chen wrote: This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.2. The major change since rc1 was to include the fix for CTAKES-359 - UMLS Authentication failing despite correct username and password. For more detailed

Re: CTAKES mirroring on github.

One of the visions behind the *-res projects was to separate out the resources from code. In theory, one can filter out all *-res projects from their git repo and pull in any version of the resources from maven central... I won't have enough bandwidth at the moment to try it out or work on the

Re: UMLS Authentication failing despite correct username and password

Michal, Thanks for pointing that out (It would have been nice if they sent out a notice about the change in the API call). Would be great if someone could open a Jira and verify this fix solves the issue... I think we should push out this critical patch asap- I can include it in 3.2.2 and create

[VOTE] Release Apache cTAKES 3.2.2 (rc1)

This is a call for a vote on releasing the following candidate (rc1) as Apache cTAKES 3.2.2. The major changes include: - Improved optional Temporal models (Time + Event Relationships models now available) - Other bug fixes/enhancements from Jira (see release notes Jira link below). I manually

Re: Command-line tool for cTAKES

If you already have the CPE running, you can pass the descriptor to the command line: *org.apache.ctakes.ytex.tools.RunCPE or * *org.apache.ctakes.core.cpe.CmdLineCpeRunner or* *org.apache.uima.examples.cpe.SimpleRunCPE

Re: Image to text conversion

Sekhar, There are a few open Jira's: I think it would be a great contribution if you get this to work: - CTAKES-189 https://issues.apache.org/jira/browse/CTAKES-189 GSoC: Implement OCR/Tika to standardize text input for cTAKES - - CTAKES-105

Re: Request for help:: NCBO Ontology Extraction Tool for i2b2

Sekhar, Is it happening to all of the ontologies you mentioned or just one? Those ontologies do not seem very big or deep. Did you notice in the logs if something in the ontology having some sort of circular reference or causing an infinite loop? I think lori from i2b2 may be better at answering

Re: Include the smoking status detection in AggregatePlaintextFastUMLSProcessor.xml

? Thanks, Tom On Sat, Apr 18, 2015 at 12:53 AM, Pei Chen chen...@apache.org wrote: Tom, I would put it at the end of the pipeline (at a min, it should be behind sectionizer, sentence, tokenizer, lvg). I would remove ExternalBaseAggregateTAE as this simulates

Apache cTAKES Hackathon: Containers- Docker + Kubernetes?

Would folks be interested in joining a hackathon nearby Boston? Exact Time and place TBA. Goal: Get cTAKES to work with Docker and Kubernetes and have a working example in sandbox. Deploying cTAKES is not so straightforward and difficult to manage, let alone in a distributed environment.

cTAKES @ ApacheCon 2015 next week

Just a reminder- Jay and I are planning to have a session (Tues) at Apache Con 2015 on using cTAKES in a Big Data context using Spark/Hadoop. If you happen to be there, feel free stop by the session. Or If you're in the neighborhood and want to meet up over coffee, feel free to drop us a note.

Re: Question about how to interpret Ctakes output

[+dev] Yu, Check out the type system: http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml Note: I believe what you really want is *org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation and not

Re: Running cTAKES via command line

or* *org.apache.uima.examples.cpe.SimpleRunCPM (requires uima examples jar)* On Fri, Apr 3, 2015 at 11:18 AM, Pedro Teixeira teixeir...@gmail.com wrote: Pei Chen chenpei@... writes: There were a couple of recent threads about this [1]. In particular search for: CmdLineCpeRunner.java

Re: Running cTAKES via command line

There were a couple of recent threads about this [1]. In particular search for: CmdLineCpeRunner.java and RunCPE.java [1] http://mail-archives.apache.org/mod_mbox/ctakes-dev/201502.mbox/%3ccahnnhnzfde5mf6ddv6y2r4jyygua1a43srdnzrskjqwddti...@mail.gmail.com%3e We should probably add it to the

Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility

Hoang, 3.0 was released a long time ago (02/2013). (according to the tag/history, it did't have the null fix until 6/2013 3.1?)

Re: Dependency Parser model data

Ephi, The ClearNLP models in the current cTAKES releases (since 3.1.0 [1]) should contain much more. They should contain at least MiPACQ and SHARP training data. Could you point us to the documentation so we can update it? I believe the break down was: - Clinical questions: 1,600

Re: cTakes setup

Mitch, -The dev@ and user@ mailing lists are archived and searchable; it is probably the best for searching archived discussions. -Could you clarify what you are trying to achieve or the issue that you are experiencing with the -Xmx? There are models and dictionaries that get loaded into memory-

Re: Hello cTAKES Mailing List

Raymond, Probably a combination of UMLS *Consumer Health Vocabulary + Custom Dictionary (as Sean described) *may work for the use case*:* OAC CHV connects informal, common words and phrases about health to technical terms used by health care professionals. It includes jargon, slang, ambiguous, and

Re: cTakes question

[+dev] Yu, Yes, you can run it from the command line in many ways. 1) You can write a Java class that does it for you. Similar to http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java 2) Run the CPE

Re: question about CTAKES

[+dev] I think that's a current limitation in the new Polarity Classifier. It's ML based, so most likely 'Deny XYZ' or 'Negative for XYZ' is probably not in the training data. There are a couple of things I would suggest: 1) Post the questions/examples to dev@ctakes.apache.org - perhaps others

Re: UMLS Integration

://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html The error seems to be related to incomplete or corrupted zip files? Pei Chen Wired Informatics http://www.wiredinformatics.com 265 Franklin St Ste 1702 Boston, MA 02110 tel: (617) 433-7544 pei.c...@wiredinformatics.com

Re: revamping the Apache cTAKES website

development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana guergana.sav...@childrens.harvard.edu wrote: There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original

Re: Question about running cTakes, urgent!

for your patience. Here is the result I run the AggregatePlaintextFastUMLSProcessor.xml by using the real medical note. But I cannot find the negation result. Yu Liang CHIBI On Dec 12, 2014, at 3:59 PM, Pei Chen chen...@apache.org wrote: Yes, Negation is handled by the new

[VOTE] Release Apache cTAKES 3.2.1 (rc2)

This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.1. The major changes include: - New optional Temporal component (Time + Event Relationships models now available) - Other bug fixes/enhancements from Jira I manually downloaded the bin as well as

Re: UMLS validation url

-ws.nlm.nih.gov/restful/isValidctakes.umlsuserUMLSUser will do the trick. Pei Chen Wired Informatics http://www.wiredinformatics.com 265 Franklin St Ste 1702 Boston, MA 02110 tel: (617) 433-7544 pei.c...@wiredinformatics.com On Mon, Nov 24, 2014 at 3:12 PM, Pei Chen chen...@apache.org wrote

Re: Chest pain absent. - polarity

Petr, Which version of cTAKES are you using? 3.2.0 or latest 3.2.1-rc1/trunk? Both default to use a Machine Learning based polarity algorithm. If it is missed, more training examples is probably the way to go. The latest one uses clearTK and trained with different features and training data so I

Re: CTakes on github.

Sounds good. Jay, Barring any objections from the group, would you mind opening a Jira with INFRA to set that up (read only git mirror) for cTAKES? --Pei On Thu, Oct 30, 2014 at 12:40 PM, jay vyas jayunit100.apa...@gmail.com wrote: Hi Pei : I Agree with (A) - the hybrid approach, so anyone can

Next cTAKES release 3.2.1 - Creating a Release Candidate

There are a lot of good fixes and new enhancements in currently trunk. - Includes new Temporal Relations models (ex: Event relationships are available now- previously- only Event/Time entities discovery models were included.) -Plus a ton of bug fixes tracked in Jira I can volunteer to be RM again

upcoming cTAKES meetup - Boston...

Next Friday (halloween) - feel free to drop by if you're in the area! Lunch/drinks provided..Please RSVP via http://www.meetup.com/cTAKES/events/208836282/ --Pei

Apache cTAKES 3.2.1 release preperation

There is a 3.2.1 release slated for end of Oct. The major changes are: uimafit 2.1 upgrade, cleakTK upgrade, New temporal relations models. Below is a summary of what was scheduled to go in (some may be still unresolved). Feel free to edit/update Jira if you believe something should be

Re: Boston cTAKES Meetup

, etc. I wish I would be there, but it is very hard tor is not possible for me to be there. Prakash Poudyal Portugal On Tue, Sep 23, 2014 at 3:31 AM, Tim O'Connell tim.oconn...@gmail.com wrote: thanks Pei. On Mon, Sep 22, 2014 at 7:17 PM, Pei Chen chen...@apache.org wrote

Boston cTAKES Meetup

Please feel free to join the Boston Meet up group: Upcoming Free Event: http://www.meetup.com/cTAKES/events/208836282/ (If possible, please feel free to RSVP so we can get an approx headcount) Feel free to chime in if you have anything specific that may be of interest to you: ex: cTAKES intro,

Re: Boston cTAKES Meetup

in Vancouver)? Best, Tim On Mon, Sep 22, 2014 at 2:40 PM, John Green hephaestus.stu...@gmail.com wrote: Will this be recorded? — Sent from Mailbox https://www.dropbox.com/mailbox On Mon, Sep 22, 2014 at 4:30 PM, Pei Chen chen...@apache.org wrote: Please feel free to join the Boston Meet up

Re: Ctakes to process 5000K recoreds

Nick, When you mean no medication is being annotated, I presume you mean the medication attributes (i.e. dosage, frequency, etc.) are not being annotated? I think the DrugNER needs a list of section names in the config; I think it includes SIMPLE_SEGMENT. I am very surprised that

Re: Permutations

Hi Kim, Thanks for pointing that out. https://issues.apache.org/jira/browse/CTAKES-310 has been opened for this. If you commit the changes, we can see if we can include in the 3.2.1 patch release. I was looking at the changelist for this file, and it may look like some of these optimizations may

Re: MedicationMention and new Mention

Harpreet, MedicationMention attributes such as .medicationfrequency .medicationDosage Can be filled via the DrugMentionAnnotator [1]. If I recall correctly, I believe you can just add that annotator after the DictionaryLookup in your pipeline. [1]

Re: managing ctakes resources on classpath

I'm not too privy to the ytex config details, but yes you're right, it's caused by the xdl.xsd being null. However it looks like it exists in ytex-res.jar but the call being made uses Class.getResource which won't be able to read in from the jar as an InputStream. 1) We can make ytex read in

cTAKES min requirements

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 trivial, but I still know a few unfortunate souls still on 32 bit systems… any

org.apache.ctakes.ytex.umls.dao.UMLSDaoTest

Hi VJ, While on the subject of unit tests- I didn't get a chance to dig deeper and was hoping you would know the cause of this unit test failure: mvn clean install 2014-08-25 13:33:50,830 WARN net.sf.ehcache.CacheManager - Creating a new instance of CacheManager using the diskStorePath

Re: Microsoft - MSDN - Is the support continuing for ASF committers?

Just an fyi - link for MSDN subscription license(s) for committers http://mail-archives.apache.org/mod_mbox/www-community/201305.mbox/%3c518b85e7.7000...@lehmi.de%3E https://svn.apache.org/repos/private/committers/donated-licenses/msdn-subscription.html

Re: [VOTE] Release Apache cTAKES 3.2.0

From: Pei Chen [chen...@apache.org] Sent: Monday, July 07, 2014 12:06 PM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 Thanks for testing this Tim. I could recreate this on my mac now (worked previously on windows on luck

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