Re: Parse Medical Research Papers

UMLS SemRep and Semantic Medline are probably better resources for parsing papers with respect to Subject, Predicate, Object. https://semrep.nlm.nih.gov/ https://skr3.nlm.nih.gov/SemMed On Mon, Jun 18, 2018 at 2:40 AM, Don Flinn wrote: > I want to parse medical research papers and am looki

Re: substance abuse and smoking

Todd: I'm working with a non-profit supporting patients with substance abuse problems. I think Smoking module is very different, and not really generalizable to substance abuse problems in a straightforward way. *In short: substance abuse is more a biomedical curation task than an informatics task

Re: Trying to Understand cTAKES [EXTERNAL]

Don You may want to see "semantic medline" and semrep from NLM-- in general ctakes is better for physician notes whereas metamap may be better on literature. Extracting predicate relationships-- you can even download a huge database of preprocessed papers On Feb 27, 2018 10:43 AM, "Don Flinn" w

( REPRODUCED , intermittent) Re: Mac/download link broken

REPRODUCED issue (intermittent) from http://ctakes.apache.org click "download" http://ctakes.apache.org/downloads.html --> HTTP 404 http://ctakes.apache.org/[preferred]/ctakes/ctakes-4.0.0/apache-ctakes-4.0.0-bin.tar.gz Appears to be fixed now, problem

Re: Using cTakes for Identified Patient Information

+1 Sean and Peter FWIW: ctakes has been used as a system for HIPAA de-identification, meaning, removing PHI from clinical text. So in at least one sense, cTakes can improve an institutions readiness to use clinical data under HIPAA. On Wed, Nov 2, 2016 at 5:09 PM, Finan, Sean < sean.fi...@childr

RE: Hardware Requirement

Hi Vicky: if you find yourself stick, experimenting with java opts settings can get you down pretty low, and you can slim down to the barest of needs (pipelines and dictionaries) if needed. On Jun 20, 2016 11:46, "Finan, Sean" wrote: > Hi Vicky, > You can view the current requirements here: > > h

Google SyntaxNet open source : state-of-the-art results on standard corpus

http://googleresearch.blogspot.com/2016/05/announcing-syntaxnet-worlds-most.html?m=1 *So How Accurate is Parsey McParseface (**SyntaxNet)**?* *"... *recovers individual dependencies between words with over *94% accuracy*, beating our own previous state-of-the-art results, which were already better

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

*** For cross-validation, you can evaluate de-identified notes data from i2b2 challenge** * https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-scrubber-deid/data/models/ *Methods for model generation of FeatureSet described here: * *Improved de-identification of physician notes through integr

Re: Does cTakes included RxNormId in the output?

Concept unque identifier (cui) is umls wide code, the value most often retrieved for ctakes users. You want the vocabulary (sab) specific code to get rxnormid On Feb 12, 2016 3:47 AM, "Phan Hồng Phúc" wrote: > Hi, > > I try to find RxNormId in the output but not found yet. I am not sure if it >

Re: ctakes blog

5655 | | Steroid | 3919 | | Sign or Symptom | 2909 | | ... | ... | On Tue, Dec 8, 2015 at 2:19 PM, andy mcmurry wrote: > +1 I would be happy to write about the experience of creating t

Re: ctakes blog

+1 I would be happy to write about the experience of creating the medgen (medical genetics) database, especially useful for cancer and cardio On Dec 8, 2015 2:04 PM, "David Kincaid" wrote: > That is a great idea! I'd be happy to help provide some content as someone > who has been trying to use cT

Re: Boston cTAKES Hackathon?

Pei: Are you planning to record the docker tutorial? Would be a big bonus for the new-user guides On Thu, Oct 8, 2015 at 12:03 PM, Pei Chen wrote: > http://www.meetup.com/cTAKES/events/225926425/ > has been set up... > > On Fri, Sep 18, 2015 at 11:46 AM, Pei Chen wrote: > > Yes, we can plan for

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

caution: Im not sure you can convert GPL3 to ASL2 anyone know for sure? On Thu, Oct 8, 2015 at 12:03 PM, Chen, Pei wrote: > This is great news! > > What is the current status and procedure? Is there an explicit > contribution to cTAKES? Is there an ICLA? What about the license of the > sourcefor

Re: [cancer-informatics] Fwd: BD2K Coordination Center Solicits Hackathon Proposals

9, Mailstop: 168-527 > Email: chris.a.mattm...@nasa.gov > WWW: http://sunset.usc.edu/~mattmann/ > ++ > Adjunct Associate Professor, Computer Science Department > University of Southern California, Los Angeles, CA 90089 USA > +++++

Re: [cancer-informatics] Fwd: BD2K Coordination Center Solicits Hackathon Proposals

mputer Science Department > University of Southern California, Los Angeles, CA 90089 USA > ++++++ > > > > > > -Original Message- > From: andy mcmurry > Reply-To: "u...@ctakes.apache.org" > Date: Friday, September 18, 2015 at 4:24 PM > To: "dev@ctakes.ap

Re: [cancer-informatics] Fwd: BD2K Coordination Center Solicits Hackathon Proposals

+1 , I support the idea of cTAKES as an intermediate step for other annotation sources, data "mash up". Phenotypes -- Genes, etc. On Thu, Sep 17, 2015 at 2:52 PM, Wilson, Brian < bwil...@tuftsmedicalcenter.org> wrote: > > > > Food for thought :) > > > > > > > The Big Data to Knowledge Coordinatio

Re: CTAKES-377 : Upgrade to Java 8

+1 long live Java 8 ! On Fri, Sep 18, 2015 at 7:43 AM, Jay Vyas wrote: > +1 for sure > > > On Sep 18, 2015, at 10:06 AM, Ted Strall > wrote: > > > > Going to Java 8 can provide a lot of benefit to an application like > cTAKES. > > The new features added to Java 8 are a game changer in terms of

Re: Apache cTAKES hosted demos and examples

Pei: this is wonderful! Thanks for doing this! On Fri, Jun 19, 2015 at 8:32 AM, Pei Chen wrote: > 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/

Downloads link broken

Homepage points to http://ctakes.apache.org/downloads.cgi should be http://ctakes.apache.org/downloads

Fwd: Re: Medical de-identification

ubject: Re: Medical de-identification To: "andy mcmurry" Cc: I would certainly be interested into "production grade code". The project also sounds interesting. How do I start working on it? I know Java well. What else would I need to know before starting on this project? On Fri,

RE: revamping the Apache cTAKES website

+1 !! Very nice On Dec 15, 2014 2:32 PM, "Chen, Pei" wrote: > Check out a mockup of a new website proposal: > http://svn.apache.org/repos/asf/ctakes/site/new/index.html > Based off bootstrap (Idea borrowed from the Spark folks..). > > Couple of key pieces of info: > - 10% of visitors are on mobil

Re: gold standard annotations for Apache cTAKES sample notes

This is great, thanks John green ! On Dec 5, 2014 8:32 AM, "Savova, Guergana" < guergana.sav...@childrens.harvard.edu> wrote: > Thanks to John Green, we now have sample clinical notes in cTAKES. Many > thanks, John, for your effort! > > We will take these notes and will start generating gold annot

Re: Announcement: UMLS MedGen-MySQL dataset now available as open access download

I understanding that right? > > > > > > JG > > — > > Sent from Mailbox > > > > On Thu, Nov 13, 2014 at 1:40 PM, andy mcmurry > > > > wrote: > > > > > I'll crunch the numbers -- in the meantime I can tell you that > &g

Re: Announcement: UMLS MedGen-MySQL dataset now available as open access download

triy" < dmitriy.dlig...@childrens.harvard.edu> wrote: > Andy, thank you for this resource! > > Do you have an estimate of what percentage of UMLS concepts were left out? > > Dima > > > > > On Nov 11, 2014, at 16:02, andy mcmurry wrote: > > > Hello! &g

Announcement: UMLS MedGen-MySQL dataset now available as open access download

ee the install be as simple as apt-get install to end up > with some working dictionary that have more than a handful of entries to > get them started. > > Regards, > James Masanz > > -Original Message- > From: andy mcmurry [mailto:mcmurry.a...@gmail.com] > Sent: Tu

Re: to map UMLS CUI with normalized form

For bioinformatics folks *Preferred disease names are already mapped by the NCBI* ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/disease_names On Mon, Sep 1, 2014 at 2:32 PM, Peter Szolovits wrote: > A single CUI may have many different preferred names in different > vocabularies. If you have a m

Recommendation for ctakes default (UMLS) dictionaries

Greetings ctakes-dev: *UMLS license restrictions have been getting more lax over the years -- *much of the UMLS can be downloaded directly from the NCBI official FTP site. In fact, the NIH (and implicitly the NLM) *have already made the standard terms public for some medical specialities*. For

Fwd: [jira] [Created] (UIMA-3969) Add JSON Serialization for CASs and UIMA Descriptors

Interesting thread in UIMA core about JSON Serialization CAS and Descriptors. Begin forwarded message: > From: Marshall Schor > Subject: Re: [jira] [Created] (UIMA-3969) Add JSON Serialization for CASs and > UIMA Descriptors > Date: August 25, 2014 at 8:33:54 PM PDT > To: d...@uima.apache.org

Re: Youtube Channel "Apache cTakes"

*How about Guergana and Japing at the Harvard Club? * We even had it professionally videotaped. It is currently on Vimeo but since I wrangled the funds to have it filmed, I'm OK with it being distributed in whatever ways this community sees fit. http://vimeo.com/24829353 On Tue, Aug 12, 2014

Re: [VOTE] Release Apache cTAKES 3.2.0

The LVG is particularly important, users are most likely to compare cTAKES and MetaMap (or other) performance on the NER task and the LVG clearly helps. Requiring a new user to understand LVG is the hard part, the download isn't a tough requirement but I wonder how many new users would even know to

Re: LVG Thread Safety

I wonder how much cTAKES performance changes with even minor changes to LVG. In principle, thread safety shouldn't change the output, but even minor updates (LVG.2014) makes me wonder. Thoughts? On Jun 23, 2014, at 11:58 AM, "John Green" wrote: > Nice!— > Sent from Mailbox for iPhone > >

Re: Preparing for an Apache cTAKES 3.2 Release?

"2" doesn't mean much. The newer NER should have in its name the Behavior... Perhaps something like MetaMap Usage "--allow_overmatches" or "--allow_concept_gaps" or .other? Since yTex already provides a pluggable *DictionaryLookup, *that see

Re: new dictionary lookup {was RE: lvg entries]

Highly Relevant *DNorm: disease name normalization* http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810844/ "Disease names are often created by combining roots and affixes from Greek or Latin (e.g. ‘hemochromatosis’)" On Mon, Apr 21, 2014 at 8:57 AM, Masanz, James J. wrote: > Sean, > > W

Re: lvg entries

reate the static factory > methods like we recently discussed. Should I go ahead and change this to > make default behavior be false? > > Tim > > > On 04/18/2014 12:47 AM, andy mcmurry wrote: > > There is a lot of config handling, maybe PostLemmas is being set to > &

Re: lvg entries

There is a lot of config handling, maybe PostLemmas is being set to true or configInit() is not setting up the NLM wrapper incorrectly. ctakes-lvg *README* Note: as distributed, PostLemmas is set to false. This is done to reduce the size of the CAS. Set PostLemmas to true to have org.apache.ctak

Re: Apache cTAKES Example Application?

Lowering the barrier to entry = worth the effort Notice the NCBO users mailing list has solid routine comments and discussion about the VM "appliance" they distribute. On Wed, Apr 16, 2014 at 9:37 AM, Pei Chen wrote: > We spent some time in the past to make it easier for users to launch the >

Re: Ctakes-data-vis

It looks great! The transitions are smooth and the hierarchical browsing is straightforward. The only edit I recommend I have is about spacing -- The information often exceeds the space of a single page. On Sat, Apr 5, 2014 at 12:13 PM, John Green wrote: > Had to refresh my svn skills as its bee

Re: ctakes-vm.apache.org

e if folks decided to integrate into > >> cTAKES... and possibly save any potential IP/License questions... > >> > --Pei > >> > ____ > >> > From: John Green [john.travis.gr...@gmail.com] > >> > Sent: Wednesday,

Re: ctakes-vm.apache.org

platform to spit > out the json for the d3js graphic im using. > > > > > John > > -- > Sent from Mailbox for iPhone > > On Thu, Mar 20, 2014 at 5:31 AM, andy mcmurry > wrote: > > > Yes! I have been working full time on the "apt-get install" tas

Re: ctakes-vm.apache.org

Yes! I have been working full time on the "apt-get install" task specific to medical genetics: http://www.ncbi.nlm.nih.gov/medgen Right now, millions of $$$ are invested in getting phenotype concepts -- indications, diseases, problem lists -- linked to patient test results including DNA / RNA / et

Update: UMLS, cTAKES, and UIMA for applications in genomics

Hi all: I'm writing to update about my efforts to make a cTAKES "out of the box" VM with UMLS support. My specific use cases are for annotating DNA test results, so both publication text and patient notes are important towards this goal. cTAKES VM. = Wrote bash scripts to download

Re: Clojure, having its origins in LISP, is a better fit for serious NLP work

MC On Wed, Jan 29, 2014 at 9:43 AM, Steven Bethard wrote: > On Wed, Jan 29, 2014 at 5:24 AM, andy mcmurry > wrote: > > Clojure, having its origins in LISP, is a better fit for serious NLP > work than Groovy > > Sorry, I have to call this one out. I don't think havin

Re: Represent your project at ApacheCon

I'm hoping to attend. If I were to present, it would be using NLP to find evidence of DNA mutations causing disease. Interesting topic (for me at least) but I'm not sure if ApacheCON would be into it. PS: the radio silence is because I've been working on both the VM and a wrapper for REST that run

Happy thanksgiving !

Sharing is caring! Happy thanksgiving to the ctakes crew. Thanks for everything, you are appreciated

Re: Following up per James Masanz suggestion: iDASH

I will ask them as well. This is a plan for me for sure. On Tue, Nov 12, 2013 at 8:31 AM, Masanz, James J. wrote: > > Are there any plans to create as an Amazon EC2 instance? Just curious. > > > -Original Message- > From: dev-return-2201-Masanz.James=mayo@ctakes.apache.org [mailto:

Re: cTAKES user interface

Ricard: Groovy idea. Virtual Machine could benefit from that as well. *## IMHO: These are parallel tasks that I think are higher priority than new features. *It isn't as glamorous as playing Jeopardy, but deploy issues are keeping users out -- if I were to guess A LOT of the potential user base l

NCI references out of date

HI Troy et al: I noticed that the NCI is still referring to cTakes 2.5. Should we A) update the other sites with each new cTakes version B) redirect to apache ctakes https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5 I dont mean to harp on this issue, but it is the front door that I keep findi

RE: how do you feel about putting public presentations on ctakes.apache.org ?

we can add following links: > > > >https://code.google.com/p/uimafit/wiki/GettingStarted > >http://knowtator.sourceforge.net/quickstart.shtml > > > >And some links related to "SVM" and "MaxEnt" related information > >etc.,(Which were referred by original imp

Re: Next cTAKES release (3.1)?

d > be: > >>>> i) Make the typesystem forefront in documentation -- generate > javadocs and > >>>> have as a link on the ctakes frontpage/sidebar > >>>> ii) Similar to the way that we are aiming to have tests in every > module, also &g

Re: how do you feel about putting public presentations on ctakes.apache.org ?

t;SVM" and "MaxEnt" related information >> etc.,(Which were referred by original implementer). >> >> This way people who want to extend/add new features and referring existing >> implementation will be able to go through these to get understanding on >> what is happening

how do you feel about putting public presentations on ctakes.apache.org ?

Argument FOR: Videos can also be very educational for new users! For example, this cTAKES description by Guergana : https://vimeo.com/24829353 Publishing our slides or video -- for example recent the NLP presentations from the i2b2 user group -- gives folks a very real sense of the kinds of pr

Re: Next cTAKES release (3.1)?

worth asking whether you >>> agree with my "diagnosis" and "treatment" or whether you think there are >>> different problems/solutions that should be higher priority. >>> >>> Tim >>> >>> On 06/27/2013 10:59 PM, Giriv

Re: Next cTAKES release (3.1)?

PM, Girivaraprasad Nambari wrote: >>> Hi Vijay and Andy, >>> >>> Thanks for sharing those examples. >>> >>> "Trouble is, privacy requires that these examples be made up by hand" >>> >>> Agree with this statement and this i

Re: Next cTAKES release (3.1)?

le of >> entries (5-10 small entries), not more than that (with explicit statement >> like "ONLY EXAMPLE", NOT GOOD FOR REAL USAGE). I understand handcrafting >> these may not be easy because we are not medical domain experts, but I feel >> worth time, because it b

Re: Next cTAKES release (3.1)?

in more user community. > > Thank you, > Giri > > > > > > On Thu, Jun 27, 2013 at 10:25 PM, Andy McMurry wrote: > >> GREAT ! >> >> The i2b2 data though isn't publicly distributable, you still need to >> request access to it since it

Re: Next cTAKES release (3.1)?

r the code should be > reproducible and made publicly available, but that's a different issue). > > When we get around to upgrading YTEX to cTAKES 3.1, we would like to > upgrade these samples as well. > > Best, > > VJ > > > > On Thu, Jun 27, 2013 at

Re: Next cTAKES release (3.1)?

ey > adopt a system and Machine Learning/NLP is ocean. Some documentation in > this area will same lot of time for us. > > I wish there will be some activity in this area from ctakes core team. > > Thank you, > Giri > > > > On Thu, Jun 27, 2013 at 5:11 PM, Andy Mc

Re: Next cTAKES release (3.1)?

ctakes is at a point where we have a LOT of features but it is still hard to get started. Judging from the mailing lists a lot of how cTakes works is not obvious and requires hand holding. This is very typical in early FOSS projects. Lowering the time to get invested in ctakes gets more user

Re: [SECURITY] Frame injection vulnerability in published Javadoc

FYI: Java 6 is END OF LIFE. I know this also applies to Java 7, just an FYI. http://developers.slashdot.org/story/13/06/20/1819245/java-6-eold-by-oracle On Jun 20, 2013, at 2:40 PM, Pei Chen wrote: > FYI > We should probably update our javadocs for the next release... > > -- Forwar

Re: docs on running Clinical Document Pipeline from Java?

Note: The WEKA gui reports the command line arguments for any GUI task. It could be a very helpful timesaver if cTAKES had a similar feature. Otherwise, I fear we will be writing Main methods and docs for each and every cTAKES task. What do you all think? --- Real world example of how t

* Public downloads link offline *

Problem running mirror.cgi; if it persists, contact . In the meantime, try Traceback (most recent call last): File "/www/www.apache.org/dyn/mirrors/mirrors.cgi", line 143, in mirrorwrap return mirrorsapp(environ, start_response) File "/www/www.a

Re: supported java releases in current ctakes development and future releases (3.1 and later)

Java 1.5 is end of life UIMA will be forced to upgrade soon enough. Until then, the most routine problem I can think of is Class will have all GenericTypes stripped once we touch UIMA type system code. On May 23, 2013, at 12:34 PM, Andy McMurry wrote: > will this fit with the UIMA j

Re: supported java releases in current ctakes development and future releases (3.1 and later)

will this fit with the UIMA java compatibility? If so, +1 ! On May 23, 2013, at 11:06 AM, "Coarr, Matt" wrote: > I know there was a small discussion about documentation back in February > about including supported platforms in the developer guide and faq. And I > know that the ctakes 3.0 d

Re: Sharing trained models while protecting confidentiality

Britt and I (ctakes committers) work on exactly this problem. We have used cTakes to train models for HIPAA de-identification. In a nutshell: the answer depends what the IRB considers "de-identified". Hashing is not allowed by any IRB that I am aware of. On May 18, 2013, at 12:43 PM, Alexande

Re: cTAKES - Context Annotation

RE: Context Dependent Annotation I had needs for fast local write (Consumer) that could directly be imported into a SQL database for further analysis independent of cTakes. Consuming annotations are MUCH faster than what I was doing before Supports fast CSV->SQL inserts for the following typ

Re: roadmap for Apache cTakes "big data" processing

PM, "Chen, Pei" wrote: > Has anyone tried Mahout recently? > Last time I tried, it was still closely tied to the Hadoop file system. > > Sent from my iPhone > > On Apr 28, 2013, at 7:44 PM, "Andy McMurry" wrote: > >> I encourage committers to check

Re: roadmap for Apache cTakes "big data" processing

On Apr 27, 2013, at 9:05 PM, "Chen, Pei" > wrote: > >> +1 for UIMA-AS >> >> >> On Apr 27, 2013, at 9:25 PM, "Andy McMurry" wrote: >> >>> I'm writing to gauge community interest and intent for parallel processing >>> wit

roadmap for Apache cTakes "big data" processing

I'm writing to gauge community interest and intent for parallel processing with cTakes. Apache UIMA is planning "Async Scaleout" as a replacement for CPM. http://uima.apache.org/doc-uimaas-what.html Apache Mahout is likely to become the defacto apache package for machine learning. http://mah

Re: ctakes twitter account

> https://twitter.com/apachectakes ApacheCtakes is better -- conveys some meaning to someone who has no exposure to cTakes. assuming that the twitters is for public messaging, that is important. my 2 cents, --A On Apr 10, 2013, at 12:05 PM, Dmitriy Dligach wrote: > FYI: > > I tried to

Re: Apache cTAKES Links...

Recommend using the official SVN "switch" command http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html On Apr 5, 2013, at 12:46 PM, "Halgrim, Scott" wrote: > I'm going to try to figure this out on my own as well, but thought it might > save me some time if I asked here: > > What's t

Re: cTakes with java web application

Since we are on the topic of "fronting" the application to a high performance backend cluster, I invite you all to check out our Apache friends at MAHOUT https://cwiki.apache.org/confluence/display/MAHOUT/Algorithms On Apr 2, 2013, at 9:56 AM, Kannan Thiagarajan wrote: > Kim, > > Thanks. I