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

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

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"

( 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,

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 <

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

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

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

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

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 <mcmurry.a...@gmail.com> > Reply-To: "u...@ctakes.apache.org" <u...@ctakes.apache.org> > Date: Fri

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

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

Downloads link broken

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

Fwd: Re: Medical de-identification

5:02 AM Subject: Re: Medical de-identification To: andy mcmurry mcmurry.a...@gmail.com 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

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 annotations

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

, 2014 6:19 AM, Dligach, Dmitriy 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 mcmurry.a...@gmail.com wrote

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

would love to see 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: Tuesday, September 09

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 m...@schor.com 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:

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

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 john.travis.gr...@gmail.com wrote: Nice!— Sent from

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 http://metamap.nlm.nih.gov/Docs/MM09_Usage.shtml --allow_overmatches or --allow_concept_gaps or .other? Since yTex already provides a pluggable *DictionaryLookup, *that seems like

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.

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

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 john.travis.gr...@gmail.comwrote: Had to

Re: ctakes-vm.apache.org

. John -- Sent from Mailbox for iPhone On Thu, Mar 20, 2014 at 5:31 AM, andy mcmurry mcmurry.a...@gmail.com wrote: 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

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 /

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

:43 AM, Steven Bethard steven.beth...@gmail.comwrote: On Wed, Jan 29, 2014 at 5:24 AM, andy mcmurry mcmurry.a...@gmail.com 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 having origins in LISP

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

Happy thanksgiving !

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

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

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

2, 2013 at 7:26 PM, Andy McMurry mcmurry.a...@gmail.com wrote: 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

Re: Next cTAKES release (3.1)?

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 8:32 PM, Andy McMurry mcmurry.a...@gmail.com wrote: +1 suggestion

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

Re: Next cTAKES release (3.1)?

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 McMurry mcmurry.a...@gmail.comwrote: ctakes is at a point where we have a LOT of features but it is still hard to get started. Judging from

* Public downloads link offline *

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

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