, given the
current talk of examples, if any domain specific examples needed generated I am
domain knowledgable enough that I could pound out a few free text notes made to
order.
Let me know, you all may already have docs on hand willing todo this, but if
not...
John Green
Sent from my iPhone
On
e:
> Agreed that you could definitely help out, and that would be a great way
> to do so. We don't really have "examples" right now, more like just short
> test sentences for showing simple results and verifying that nothing has
> been broken by changes. I think reg
test notes that have been collected over
>> the years:
>> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/
>>>
>>>
>>> From: Tim Miller [timothy.mil...@childrens.harvar
Just got some free time. I have a number of example free-text per previous
discussions to upload. They're quality but not annotated. Do I need someone
to commit for me?
Thanks,
J Green
://issues.apache.org/jira/browse/ctakes.]
> Then we can make the commits for you.
> This is awesome... do anyone have the gold standard annotation
> guideline(s) handy? Would be great to have those test notes annotated as
> well as examples.
>
> --Pei
>
>
>
> On Sat, Au
So far I have about 15 notes done. Im submitting them slow as, after I said
they were done I decided one last review of each for gross errors and
completeness would be in order. Im slowly working through the proof read of
each now. Just FYI if anyone was wondering.
I don't know what the coders can
, John.
> --Guergana
>
> -Original Message-
> From: John Green [mailto:john.travis.gr...@gmail.com]
> Sent: Wednesday, August 21, 2013 12:56 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctakes-examples project?
>
> So far I have about 15 notes done. Im submittin
Message-
> > From: John Green [mailto:john.travis.gr...@gmail.com]
> > Sent: Thursday, August 22, 2013 6:52 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: ctakes-examples project?
> >
> > @Guergana: Glad to be getting involved in the project ma'am!
&
Just out of curiosity, how was the training data originally built? I mean, who
separated the lines? By hand? Regex?
Question two: has anyone made attempts at adding project gutenberg to the
training data for things like sentence detection? Wide variety of punctuation
in the y
org
> [mailto:dev-return-1889-Masanz.James=mayo@ctakes.apache.org] On Behalf Of
> John Green
> Sent: Monday, August 26, 2013 11:46 AM
> To: dev@ctakes.apache.org
> Subject: Re: apostrophe and sentence detector
> Just out of curiosity, how was the training data originally built
>> The Apache cTAKES Team is happy to announce the addition of John Green as
>> new committer.
>>
>> In his own words, 'I'm a third year medical student rounding the bend
>> toward my MD. I used to be a computer programmer, however, and continue
Pei, or anyone else - Where should I upload example cases? Continue with
the same Jira item? I apologize I dont have time to investigate on my own,
the hospital is keeping me very busy.
Do you know if those other cases were annotated? I'm just curious if this
has been any benefit.
Thanks,
JG
Hey all, a couple of things:
1) Ill polish off those example notes as I push through the final lap of my
clinical experiences of medical school. It should leave a very
representative set across disciplines.
2) I work for the DoD and have latched on to several IRB approved projects
within that com
Pei and Tim - Good questions.
The bottom line is that OPQRST is the algorithm that every clinician uses
to characterize the history of a sign, symptom or constellation of
symptoms. Each letter has multiple meanings, but generally they're grouped.
O for onset, was it quick or slow in onset, P for p
ready. I must admit, I am
still in my infancy with understanding cTakes, UIMA, etc.
JG
On Thu, Oct 31, 2013 at 12:00 PM, John Green wrote:
> Pei and Tim - Good questions.
>
> The bottom line is that OPQRST is the algorithm that every clinician uses
> to characterize the history of a
This is a very good point. I can attest as a new user, these hurdles
mentioned by Andy seem paramount to broader adoption. Just by-the-by I
loved the Linux analogy Andy. At least, to a greater or lesser degree, it
survived!
JG
On Tue, Oct 29, 2013 at 7:33 PM, andy mcmurry wrote:
> Ricard:
>
> G
c/articles/PMC2655994/
> It discusses the use of nlp to create something like a problem list.
>
> Sean
>
>
>
>
> From: John Green [john.travis.gr...@gmail.com]
> Sent: Thursday, October 31, 2013 12:02 PM
> To: dev@ctakes.apache.or
/articles/PMC2655994/
> It discusses the use of nlp to create something like a problem list.
> Sean
> ____
> From: John Green [john.travis.gr...@gmail.com]
> Sent: Thursday, October 31, 2013 12:02 PM
> To: dev@ctakes.apache.org
> Subject: Re
for iPhone
On Thu, Oct 31, 2013 at 7:22 PM, John Green
wrote:
> Sean - quick note: after looking at the above two resources, a couple of
> points. The first resource confirms what I expected, that the vocabulary
> exists in ctakes. The second confirms what I suspected: that novel a
em list, but I haven't looked at it.
> http://www.nlm.nih.gov/research/umls/Snomed/core_subset.html
>
> This might be a paper of interest to you:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655994/
> It discusses the use of nlp to create something like a problem list.
>
> Sea
is probably well known stuff
> Bad assumption ... insert emoticon here ...
>
> >working back from the known natural history of diseases would possibly
> be a route to a solution.
> Now that is a challenge!
>
> Cheers for the inspiration and enthusiasm,
> Sean
>
>
>
outside the domain.
> I hope that I am starting to get on the same page, and I am enjoying this
> chat - it is different from my normal engagements, which is always nice.
> Cheers,
> Sean
> From: John Green [mailto:john.travis.gr...@gmail.com]
> Sent: Monday, November 04, 2013 5
l present" time (including all
the UIMA documentation/Lucene documentation etc)?
As is the patent phrase in moments like these: forgive me if this has been
asked before.
John Green
scripts may be an easy way to get started with some programming
> experience and one can easily start poking at the code to see what the
> components are doing.
> Just an idea...
>
> > -Original Message-
> > From: John Green [mailto:john.travis.gr...@gmail.com]
> &g
I was in passionate agreement with this post by Andy, by the by.
JG
—
Sent from Mailbox for iPhone
On Wed, Dec 4, 2013 at 6:29 PM, Andrew McMurry
wrote:
> Most Open Source frameworks come with an "project-examples.zip" folder.
> I can't help but think that the Groovy parser code and ctake
I found the above that Pei mentioned helpful, but also the brief UIMA tutorial
on their page as well as the original 2010 ctakes JAMIA article helpful for a
big picture look.
JG
—
Sent from Mailbox for iPhone
On Tue, Dec 24, 2013 at 11:28 AM, Chen, Pei
wrote:
> I think the type system do
to point out where you think the documentation is
> most scattered and maybe we can address that.
>
> -- James
>
> -Original Message-----
> From: dev-return-2334-Masanz.James=mayo@ctakes.apache.org [mailto:
> dev-return-2334-Masanz.James=mayo@ctakes.apache.org] On Behalf Of
Anyone working on Jira item cTakes-247? If not, I was gonna tackle it. And
if no one is, is everyone OK with a python script that auto-runs the XSLT
transformations with some pretty css/javascript?
JG
I've done a cursory search and come up short: has anyone written anything
to convert the annotations from the pipeline to the Brat *.ann format?
Thanks,
JG
Completely non-contributory, but it is odd/humorous to see the headaches
that quickly written notes we do in the 5 minutes post-encounter lead to in
free-text analysis.
JG
On Thu, Feb 6, 2014 at 1:27 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Right, got it. I just wanted to l
e-system/src/main/resources/org/apache/ctakes/typesystem/types/
> The content (Descriptions) probably needs to be filled in more...
> --Pei
>
> > -Original Message-
> > From: John Green [mailto:john.travis.gr...@gmail.com]
> > Sent: Thursday, February 06, 201
7, 2014 at 1:43 PM, Chen, Pei wrote:
> I think some of the OpenNLP folks did some work with the Brat annotation
> tool,
> but I don't think anyone has worked on it with cTAKES-I would be curious
> on your analysis though...
>
>
> > -Original Message-
> > Fr
ect: RE: Brat
>
> I think some of the OpenNLP folks did some work with the Brat annotation
> tool,
> but I don't think anyone has worked on it with cTAKES-I would be curious
> on your analysis though...
>
>
> > -Original Message-
> > From: John Green [m
That's really great, thank you! I will try and get it up and running this
week.
JG
On Sat, Feb 8, 2014 at 7:29 AM, Richard Eckart de Castilho <
richard.eck...@gmail.com> wrote:
> On 08.02.2014, at 13:20, John Green wrote:
>
> > What I was
> > thinking was Brat
I know there has been some chatter about sectionizers. From what I
understand Paula is doing, and from what I understand YTEX does, they are
all regular expression based, correct?
Has anyone added to rule based matching a statistical/Markov type
sectionizer? E.g. one trained from a bunch of notes?
To answer my own question, and for anyone searching the mail archives in
the future, I haven't fully explored it yet, but it seems that Vanderbilt
already did this with SecTag.
JG
On Sun, Feb 9, 2014 at 9:29 PM, digital paula wrote:
> John,
>
> I've been out of the loop for a few weeks now w/th
I'm sure most of you know what he presents esp because he's from Mayo, but
great talk:
http://webcast.jhu.edu/Mediasite/Play/0fd833143fcc4bd5954bcab801bba6da1d
If that url doesnt work:
http://www.icm.jhu.edu/seminars/index.php?pageid=5
and look for Christopher Chute
Professor of Biomedical Infor
Finally got around to looking at these: work great on ubuntu 13.1
JG
—
Sent from Mailbox for iPhone
On Tue, Dec 24, 2013 at 3:48 PM, Masanz, James J.
wrote:
> I checked in 2 groovy scripts under
> ctakes-core\scripts\groovy\
> I checked into trunk. Will gladly move or remove if needed.
> Th
Andy: this is very interesting and exciting.
I hacked out a script that makes a visually appealing representation of the
aggregate pipeline in d3js that, at least for a clinician, is a nice overall
summary of the meta data generated from the pipeline. Its really no more than a
parser of the
, 2014 8:33 AM, "John Green" wrote:
>> Andy: this is very interesting and exciting.
>>
>>
>>
>>
>> I hacked out a script that makes a visually appealing representation of
>> the aggregate pipeline in d3js that, at least for a clinician, is a n
ou can also put it directly in sandbox
> https://svn.apache.org/repos/asf/ctakes/sandbox/
> It may make it easier in the future if folks decided to integrate into
> cTAKES... and possibly save any potential IP/License questions...
> --Pei
> __
Hmm. Been awhile since Ive committed to anything with svn. Seems I botched my
import and rather than it creating my subdir ctakes-data-vis added all my files
to ./sandbox project root.
Gimme a min and ill fix it or Pei if you beat me to it, sorry, should have gone
in ctakes-data-vis.
Apolog
Well, dang. I think I can fix my mistake but it seems one of my files needs
unlocked. Rather than compound things here, Pei, you mind extricating me from
this by moving those files to a subdir called ctakes-data-vis?
Sorry about that.
JG
—
Sent from Mailbox for iPhone
Please disregard Pei. The lock error I was getting threw me. All is corrected.
Jg
—
Sent from Mailbox for iPhone
Had to refresh my svn skills as its been years. As a result not much cleaning
up got done Andy/Pei. The code is solid though and I sent four different ways
to view the json up too; collapsable dendrogram is the most useful.
The script could easily be re written to iterate through a directory as
s.
> It requires passwordless ssh so you'll need to ssh-keygen and save them via
> http://id.apache.org.
> --Pei
>> -Original Message-
>> From: John Green [mailto:john.travis.gr...@gmail.com]
>> Sent: Thursday, April 03, 2014 6:05 PM
>> To: dev@ct
d. 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 been years. As a result not much
>> cleaning up got done Andy/Pei. The
+1!
Im mainly using ctakes as middleware, which is totally inline with this.
What is NCBO?
JG
—
Sent from Mailbox for iPhone
On Wed, Apr 16, 2014 at 6:53 PM, andy mcmurry
wrote:
> Lowering the barrier to entry = worth the effort
> Notice the NCBO users mailing list has solid routine c
t; We can certainly load up cTAKES and it's resources.
> If it's a web app, we can prompt the user to enter umls credentials if they
> choose the umls resources?
> --Pei
>> -----Original Message-
>> From: John Green [mailto:john.travis.gr...@gmail.com]
>> S
Where do we stand on the web demo? Ive been off on other projects and Im
looking to digging into ctakes again, picking up where I left off, for an
application for my med school. I think my work there could overlap with a demp
server.
In regards to thread safety: it sounds like from the chatter
e to install tomcat on the demo vm properly yet]. Feel
> free to give it a shot if you have time.
>> -Original Message-
>> From: John Green [mailto:john.travis.gr...@gmail.com]
>> Sent: Wednesday, June 18, 2014 1:22 PM
>> To: dev@ctakes.apache.org
>> Subj
Nice!—
Sent from Mailbox for iPhone
On Mon, Jun 23, 2014 at 2:57 PM, Chen, Pei
wrote:
> +dev@
> Chris,
> This awesome news. Yes we'll be happy to try out the fix.
> Thanks again,
> Pei
> https://issues.apache.org/jira/browse/CTAKES-151
> From: Lu, Chris (NIH/NLM/LHC) [C] [mailto:c...@mail.nih.g
I got the semantic similarity web app running in ytex. Im still learning umls
terminology, but I believe it says that out of the box its concept graphs are
limited to the free set from umls? Does this mean without permissions? Similar
to ctakes with umls rights? The concepts available seem limit
Pei - Im finally getting around to working with ytex. There are some things Id
like to clarify in the install for beginners like me. How do I edit the
confluence wiki?
JG
Sent from my iPhone
t;
> All YTEX packages moved from the ytex namespace into org.apache.ctakes.ytex
> - can you tell me which document you were looking at that mentioned
> ytex.kernel.dao.ConceptDaoImpl? I thought I had fixed this in the
> documentation.
>
> HTH,
>
> -vj
>
>
> On
for using them (this makes sense as the command line output makes no
mention of loading them) but I can find where what is loaded is defined.
I hope that wasnt too poorly explained,
Thanks,
John
On Sun, Jun 29, 2014 at 9:10 PM, John Green
wrote:
> Hi Vijay, thank you for your time.
>
Correction: "cant find where what is loaded is defined".
On Sun, Jun 29, 2014 at 9:30 PM, John Green
wrote:
> Successfully ran command to build the concept graph, however, it seems to
> be failing silently. The version issued with ytex is 10m. I expected, worst
> case, for
Thanks Pei!—
Sent from Mailbox for iPhone
On Sun, Jun 29, 2014 at 10:37 PM, Pei Chen wrote:
> jtgreen has been added to the confluence wiki.
> --Pei
> On Sun, Jun 29, 2014 at 2:03 PM, John Green wrote:
>> Pei - Im finally getting around to working with ytex. There are some
>&
If someone has a free minute, which, judging from my own life is probably
not the case - where in the groovy scrips in sandbox do you define the
consumer to use? There is one comment that says "dont put the .xml here"
then there is a path to the dictionary ae. Im working by ssh from the
hospital a
T.zip
> > > <
> > >
> >
> http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip
> > > >
> > > 'over'
> > > your installation. This contains:
> > >
> > >- Concept Graphs de
ces run as well
>
> On Friday, July 4, 2014, John Green wrote:
>
> > Vijay - Ha! Ok. Works perfect with cuis.
> >
> > Is there a way to run the web application as a RESTful API? You mention
> > this as a service on your yale box, but I dont see a way to deploy it
ot;annotator" as a consumer and convention is AFAIK to call them writers in
> this case.
>
> Hope that helps,
> -- James
>
> -Original Message-
> From: John Green [mailto:john.travis.gr...@gmail.com]
> Sent: Tuesday, July 01, 2014 7:15 PM
> To: dev@ctakes.apache.o
o say the same thing.
> >
> > cTAKES_clinical_pipeline.groovy is in ctakes-core/scripts/groovy
> >
> > In that script, line 321 is where the writer is specified. There is no
> separately defined "consumer" in the same sense that the CPE GUI has
> consumers that are
The Ytex DBConsumer - If someone has a free moment, could they give me a
hint at how I can plug into a mysql DB with the ytex DB consumer? For
example, taking the default ytex pipeline and sending it to a db.
If I get pointed in the right direction such that I figure it out Ill
update the confluen
to and your database as documented here:
> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
> -vj
> On Tue, Jul 15, 2014 at 2:16 AM, John Green
> wrote:
>> The Ytex DBConsumer - If someone has a free moment, could they give me a
>> hint at how I can p
; See
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+YTEX+DBConsumer
> You will have to set up ctakes to and your database as documented here:
> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
> -vj
> On Tue, Jul 15, 2014 at 2:16 AM, John Green
uld probably add to the docs to use the component descriptor:
> YTEX_HOME\desc\ctakes-ytex-uima\desc\analysis_engine\DBConsumer.xml
> On Tue, Jul 15, 2014 at 2:53 PM, John Green
> wrote:
>> Ok. I must have missed something. I did read both of those. Ill go back
>> and look again.
>
Is there a generally accepted procedure for identifying why an annotation
wasnt made?
JG
t the
> dictionary, if not then I go back to the chunker to figure out why the
> lookup window wasn't found, etc.
> Tim
> On 07/16/2014 03:01 PM, John Green wrote:
>> Is there a generally accepted procedure for identifying why an annotation
>> wasnt made?
>>
>> JG
>>
f
> annotation you are most interested in.
>
> -Original Message-
> From: John Green [mailto:john.travis.gr...@gmail.com]
> Sent: Wednesday, July 16, 2014 2:01 PM
> To: dev@ctakes.apache.org
> Subject: Procedure
>
> Is there a generally accepted procedure for identifying why an annotation
> wasnt made?
>
> JG
>
n,
> but doesn't associate those with a named entity that has a cui.
> The example of "pulsatile abdominal mass" listed the same 3 words in the same
> order for the dictionary entry and the text that was processed, so I'm not
> clear what you meant about word order
olutions] <http://imatsolutions.com>
> Bruce Tietjen
> Senior Software Engineer
> [image: Mobile:] 801.634.1547
> bruce.tiet...@imatsolutions.com
> On Thu, Jul 17, 2014 at 11:57 AM, John Green
> wrote:
>> I didnt see how it appeared in dictionary, I just looked at the cui
quot;.
> Also note that intervening words can be OK, up to a limit, but all words
> within the term must appear within a single LookupWindow.
> Hope that is helpful
> -- James
> -Original Message-
> From: John Green [mailto:john.travis.gr...@gmail.com]
> Sent: Thursd
As a clinician Id really like to see the types that Melissa has elicited from
physicians.
By the by: Id call apgar, or duke, or has bled score, or chads vasc, or childs
criteria, or anything else like them risk classifiers or prognosticators or
decision models or something like that (the line
What exactly needs updated? I have not had the time (unfortunately) to help
with this project very much because of the steep learning curve on the
technology. I'm currently on some protected research time working with
cTakes as of this week and would be happy to help with some grunt work.
JG
On
ay/CTAKES/cTAKES+3.1.1
> And just add the YTEX and/or any new changes to it...
> Would be grateful for any help here...
>> -Original Message-
>> From: John Green [mailto:john.travis.gr...@gmail.com]
>> Sent: Tuesday, July 22, 2014 2:37 PM
>> To: dev@ctakes.ap
Well Pei, I guess we were editing at the same time 5 hours ago. I kept
getting this error, and I couldn't figure it out because nothing was in the
index yet:
Cause
com.atlassian.confluence.pages.DuplicateDataRuntimeException: A page
already exists with the title cTAKES 3.2 Component Use Guide in
inal Message-
>> From: John Green [mailto:john.travis.gr...@gmail.com]
>> Sent: Wednesday, July 23, 2014 9:11 PM
>> To: dev@ctakes.apache.org
>> Subject: Wiki
>>
>> Well Pei, I guess we were editing at the same time 5 hours ago. I kept
>> getting
>
This sounds just like jira ctakes-306.
JG
—
On Fri, Jul 25, 2014 at 1:04 PM, John Green
wrote:
> —
> -- Forwarded message --
> From: "Natalia Connolly"
> Date: Fri, Jul 25, 2014 at 12:35 PM
> Subject: UMLS integration with cTAKES 3.1
> To: "
Any ideas why as of cTakes 3.2.0 when I try and
use FilesInDirectoryCollectionReader.xml I get a NullPointerException?
java.lang.NullPointerException
at org.apache.uima.tools.cpm.CpmPanel.fileSelected(CpmPanel.java:1509)
at
org.apache.uima.tools.util.gui.FileSelector$1.actionPerformed(FileSelector
Please disregard, I discovered the error.
JG
On Mon, Jul 28, 2014 at 3:29 PM, John Green
wrote:
> Any ideas why as of cTakes 3.2.0 when I try and
> use FilesInDirectoryCollectionReader.xml I get a NullPointerException?
>
> java.lang.NullPointerEx
I was thinking the same thing as Steve. Thats a pretty regular onc physical
exam, why not just split sentences with regex's off a small list of defined onc
physical exam terms? The interesting case would be breast, as this term may
appear in the body of a sentence (rather than just a term), but
outstanding!—
On Thu, Aug 7, 2014 at 9:16 AM, britt fitch wrote:
> 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 availa
Nice!!! —
Sent from Mailbox for iPhone
On Tue, Aug 12, 2014 at 5:09 PM, Finan, Sean
wrote:
> cTakes now has a youtube channel named "Apache cTakes". It is empty, but if
> you have ever made a training video, presentation on a component
> (descriptors, type system, etc.), or demo of integratio
Great catch!—
Sent from Mailbox for iPhone
On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell
wrote:
> Hi folks,
> I was having an issue with the current build (from svn) of ctakes/ytex not
> identifying any annotations as some folks on this board. I traced it to
> the fact that the UMLS database h
I have not had time to implement this - to clarify out of curiosity, does this
clear up the @db.schema@ error Tim? And did you successfully run ytex with the
ctakes dictionary-lookup?
JG
—
Sent from Mailbox for iPhone
On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell
wrote:
> Hi folks,
> I was
Im trying to deploy the cTakes web-server code someone already wrote (who
wrote it btw?). Im running into deployment issues in eclipse with tomcat 7
on mac... I can get into details but for now: is it in a working state? Im
learning as I go and it looks in order and the code is solid...
Also, Pei:
Are there any acronym annotators and disambiguators? What are people doing
in production elsewhere? Im learning the heart of cTakes and UIMA by the
numbers right now and I think writing an annotator of my own will be the
best way to solidify the information. If no one has it done already, I
thought
> -Original Message-----
>> From: John Green [mailto:john.travis.gr...@gmail.com]
>> Sent: Thursday, August 21, 2014 3:06 PM
>> To: dev@ctakes.apache.org
>> Subject: Web server
>>
>> Im trying to deploy the cTakes web-server code someone already wrote (who
&
ered that as such it could serve as a nice foundation. Well, maybe a
> cornerstone.
>> -Original Message-
>> From: John Green [mailto:john.travis.gr...@gmail.com]
>> Sent: Thursday, August 21, 2014 3:43 PM
>> To: dev@ctakes.apache.org
>> Cc: dev@ctakes.apache
for iPhone
On Thu, Aug 21, 2014 at 12:05 PM, John Green
wrote:
> Im trying to deploy the cTakes web-server code someone already wrote (who
> wrote it btw?). Im running into deployment issues in eclipse with tomcat 7
> on mac... I can get into details but for now: is it in a working
tUMLSProcessor.xml (with swapping
>>> the
>>> LookupDesc_Db.xml file as above)
>>>
>>> I've even made modifications to the ytex version of LookupDesc_SNOMED.xml
>>> to get it tagging Disease Disorders, along with database modifications to
>>>
t. Co-occurence is one way of doing it, not necessarily the
> best; you need a ton of annotated data for it to work well.
> On Thu, Aug 21, 2014 at 9:08 PM, John Green
> wrote:
>> Are there any acronym annotators and disambiguators? What are people doing
>> in production elsewher
Wow, what a goldmine, thanks!
JG
—
Sent from Mailbox for iPhone
On Fri, Aug 22, 2014 at 8:31 AM, Koola, Jejo David
wrote:
> You might be interested in:
> https://sbmi.uth.edu/ccb/resources/abbreviation.htm
> On Aug 21, 2014, at 2:08 PM, John Green
> mailto:john.travis.gr.
Very good
On Wed, Aug 27, 2014 at 2:39 AM, and...@apache.org (Andy McMurry) <
mcmurry.a...@gmail.com> wrote:
> Interesting thread in UIMA core about JSON Serialization CAS and
> Descriptors.
>
>
> Begin forwarded message:
>
> > From: Marshall Schor
> > Subject: Re: [jira] [Created] (UIMA-3969)
Does anyone know of a larger set of human generated measures for semantic
simalarity than the 500+ one cited by Vijay in his paper on semantic
simalarity? The paper cited was PMID 21347043.
Jg
—
Sent from Mailbox
u/~bthomson/sim/index.html
> Dima
> On Sep 27, 2014, at 12:26, John Green wrote:
>> Does anyone know of a larger set of human generated measures for semantic
>> simalarity than the 500+ one cited by Vijay in his paper on semantic
>> simalarity? The paper cited was PMI
How large? And across how many EMRs?
JG
—
Sent from Mailbox
On Mon, Sep 29, 2014 at 6:58 PM, Ajay Jain
wrote:
> Sorry, I wasn't clear. I am working on a related project and trying to figure
> out if the code can be repurposed for a lab mention annotator for cTAKES.
> From what I have seen,
ever dataset you
> are able to provide without spending a lot of effort extracting it.
> Thanks.
> Ajay
> Sent from my iPhone
>> On Sep 30, 2014, at 5:22 AM, "John Green"
>> wrote:
>>
>> How large? And across how many EMRs?
>>
>>
&g
I've been putting off debugging this as it was a piece of this app Im
working on, but one that fit in down the road in development. Development
has progressed, and here I am. I have posted this one before, was hoping to
find fresh help.
When running ytex.sh in a distro installed at something like
1 - 100 of 130 matches
Mail list logo
