Yes, it would be great if we can fix the unit test.
So "mvn test" works fine, but if you need to install or package, we had
-skipTests=true because the unit test attempts to load resources after it's
been bundled/packaged.
We should fix update the unit test or allow load resource from stream.
It would be great if we could have a patch that allows lvg to load from
resource from steam. Thanks for looking into that Lewis. Note though- the
physical files requirement may go deeper into lvg code.
Sent from my iPhone
On Oct 15, 2015, at 2:36 AM, Lewis John Mcgibbney
that we can probably just
overwrite for new regression testing code.
From: Ted Strall [mailto:tstr...@yahoo.com]
Sent: Thursday, July 30, 2015 9:21 AM
To: Chen, Pei; dev@ctakes.apache.org
Subject: Re: Combining Knowledge- and Data-driven Methods for De-identification
of Clinical Narratives
How
Matie,
That looks to be a discrepancy.
My suggestion would be to remove: POSTagger.xml from the Chunker project and
anywhere else as it is confusing. (I think these 'mini' pipelines were there
when we supported those PEAR file deployments)
Would you mind double checking to see what the defaults
Tomasz,
Thanks for bringing those up. It would be great if you can log the real
examples into the Jira ticket and it can be incorporated into test cases going
forward (it may most likely need more training examples).
Also, FYI- If I recall correctly, there was nothing previously in cTAKES that
Tomasz,
Yes, please please feel free to open a Jira ticket for this. Also, Be sure to
include the version of the cTAKES and pipeline you're using.
It is possible that the new Subject Classifier isn't classifying this...
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Soumya,
Could you elaborate a bit on what you mean by pattern? Perhaps an example would
be helpful.
--Pei
Sent from my iPhone
On Jul 3, 2015, at 7:27 AM, Soumya Shree
soumya.sh...@citiustech.commailto:soumya.sh...@citiustech.com wrote:
Hi folks,
I need to train my system so that it should
Samir,
Which cas consumer are you using?
Sent from my iPhone
On Jun 14, 2015, at 11:24 AM, samir chabou
samir...@yahoo.commailto:samir...@yahoo.com wrote:
Hi,
When I use CPE_GUI it does not keep the input file name but it changes it to
doc0.
Example input file = test123.txt
the output file
This looks awesome.
Perhaps we can reuse the Tika server on the ctakes demo VM.
Sent from my iPhone
On Jun 6, 2015, at 8:40 PM, jay vyas jayunit100.apa...@gmail.com wrote:
This is awesome; thanks!
For some of the new ctakes projects where fplks bc are aiming at using it
with big data
Hi Tom,
Thanks for pointing that out. There was a copy and paste error on the website
links for the resources.
Should be fixed now.
-Original Message-
From: Tom Devel [mailto:deve...@gmail.com]
Sent: Friday, May 29, 2015 6:23 PM
To: dev@ctakes.apache.org
Subject: Re: Downloads link
Cancelling this rc1 so we can squeeze the UMLS validation fix into this patch
release.
Will create a rc2 for voting instead.
--Pei
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Tuesday, May 05, 2015 2:06 PM
To: dev@ctakes.apache.org
Subject: [VOTE] Release Apache
Can we use InputStreamReader instead of FileReader?
That way the resource can also be read from within a jar (potentially from
maven central, etc.) and doesn't have to be fixed to a physical file...
i.e.
Instead of new BufferedReader(new FileReader(path))
new BufferedReader(new
to have
some way for people to access all the machine learning assertion modules if
they want them.
Tim
On 04/29/2015 06:04 PM, Chen, Pei wrote:
FYI- I will plan to create a 3.2.2 branch from trunk this week in prep for
the 3.2.2 release so others can continue their work in trunk.
Feel free
2) Minor bug fixes reported in Jira
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Thursday, March 12, 2015 12:55 PM
To: dev@ctakes.apache.org
Subject: Prep for upcoming cTAKES 3.2.2 Patch Release
I was thinking of creating a 3.2.2 release for Mar (it's long passed
Great. There is a redundant Negation step in one of final sub smoking desc
xml's.
Leave the Jira as a placeholder to clean up the smoking status desc's.
Sent from my iPhone
On Apr 20, 2015, at 1:11 PM, Tom Devel deve...@gmail.com wrote:
Pei,
I did what you recommended, I run a test
I was thinking of creating a 3.2.2 release for Mar (it's long passed the
original Jan date?) I can volunteer to be the RM again.
There are still plenty of unresolved items... If you plan to have anything you
would like included in the upcoming release, please mark it in Jira and plan
the
/in/ksarma
On Wed, Dec 31, 2014 at 1:53 PM, Chen, Pei pei.c...@childrens.harvard.edu
wrote:
Hi folks,
Michelle, Sean, Guergana, and Co. have created a few mockups for the
new cTAKES website. Which option would folks prefer?
This is purely on the design intent, and layout, etc. (not actual
Hi folks,
Michelle, Sean, Guergana, and Co. have created a few mockups for the new cTAKES
website. Which option would folks prefer?
This is purely on the design intent, and layout, etc. (not actual content).
Option 1: http://mwchen.scripts.mit.edu/cTakes/mock0/index.html
Option 2:
[image: IMAT Solutions] http://imatsolutions.comhttp://imatsolutions.com
Bruce Tietjen
Senior Software Engineer
[image: Mobile:] 801.634.1547
bruce.tiet...@imatsolutions.commailto:bruce.tiet...@imatsolutions.com
On Thu, Dec 18, 2014 at 3:37 PM, Chen, Pei
pei.c
Matt,
The below change has been made in trunk:
http://svn.apache.org/r1646497
https://issues.apache.org/jira/browse/CTAKES-344
(if you make the change, be sure to also include ctakes-drug-ner in your
pom.xml)
--Pei
-Original Message-
From: Chen, Pei [mailto:pei.c
Bruce,
Thanks for this-- very useful.
Perhaps Sean Finan comment more-
but it's also probably worth it to compare to an adjudicated human annotated
gold standard.
--Pei
-Original Message-
From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com]
Sent: Thursday, December 18,
platform for rapid
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 Message-
From
That’s a typo in the fast dictionary lookup.
It should be: https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser
Jira raised for this: https://issues.apache.org/jira/browse/CTAKES-335
From: Kim Ebert [mailto:kim.eb...@imatsolutions.com]
Sent: Monday, November 24, 2014 1:28 PM
To:
Budi,
It looks like there may have been an issue with the sourceforge mirrors for
3.2.1.1 resources (the size should be about 627MB, not 200MB.)
I refreshed it… Could you try know?
Also, ensure do a merge of the resources folder (rather than replace.)
Hope that helps…
--Pei
From: Budi Wibowo
Budi,
You can also try out
ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml
available in the current 3.2.1-rc.
It contains a new dictionary lookup algorithm from Sean that is roughly 1000%
faster for each pipeline.
--Pei
From: Kim Ebert
John- I believe that was the thinking.
Andy- Just to confirm- Is the raw content of this dataset released under
ASL2.0? i.e. can you contribute it as a CSV or similar so that cTAKES may
re-tokenize it using the same PTB rules, format it for cTAKES' dictionary
lookup, etc., and then
Chen,
Does this need to go into this upcoming release or can it wait till the next
one?
Sent from my iPhone
On Nov 10, 2014, at 10:20 AM, c...@apache.org c...@apache.org wrote:
Author: clin
Date: Mon Nov 10 15:19:55 2014
New Revision: 1637884
URL: http://svn.apache.org/r1637884
Log:
RC1 ready for testing:
Binary Artifacts: https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.1/
Tag: https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.1-rc1/
Would be great if folks have time to test/verify especially if you opened any
of the Jira's below to ensure the bugs have been
, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Thursday, November 06, 2014 10:17 PM
To: 'dev@ctakes.apache.org'
Subject: RE: ctakes-dictionary-lookup-fast
The image didn't come through for me. Can you post the image somewhere
and send the url? Thanks.
From: Chen, Pei [mailto:pei.c
Hi,
The original plan was to update AggregatePlaintextUMLSProcessor.xml to use the
new ultrafast dictionary lookup in the upcoming 3.2.1 release.
However, the output is slightly different the old cTAKES dictionary where it no
longer has a SNOMED/RXNORM consumer (Returns CUI's only and doesn't
VJ,
This required a code change as well.
I updated it to use java pojo's instead. Would be good if you can help
verify/confirm:
Please see http://svn.apache.org/r1636663
import gnu.trove.set.TIntSet;
import gnu.trove.set.hash.TIntHashSet;
-Original Message-
From: Chen, Pei
Lam Vu,
Have you tried running it with -DskipTests as a temp workaround?
Tests in error:
TestClearNLPPipeLine(org.apache.ctakes.dependency.parser.ae.util.TestClearNLPAnalysisEngines):
URI
is not hierarchical
From: Lam Vu Son [mailto:lamvu...@gmail.com]
Sent: Friday, October 31, 2014 12:10 PM
Jay,
Were you proposal the A) Hybrid [1] git/svn approach (where svn is still the
primary version control, but code and full histories gets gets mirrored to git)?
OR were you proposal B) replacing SVN and using git as the primary version
control for cTAKES @ a.o [3]?
A) is fairly straightforward
.
On Wed, Oct 15, 2014 at 10:42 AM, Chen, Pei
pei.c...@childrens.harvard.edu wrote:
Steve,
This is a good catch! I was pretty sure 3rd party libs were checked but
somehow this may have been missed.
I noticed it's in the convenience binary distro as well. We need to remove
this; I'll
Steve,
This is a good catch! I was pretty sure 3rd party libs were checked but
somehow this may have been missed.
I noticed it's in the convenience binary distro as well. We need to remove
this; I'll create a Jira.
VJ, could you confirm- I actually don't think we use trove4j in ytex?
in ctakes 3.2.0
No. I have no file named beanRefContext.xml anywhere on my hard drive.
On Fri, Oct 10, 2014 at 3:45 PM, Chen, Pei
pei.c...@childrens.harvard.edumailto:pei.c...@childrens.harvard.edu wrote:
I’m not too familiar with the ytex component,
but my guess is that the ytexApplicationContext
Assuming we have a representative training set, are there any objections if we
default cTAKES to this SentenceAnnotator + Model?
For the upcoming release:
- Consolidate the existing sentence detector, ytex sentence dectector into this
new?
- Allow a config parameter to still allow an override
Applied fix in trunk r.1624031
https://issues.apache.org/jira/browse/CTAKES-311
VJ- I'm not sure if there is test coverage for this, but let us know if you
have any idea/sconcerns.
--Pei
-Original Message-
From: Tim O'Connell [mailto:tim.oconn...@gmail.com]
Sent: Monday, September 08,
(Trying to avoid passing individual jars via email)
Sent from my iPhone
On Sep 9, 2014, at 5:26 PM, Chen, Pei pei.c...@childrens.harvard.edu
wrote:
Sean-
Aren't the scripts to generate the DB already available in the sandbox area?
Sent from my iPhone
On Sep 9, 2014, at 5:24 PM
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 08/20/2014 11:52 AM, Chen, Pei wrote:
Thanks Kim- would you mind opening up a Jira to track this?
The cTAKES ClearNLP Dependency Parser and/or Test Cases most likely
need
to be updated to enable
It logs it as a warn, but fails the test.
Should there it assertNotNull only if UMLS setup else, pass the test?
That way, for those folks are doing a default 'maven clean install, they won't
have to skipTests?
// UMLSDaoTest .testGetAllAuiStr() - Check to see if UMLS is setup before
checking?
garla [mailto:vnga...@gmail.com]
Sent: Thursday, August 21, 2014 11:07 PM
To: dev@ctakes.apache.org
Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
v_snomed_fword_lookup
That would definitely make sense
On Thursday, August 21, 2014, Chen, Pei pei.c...@childrens.harvard.edu
wrote
Hi Tim,
I think these 2 types may have been clobbered accidently between these 2
revisions?
Let me know and I'll add these back in...
Natalia,
That is strange. It sounds like it isn't configured to use the right resource.
Could you double check the mappings, in particular: in your LookupDesc_Db.xml:
externalResourceKey=DbConnection to ensure it's using the right resource that
was added in your DictionaryLookupAnnotatorDB.xml?
Ah Yes,
I noticed there was a 'Copy Page Tree' feature that copied the entire pages so
it was fairly straightforward...
-Original 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
...@mayo.edu]
Sent: Friday, July 11, 2014 7:27 PM
To: 'dev@ctakes.apache.org'
Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
I agree about keeping the thread open.
-- James
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Friday, July 11
, which is why I had the 3.1.1 page mostly just
reference the
3.2 documentation.
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Tuesday, July 22, 2014 10:00 AM
To: dev@ctakes.apache.org
Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2
: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Thursday, July 10, 2014 2:12 PM
To: dev@ctakes.apache.org
Subject: RE: [VOTE] Release
I think this is due to the fact that the default lvg.properties also exits in
the ctakes-resources project, so if you download and replace, it will override
the ctakes configured one.
I think it's a bug, but probably always been there...
I'll fix up ctakes-resources on sourceforge
The maven artifacts are also available in the staging area:
https://repository.apache.org/content/repositories/orgapachectakes-1001
VJ: Just curious- how did you envision ytex users downloading the jars/war?
From the distro bin.zip or from maven central?
--Pei
-Original Message-
From:
Nick,
On why 'Enterococcus faecium' isn't returned:
I think a limitation is that cTAKES will force a mapping of the TUI's semantic
types into a semantic group. If it doesn't exist in the mapping, the
dictionary lookup won't save it.
It would probably be a nice feature to create a Other semantic
One can try the CDASegmentAnnotator. Both are rules/regex based but it's much
simpler and doesn't require the find struct 3rd party lib.
Sent from my iPhone
On Jul 1, 2014, at 10:19 PM, Harpreet Khanduja hsk5...@rit.edu wrote:
Hello,p
Thanks for getting back.
I tried again and this is the
Himanshu,
There is a RC1 available for voting (see recent [VOTE] thread from this list.)
Please feel free to try it out and vote.
It will be release once there are more than 3 +1 binding votes.
Sent from my iPhone
On Jul 2, 2014, at 2:32 PM, Himanshu Singhal himanshusinghal...@gmail.com
Thanks James.
I just did a Jira review for 3.2. There are just 2 remaining items that are
pending some clarification from respective dev. Otherwise, it should be up to
date now- any items that didn't make it to 3.2 have been updated to 3.2.1
instead now.
--Pei
-Original Message-
I presume the parameter markers should really have a property name attached to
it:
catalog=@filter.umls.catalog@ rather than @filter.umls.catalog@ byitself in
order to pass xml validation.
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Friday, June 27,
Nick,
If I'm reading it correctly, that code change essentially tells it to bypass
the OrangeBookFilter completely.
If that is the behavior you're looking for (i.e. return all of the drugs
bypassing the OrangeBookFilter, then you can just modify the lookupConsumer
className in your
: +
patternLists.createPatternList(ocMap.keySet()).toLowerCase());
return ocMap;
}
I wrote this code in my own annotator to retrieve the medication names but
this is not returning anything now. Which class should I use now to get
medication names?
-Original Message-
From: Chen, Pei
There is a demo server setup to host a web ui:
https://demo-ctakes.apache.org/
There is a code for a very simple html web UI at:
http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-web-client/
We should be able to just mvn package and drop the war file into a tomcat
instance.
[I didn't get a
Renamed to *-fast.
Again, this is only temporary... this will eventually just replace the existing
dictionary lookup (next minor release?).
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Tuesday, June 17, 2014 10:14 AM
To: dev@ctakes.apache.org
-lookup-fast? Besides being accurate and
more descriptive than 2, it might lure people into trying it and
give us some feedback.
Tim
On 06/16/2014 10:34 AM, Chen, Pei wrote:
I'm making some significant updates to trunk that may cause some
instability for this release.
It should
/main/java
org.apache.ctakes.core.resource
package.
Thank you very much.
Harpreet
On Wed, Jun 11, 2014 at 4:33 PM, Chen, Pei
pei.c...@childrens.harvard.edu
wrote:
Harpreet,
Just curious- is maven able to connect to the internet
, 2014, at 12:48 PM, Chen, Pei
pei.c...@childrens.harvard.edu
wrote:
I think James has a fair point here.
It may be worthwhile biting the bullet here and push forward.
Since this essentially will be a full replacement of the
ctakes-dictionary-lookup module, a good
Dear cTAKES enthusiast,
As you may be aware, ApacheCon will be held this year in Budapest, on November
17-23. (See http://apachecon.eu for more info.)
The Call For Papers for that conference is still open, but will be closing
soon. We need you talk proposals, to represent cTAKES at
Harpreet,
I had a closer look at your log file and it looks like you were actually trying
to run it from Eclipse IDE?
If so, just ensure that the resources do exist in the classpath.
If it's within eclipse ide, the plugin should download and unpack the umls
dictionaries automatically actually.
of
apache.snapshots has elapsed or updates are forced - [Help 1] [ERROR]
On Wed, Jun 11, 2014 at 2:17 PM, Chen, Pei
pei.c...@childrens.harvard.edu
wrote:
Harpreet,
I had a closer look at your log file and it looks like you were
actually trying to run it from Eclipse IDE?
If so, just
of it that will help users to decide when to use one
dictionary lookup component vs. the other.
-- James
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Friday, June 06, 2014 12:34 PM
To: dev@ctakes.apache.org
Subject: Preparing for an Apache
the algorithm?
Is there a description of it that will help users to decide when to use one
dictionary lookup component vs. the other.
-- James
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Friday, June 06, 2014 12:34 PM
To: dev@ctakes.apache.org
Hi,
The 3.2 release was slated to be release end of this month (Jun 21).
Since I volunteered to be the RM for this release, just like the past releases,
I was planning to create a branch/tag next week from trunk and dev can continue.
Feel free to take a look at any outstanding Jira issues [1]
Michal,
Quick Q
Do the ctakes-ytex*physical folders exist after your refresh/checkout?
https://svn.apache.org/repos/asf/ctakes/trunk/
Depending on the setup, I don't recall if 'svn up' automatically adds new
folders that were added subsequent to your original checkout or if you had to
specify
+1 for a consolidated common type system...
I would go a step further- 'Markable' seems like a pretty general concept,
maybe if folks can think of other uses, we can subclass a
MarkableCoRefMarkable?
-Original Message-
From: Steven Bethard [mailto:steven.beth...@gmail.com]
Sent:
There is a filter in the root pom.xml to only include these types inside the
jars during package time:
So essentially, all of the jars from *-res projects will be empty.
I think this was residual setting when we were still in incubator where we were
debating if resources should be included.
Are
, 2014, at 5:46 AM, Richard Eckart de Castilho r...@apache.org
wrote:
At the time a factory method becomes callable, the Maven/Ivy-magic should
already have taken place, no?
-- Richard
On 27.04.2014, at 17:52, Chen, Pei pei.c...@childrens.harvard.edu wrote:
My vote would
My vote would be for the latter. Have the Factory create pipelines instead.
It could just be a naming thing though...
+1 for building dynamic pipelines. I think this idea has been thrown around for
sometime, but it hasn't been really worked on so it would be cool to see it in
action. I think
, that would be great, add me.
Jg
--
Sent from Mailbox for iPhone
On Fri, Apr 4, 2014 at 10:15 AM, Chen, Pei
pei.c...@childrens.harvard.edu
wrote:
John,
You should have committer rights now... I would suggest opening a
Jira
item just so that it can be tracked
Ying,
Are you behind a proxy or firewall?
If you're trying to use the umls resources, it attempts to make a call to their
umls service to validate your credentials.
--Pei
-Original Message-
From: Liu, Ying [mailto:l...@advisory.com]
Sent: Wednesday, April 16, 2014 1:13 PM
To:
If I remember correctly, I think those attributes were set in
IdentifiedAnnotation via:
ctakes-template-filler/desc/analysis_engine/TemplateFillerAnnotator.xml
One can look at the logic in:
org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator [1]
Have you tried added that to the
PM, Chen, Pei
pei.c...@childrens.harvard.eduwrote:
If I remember correctly, I think those attributes were set in
IdentifiedAnnotation via:
ctakes-template-filler/desc/analysis_engine/TemplateFillerAnnotator.xm
l
One can look at the logic
Feel Free to add/edit (due 3/12/14)
Apache cTAKES (clinical Text Analysis and Knowledge Extraction System) is a
natural language processing (NLP) tool for information extraction from
electronic medical record clinical free-text.
Issues:
There are no issues requiring board attention at
Hi,
Is anyone still using the pad-term-spotter component?
Deprecating this module if it's no longer used will simplify the codebase and
reduce the effort in support...
--Pei
Don't know how we'd find out if anyone is still using it.
I think we can start with the dev@ and user@ mailing lists to see if they're
still using PAD Term spotter.
And let them know the plans of removing it in the future major release.
I can volunteer some time for that...
+1 for
and this being geared toward new folks
such as myself. But, opinions before diving would be appreciated, time
always being limited.
JG
On Thu, Feb 6, 2014 at 9:51 AM, Chen, Pei
pei.c...@childrens.harvard.eduwrote:
John,
As a starting point, you may want to check out:
http
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 [mailto:john.travis.gr...@gmail.com]
Sent: Friday, February 07, 2014
John,
As a starting point, you may want to check out:
http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/
The content (Descriptions) probably needs to be filled in more...
--Pei
-Original Message-
From: John
+1
There's an example of the configs here :)
https://issues.apache.org/jira/browse/CTAKES-98
I think we should be able to use OpenNLP's Sentence Annotator directly if we no
longer need the custom newline rule(s)
[Or if we find that a fixed rule is still required, perhaps OpenNLP can support
it
The contents -res jars/projects have been temp commented out by the parent
Pom.
-it was quite ready for prime time yet. Mainly because some of the code still
can not load resources from jars/class paths (some of which we do not have
control the 3rd party code so it's not as straight forward)
Done.
Anonymous is read-only now.
Thanks for pointing that out- I always thought that was the default.
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Tuesday, January 07, 2014 10:34 AM
To: 'dev@ctakes.apache.org'
Subject: Apache cTAKES confluence wiki
* How can I distribute the ctakes binary distribution to ytex users before the
merge? Can we make the branch build available somewhere? The binary
distribution is too large to host on the ytex google code site (max 200 MB)
Is this for testing purposes? Or official release? If it's just for
, not
both dot and underscore. I would prefer that we remove the dot
functionality since it is not operational across all environments, but it
isn't up
to me alone to remove functionality.
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Saturday
I believe Sean updated the code to also support underscore (_) as well. But the
docs just need to be updated...
On Jan 4, 2014, at 4:04 PM, Dewful dew...@gmail.com wrote:
In the documentation, in the .sh files to run ctakes;
# If you plan to use the UMLS Resources, set/export env
This is awesome VJ.
I'll take a look at it this week unless someone beats me to it
On Jan 3, 2014, at 10:22 PM, vijay garla vnga...@gmail.com wrote:
Hello All,
I have finished an initial cut at the port of YTEX to cTAKES 3.1.1. Most
of the YTEX functionality has been ported and
I think the type system doc [1] and javadoc [2] is probably the closest thing I
could think of:
It's not an xml schema of the UIMA XMI per se though...
[1]
I can ping ASF infra to see if they offer any vm's for Demo's etc. will revert
back to see what I find out.
Sent from my iPhone
On Dec 23, 2013, at 10:17 AM, Masanz, James J. masanz.ja...@mayo.edu
wrote:
Hi Andy,
It's great to see such enthusiasm!
I like all the ideas. I don't know
[moved to dev@]
Hi Paula,
My suggestion would be to open a Jira item so that it could be tracked:
https://issues.apache.org/jira/browse/CTAKES (Feel free to create a new
account).
Even cooler if you could attach the affected files with the patch(diffs) and
any tests.
--Pei
From: digital paula
James,
Would it be possible to also attach your script? I can try to replicate it
here...
--Pei
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Friday, December 13, 2013 11:34 AM
To: 'dev@ctakes.apache.org'
Subject: scala and groovy
I'm still
@ctakes.apache.org] On
Behalf Of Chen, Pei
Sent: Friday, December 13, 2013 10:48 AM
To: dev@ctakes.apache.org
Subject: RE: scala and groovy
James,
Would it be possible to also attach your script? I can try to replicate it
here...
--Pei
-Original Message-
From: Masanz, James
Also,
My 2 cents on dynamic downloading-
If the use case is for developers to have a simple script to start coding away
that is sits on top of cTAKES without having to learn about UIMA etc..., then
dynamic downloads are probably okay.
But if the goal is to make a stand-alone product w/o any
James,
If you enable the verbose debugging, it may help identify the cause:
Try removing the artifact in question from your .m2 directory and your .groovy
And then:
$grape -d install org.springframework spring-asm 3.1.0.RELEASE
Which should output the full path it will take in attempting to
Hi Dima,
I believe OrangeBook doesn't have the license restriction like UMLS- hence it
was included in
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/OrangeBook/
-Original Message-
From: Dligach, Dmitriy
.
From: Chen, Pei [pei.c...@childrens.harvard.edu]
Sent: Tuesday, November 26, 2013 4:13 PM
To: dev@ctakes.apache.org
Subject: cTAKES Groovy...
Tim had a good end user use case:
I just want to use the ctakes constituency parser and output the tree text to
console.
So I
Hi VJ,
Sounds cool. I guess once things are in the branch, we can start to take a
look to see if it makes sense to incorporate them directly into existing ctakes
modules or not?
Just curious- were the type system changes mainly adding additional fields?
Just planning ahead especially for
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