seanfinan closed issue #19: cTAKES custom dictionary setup documentation
URL: https://github.com/apache/ctakes/issues/19
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Subject: Re: [apache/ctakes] cTAKES custom dictionary setup documentation
(Issue #19) [EXTERNAL]
* External Email - Caution *
Thanks for sharing, I converted csv to bsv, then created a xml b
andytubeee commented on issue #19:
URL: https://github.com/apache/ctakes/issues/19#issuecomment-2143935250
Thanks for sharing, I converted csv to bsv, then created a xml based on your
tinyDictSpec.xml, and then used the -l flag with ./bin/runClinicalPipeline.
I didn't run into any iss
seanfinan commented on issue #19:
URL: https://github.com/apache/ctakes/issues/19#issuecomment-2142793964
https://github.com/apache/ctakes/wiki/ctakes-dictionary-lookup-fast
If you expand DictionarySubPipe
https://github.com/apache/ctakes/wiki/ctakes-dictionary-lookup-fast#dictionary-sub-
seanfinan commented on issue #19:
URL: https://github.com/apache/ctakes/issues/19#issuecomment-2142787585
There is/was documentation somewhere, but it is spread out and would take me
some time to find the latest and most accurate. However, you have have a look
at the example here
https://
andytubeee opened a new issue, #19:
URL: https://github.com/apache/ctakes/issues/19
I have a CSV file of dictionary vocabulary and concept code. Are there any
documentations on how we can set up a custom dictionary for when using
**bin/runClinicalPipeline.sh**?
Thanks
--
This is
at the code and see if I can determine what
happened there.
Thanks for reporting,
Sean
From: Kean Kaufmann
Sent: Tuesday, April 16, 2024 10:42 AM
To: dev@ctakes.apache.org
Subject: Custom dictionary no-"no" [was: Re: PREFTERMs not included in UML
Hi Sean,
I ran the dictionary creator tool from ctakes 5.0.0, and am happy to see
that preferred texts are now also lookup texts -- thank you!
However, I also note that almost all terms starting with the letters "no"
are now omitted, except for a few starting with "no fh : &qu
om
Sent: Thursday, September 17, 2020 12:45 PM
To: dev@ctakes.apache.org
Subject: RE: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
* External Email - Caution *
Hi Sean,
We tried this and unfortunately this wasn't working, Our main goal
is "code" would not be getting populated for the newly configured ICD/CPT
. Pls. find the below steps that we did for adding ICD/CPT into our profile
1. Generated a custom dictionary using METAMORPHOSYS UML installation
tool(where we provide sources as ICD10,CPT) and leverage the full set of .
@ctakes.apache.org
Subject: RE: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
* External Email - Caution *
Hi Sean,
We tried setting the exclusion tags="". PFB the changes we did
1. Set the value of String DEFAULT_EXCL
ent: Tuesday, September 15, 2020 9:06 PM
To: dev@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
[External]
Hi Abad,
The first thing that I would try for the "97112" problem is changing the parts
7;s modifier in a treebank.
> >
> > Does the question make sense?
> >
> > Peter
> >
> > On Tue, Sep 15, 2020, 9:02 AM Finan, Sean <
> > sean.fi...@childrens.harvard.edu>
> > wrote:
> >
> > > I should mention that going the Paragraph r
impact
> > term
> > lookup.
> >
> > From: abad.ay...@cognizant.com
> > Sent: Tuesday, September 15, 2020 11:54 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: Building a new custom dictionary or Updating/Adding
&g
ent: Tuesday, September 15, 2020 11:54 AM
> To: dev@ctakes.apache.org
> Subject: RE: Building a new custom dictionary or Updating/Adding values to
> the existing dictionary in cTAKES [EXTERNAL]
>
> * External Email - Caution *
>
>
> Thank you Sean for the response. We shall d
I should mention that going the Paragraph route would only impact term lookup.
From: abad.ay...@cognizant.com
Sent: Tuesday, September 15, 2020 11:54 AM
To: dev@ctakes.apache.org
Subject: RE: Building a new custom dictionary or Updating/Adding values to
.@cognizant.com
Sent: Tuesday, September 15, 2020 11:54 AM
To: dev@ctakes.apache.org
Subject: RE: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
* External Email - Caution *
Thank you Sean for the response. We shall definitely try t
ds
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan, Sean
Sent: Tuesday, September 15, 2020 9:06 PM
To: dev@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
[Exter
ds to be changed to fit your data.
Sean
From: abad.ay...@cognizant.com
Sent: Tuesday, September 15, 2020 11:15 AM
To: dev@ctakes.apache.org
Subject: RE: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES [EXTERNAL]
Kindly advise.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan, Sean
Sent: Monday, September 14, 2020 9:35 PM
To: dev@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dict
his seems like a lot to check, but dictionary lookup is not a
simple beast.
Sean
____
From: Finan, Sean
Sent: Monday, September 14, 2020 12:04 PM
To: dev@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existi
en spaces. This would carry forward for the other entries, such as:
INSERT INTO CUI_TERMS VALUES(4352,3,4, ‘F84 . 1 pdd’, ‘pdd’)
Sean
From: abad.ay...@cognizant.com
Sent: Monday, September 14, 2020 11:32 AM
To: dev@ctakes.apache.org
Subject: RE: Building a
B598]
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
From: Remy Sanouillet
Sent: Tuesday, June 2, 2020 7:23 AM
To: dev@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES
[External]
Hi Abad,
• How can we point cT
It works!
I've added one entry "bed" with my new dictionary and blacklisting it from
disorders, S&S, procedures, etc to the case sensitive version
When I spell it bed, it is blacklisted.
When I spell it BED, I get
"ontologyConceptArr": [{
"_type": "UmlsConcept",
"codingScheme"
>From codebase 4.0.1
org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer line 98,
but you'll see it referenced everywhere in the file.
Oddly enough it is not abstracted out so it could be used in the
PrecisionTermConsumer.
I'm just testing it.
Peter
Peter
On Tue, Aug 4, 2020 at
Where in the source code is this feature implemented?
On Tue, Aug 4, 2020 at 7:30 PM Peter Abramowitsch
wrote:
> Blacklist format
> Actually I got it inverted, its:
>
> semantic_code1, semantic_code2,...|text1
> semantic_code1, semantic_code2,...|text2
>
> Peter
>
> On Tue, Aug 4, 2020 at 4:16 P
Blacklist format
Actually I got it inverted, its:
semantic_code1, semantic_code2,...|text1
semantic_code1, semantic_code2,...|text2
Peter
On Tue, Aug 4, 2020 at 4:16 PM Peter Abramowitsch
wrote:
> Ok Thanks Jeff. I'm glad I wasn't missing something important.
>
> There already is a blacklist
Ok Thanks Jeff. I'm glad I wasn't missing something important.
There already is a blacklist text mechanism which suppresses identification
of specific text by clinical domain.
Looking at the code it collects entries like
cTakesSemanticCode,texta,textb,textc
NE_TYPE_ID_DRUG, jasmine, coriander, bl
Hi Peter,
To your question about sno_rx_16ab I suspect that the CUI is new since
2016, or if it existed in UMLS back then, it was not associated with a term
in snomed or rxnorm at that time.
To those solutions, if you are able to use the trunk I know Sean said there
was a suppression text feature
Hi Jeff et al
To take up the thread from a few days ago where a simple english word such
as bed, soft, shop also maps into a legitimate but rarely used acronym and
shows up in the same POS as a potentially interesting entity, what is the
mechanism you would use to disambiguate?
This problem only
And of course, once you get a great set of terms, you get to play with the
> valid parts of speech. You decide on grabbing every term or only the
> longest overlapping terms. Allow discontinuous spans or require continuous
> spans.
>
> Fun.
>
>
>
> ___
d of course, once you get a great set of terms, you get to play with the
valid parts of speech. You decide on grabbing every term or only the longest
overlapping terms. Allow discontinuous spans or require continuous spans.
Fun.
____
From: Peter Abramow
or mixed case.
>
> When the annotator engine iterates over the text, it checks one table
> (classic) or the other (caps) depending upon the case of the text in the note.
>
> It sounds like minor work, but it requires a new engine, new dictionary, and
> new dictionary creator. None of t
t; that are lower and/or mixed case.
>
> When the annotator engine iterates over the text, it checks one table
> (classic) or the other (caps) depending upon the case of the text in the
> note.
>
> It sounds like minor work, but it requires a new engine, new dictionary,
> and
work, but it requires a new engine, new dictionary, and
new dictionary creator. None of this is difficult, but it requires time.
Anyway, I hope that some of this helps.
Sean
From: Peter Abramowitsch
Sent: Saturday, August 1, 2020 11:35 PM
To: dev@
Hi Jeff thanks for your suggestions,
I spent some time in the script file and sure enough, my 2020 UMLS
extraction actually has these two entries:
INSERT INTO CUI_TERMS VALUES(3542022,0,1,'soft','soft')
INSERT INTO PREFTERM VALUES(3542022,'SHORT STATURE, ONYCHODYSPLASIA, FACIAL
DYSMORPHISM, AND
Sorry, I meant suggest to search for 'soft' in the dictionary file not
'short'
grep -i ,\'soft\', *.script
On Sat, Aug 1, 2020 at 7:47 PM Jeffrey Miller wrote:
> Hi Peter,
>
> To my knowledge, there isn't any drastic difference in the behavior of the
> dictionary gui creator and the way the sno
Hi Peter,
To my knowledge, there isn't any drastic difference in the behavior of the
dictionary gui creator and the way the sno_rx dictionary was created. I
originally thought there was, but I realized the difference was that I had
not installed all of UMLS to my machine (just the vocabularies I w
Hi All
Having created a new dictionary from the 2020AA UMLS and added Genes and
Receptors to the dictionary-creator's default selections, I have a curious
problem where cTakes now assigns the most bizarre acronyms to ordinary
words used in POS contexts where it shouldn't find Mentions.
Here are
sion.
Thanks,
Sean
From: Jeffrey Miller
Sent: Friday, July 31, 2020 12:44 PM
To: dev@ctakes.apache.org
Subject: Re: Problem trying to load a custom dictionary [EXTERNAL] [EXTERNAL]
* External Email - Caution *
How would I go about getting edit access to the Wiki (is that the p
> > > > The wiki needs additional and more thorough information. If
> anybody
> > > can
> > > > > volunteer to work on it I (and future users) would really
> appreciate
> > > it!
> > > > >
> > > > > Thanks,
> &
> > > > volunteer to work on it I (and future users) would really appreciate
> > it!
> > > >
> > > > Thanks,
> > > > Sean
> > > >
> > > >
> > > >
> > > > Fro
> Thanks,
> > > Sean
> > >
> > >
> > >
> > > From: Peter Abramowitsch
> > > Sent: Thursday, July 30, 2020 9:02 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: Problem trying to
Cheers!
From: gandhi rajan
Sent: Friday, July 31, 2020 10:33 AM
To: dev@ctakes.apache.org
Subject: Re: Problem trying to load a custom dictionary [EXTERNAL] [EXTERNAL]
* External Email - Caution *
Hi Peter,
We can work together on this if you are
can
> > volunteer to work on it I (and future users) would really appreciate it!
> >
> > Thanks,
> > Sean
> >
> >
> >
> > From: Peter Abramowitsch
> > Sent: Thursday, July 30, 2020 9:02 PM
&
itsch
> Sent: Thursday, July 30, 2020 9:02 PM
> To: dev@ctakes.apache.org
> Subject: Re: Problem trying to load a custom dictionary [EXTERNAL]
>
> * External Email - Caution *
>
>
> Thanks Jeff
>
> That worked!
>
> Seems like something that should get fixed in the PiperCreato
rying to load a custom dictionary [EXTERNAL]
* External Email - Caution *
Thanks Jeff
That worked!
Seems like something that should get fixed in the PiperCreator and in the
documentation.
With a life of assuming that every mistake is my own error, the last thing
I would have expected
tionary location is
> LookupXml instead of DictionaryDescriptor
>
> Jeff
>
> On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch <
> pabramowit...@gmail.com>
> wrote:
>
> > A couple of questions about installing a custom dictionary in lookup
> fast.
> > I hope I&
Descriptor
Jeff
On Thu, Jul 30, 2020 at 6:49 PM Peter Abramowitsch
wrote:
> A couple of questions about installing a custom dictionary in lookup fast.
> I hope I'm not too far off the track.
>
> I've used the dictionary creator with a UMLS install to create the
> dictionary
A couple of questions about installing a custom dictionary in lookup fast.
I hope I'm not too far off the track.
I've used the dictionary creator with a UMLS install to create the
dictionary script, prop file, and xml file in my ctakes resources tree
1. Do I have to manually run this
?
> Basically it’s a one-to-one mapping between CUI and PREFTERM . Correct me
> if am wrong on this understanding.
>
>
>
>
>
> Thanks & Regards
>
> [image: cid:D3145E69-CD94-48C1-877F-5134EEAFB598]
>
> *Abad Ayyub*
>
> Vnet: 406170 | Cell : +91-944
Friday, May 29, 2020 9:25 PM
To: dev@ctakes.apache.org
Cc: u...@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating/Adding values to the
existing dictionary in cTAKES
[External]
Hello Abad,
The short answer is, yes, the sno_rx_16ab can be "hacked". A couple of c
not recogonised by cTAKES. I see there are some
>> filters working on top of the available entries in dictionary(ctakes-gui
>> and ctake-gui-res). Will that be because of these filters the tokens are
>> not recognized as expected. Could you pls. share us what exactly these
>>
,RINDEX,TCOUNT and PREFTERM. Is it fine if I can give any random value
> for the TUI/CUI/RINDEX/TCOUNT. I could also see options to create custom
> bsv dictionaries but couldn’t see much documentation for it. Kindly advise
> which is the better option from the below 3.
>
>
>
> o G
e if I can give any random value for the
TUI/CUI/RINDEX/TCOUNT. I could also see options to create custom bsv
dictionaries but couldn't see much documentation for it. Kindly advise which is
the better option from the below 3.
o Generate a custom dictionary using METAMORPHOSYS UML installat
t you never know.
Sean
From: Chahal Arora
Sent: Wednesday, December 27, 2017 3:59 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql [EXTERNAL]
Hi Sean,
I am not trying to run it with multiple threads and in fact, I haven't changed
lto:chahal.ar...@raxa.com]
> Sent: Wednesday, December 27, 2017 7:53 AM
> To: dev@ctakes.apache.org
> Subject: Re: Custom Dictionary connected to mysql [EXTERNAL]
>
> Hi Gandhi, Sean, and James
>
> Thank you all for your help.
>
> It ran fine but after some time, I started gettin
increases.
Sean
-Original Message-
From: Chahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Wednesday, December 27, 2017 7:53 AM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql [EXTERNAL]
Hi Gandhi, Sean, and James
Thank you all for your help.
It ran fine but
you modify your database.
> > > Sean
> > >
> > >
> > > -Original Message-
> > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> > > Sent: Thursday, December 21, 2017 11:06 AM
> > > To: dev@ctakes.apache.org
[mailto:gandhi.natara...@arisglobal.com]
> > Sent: Thursday, December 21, 2017 11:06 AM
> > To: dev@ctakes.apache.org
> > Subject: RE: Custom Dictionary connected to mysql [EXTERNAL]
> >
> > I feel Sean and Tim will be the right persons to answer this.
> >
> >
>
you are ok with
> the case insensitivity then I propose that you modify your database.
> Sean
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Thursday, December 21, 2017 11:06 AM
> To: dev@ctakes.apache.org
>
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, December 21, 2017 11:06 AM
To: dev@ctakes.apache.org
Subject: RE: Custom Dictionary connected to mysql [EXTERNAL]
I feel Sean and Tim will be the right persons to answer this
I feel Sean and Tim will be the right persons to answer this.
Regards,
Gandhi
-Original Message-
From: Chahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Thursday, December 21, 2017 7:32 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql
Hi Gandhi, Thank you
solete now and request you to consider only ctakes-web-rest
> module in https://github.com/GoTeamEpsilon/ctakes-rest-
> service/tree/master/ctakes-web-rest
>
> Regards,
> Gandhi
>
> From: Chahal Arora [mailto:chahal.ar...@raxa.com]
> Sent: Tuesday, December 19, 2017 8:20 PM
>
ahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Tuesday, December 19, 2017 8:20 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql
Hi Gandhi,
With updated customDictionary.xml all errors were gone.
I am not sure about the schema of the tables used. I have taken refe
rrors in tomcat console?
>
> Regards,
> Gandhi
>
> From: Chahal Arora [mailto:chahal.ar...@raxa.com]
> Sent: Tuesday, December 19, 2017 6:09 PM
> To: dev@ctakes.apache.org
> Subject: Re: Custom Dictionary connected to mysql
>
> Hi,
>
> I have updated the customDiction
Not able to see any tomcat logs attached.
Do you see any errors in tomcat console?
Regards,
Gandhi
From: Chahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Tuesday, December 19, 2017 6:09 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql
Hi,
I have updated the
gt; I was working on moving the terms from custom dictionary BSV file to MySQL
> database in LabValueFinder. I am able to connect to the database but not
> sure about the database schema.
>
> Is there an example available where the custom dictionary is connected to
> mysql database
Hi All,
I was working on moving the terms from custom dictionary BSV file to MySQL
database in LabValueFinder. I am able to connect to the database but not
sure about the database schema.
Is there an example available where the custom dictionary is connected to
mysql database instead of a bsv
Hi Sean,
Now it works like a charm. Thanks again for your assistance.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, November 30, 2017 2:28 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file
, November 29, 2017 3:27 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Sean,
I was able to make the custom dictionary XML work with "LookupXml" parameter.
But I face another issue in the rest implementation in this new approach using
Piper
Hi Sean,
I was able to make the custom dictionary XML work with "LookupXml" parameter.
But I face another issue in the rest implementation in this new approach using
PiperFileReader. If I use the following lines of code, for each post request
it makes a db connection once again
...@childrens.harvard.edu]
Sent: Wednesday, November 22, 2017 1:21 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Gandhi,
You don't need to add that code. There is already a parameter named
"LookupXml" that can be used.
That being said
: Wednesday, November 22, 2017 1:21 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Gandhi,
You don't need to add that code. There is already a parameter named
"LookupXml" that can be used.
That being said, I just took a look at the code in
sponse from the HtmlTextWriter,
but I don't know how quick and easy that would be to implement.
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 1:36 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom D
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Gandhi,
You don't need to have sno_rx_16ab* . I don't know exactly how you are
configured, but if you have another dictionary that you want to use instead of
the default sno_rx then you ju
Cheers!
-Original Message-
From: Sirisha Pulivarthi [mailto:sirisha_pulivar...@horizonblue.com.INVALID]
Sent: Tuesday, November 21, 2017 10:48 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi
We can point to the custom xml file explicitly
lay/CTAKES/Dictionary+Creator+GUI
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 10:44 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Sean,
When we try
custom Dictionary Descriptor file [EXTERNAL]
Hi Sean,
When we try to deploy cTAKES as web application, it always looks for
sno_rx_16ab.xml by default on server start. So do you mean we should also have
sno_rx_16ab.xml as well as custom xml file in the resources folder all the time?
Regards,
Gandhi
, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 8:42 PM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Sandeep,
Adding a custom dictionary should never require code modification.
The dictionary creator gui will create
Hi Sandeep,
Adding a custom dictionary should never require code modification.
The dictionary creator gui will create a custom dictionary and its .xml
configuration file and place them in your ctakes resources/ directory. No code
changes necessary.
https://cwiki.apache.org/confluence/display
Hi,
Is there currently any way to use a custom dictionary descriptor file without
making changes to the code or by rebuilding the ctakes-dictionary-lookup-fast
jar file.
Regards,
Sandeep
This email and any files transmitted with it are confidential and intended
solely for the use of the
Hi Kathy,
When you use the dictionary generator GUI to generate the custom dictionary, it
will create a XML file under
\resources\org\apache\ctakes\dictionary\lookup\fast folder. Say fo
r example, while generating custom dictionary if you would have given the name
as 'customdictionary&#
thew Vita [mailto:matthewvit...@gmail.com]
>> Sent: Wednesday, October 11, 2017 11:00 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: HSQLDB out of memory with custom dictionary
>>
>> Hi Kathy and Gandhi,
>>
>> I started to put together a more formal solut
me know if you are looking for any specific
> additional info.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Wednesday, October 11, 2017 11:00 AM
> To: dev@ctakes.apache.org
> Subject: Re: HSQLDB ou
11, 2017 11:00 AM
To: dev@ctakes.apache.org
Subject: Re: HSQLDB out of memory with custom dictionary
Hi Kathy and Gandhi,
I started to put together a more formal solution for this here:
https://github.com/GoTeamEpsilon/cTAKES-HSQLDB-to-MySQL-Dictionary - It is not
perfect but it makes things a
ment on performance comparison
> as I have no clue on this.
>
>
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Kathy Ferro [mailto:healthcare1...@gmail.com]
> Sent: Tuesday, October 10, 2017 9:26 PM
> To: dev@ctakes.apache.org
> Subject: Re: HS
-Original Message-
From: Kathy Ferro [mailto:healthcare1...@gmail.com]
Sent: Tuesday, October 10, 2017 9:26 PM
To: dev@ctakes.apache.org
Subject: Re: HSQLDB out of memory with custom dictionary
Gandhi,
My name is Kathy Ferro.
Matthew and I are trying to accomplish the thing. I got the scripts loaded
into
split the file. This is the easiest approach I
> feel.
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Tuesday, October 10, 2017 10:47 AM
> To: dev@ctakes.apache.org
> Subject: Re: HSQLDB out of memory with
with custom dictionary
Gandhi,
I really appreciate this information. I have started working out the schema and
plan on writing a program that will automatically prepare a script to work with
MySQL. Work in progress. Can you do a quick review of my MySQL schema so far?
CREATE SCHEMA CTAKES_DATA;
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Matthew Vita [mailto:matthewvit...@gmail.com]
> Sent: Monday, October 09, 2017 10:41 AM
> To: dev@ctakes.apache.org
> Subject: Re: HSQLDB out of memory with custom dictionary
>
> Gandhi,
>
> Thank you
hewvit...@gmail.com]
Sent: Monday, October 09, 2017 10:41 AM
To: dev@ctakes.apache.org
Subject: Re: HSQLDB out of memory with custom dictionary
Gandhi,
Thank you for the reply. Do you have any documentation on how to accomplish
this?
Thanks,
Matthew Vita
www.matthewvita.com
On Sun, Oct 8, 2017
Sunday, October 08, 2017 6:02 AM
> To: dev@ctakes.apache.org
> Subject: HSQLDB out of memory with custom dictionary
>
> Hi Sean, Tim, cTAKES Community,
>
> I have put together what I am considering a pretty standard dictionary
> with sources from the following:
>
>
>-
&g
: Sunday, October 08, 2017 6:02 AM
To: dev@ctakes.apache.org
Subject: HSQLDB out of memory with custom dictionary
Hi Sean, Tim, cTAKES Community,
I have put together what I am considering a pretty standard dictionary with
sources from the following:
-
MEDLINEPLUS
-
MSH
-
NCI
Hi Sean, Tim, cTAKES Community,
I have put together what I am considering a pretty standard dictionary with
sources from the following:
-
MEDLINEPLUS
-
MSH
-
NCI
-
NDFRT
-
CHV
-
CSP
-
ICPC2P
-
MEDCIN
-
SNOMED
-
RXNORM
-
Hi,
I am trying to build a custom dictionary (our own, and not UMLS subset one) and
below are steps how far we reached.
1. Used a program to develop Lucene form of custom dictionary.
Output - LuceneIndexDirectory
2. Made changes to LookupDESC.XML file to configure our own
e .bsv paths in the
xml files. I thought that I had fixed that ...
Sean
-Original Message-
From: Kumar, Avanish [mailto:avanish.ku...@optum.com]
Sent: Tuesday, June 20, 2017 3:52 AM
To: dev@ctakes.apache.org
Subject: Custom Dictionary [EXTERNAL]
Hi,
I want to make a custom dictio
Hi,
I want to make a custom dictionary using pipe delimited file and configure
the lookup-descriptor to lookup from that file. Do anyone have any idea about
how to do that? I had searched about it but couldn't find a detailed
description on that.
Thanks,
Avanish
This e-mail, incl
" and then tried to connect to the DB by changing
> > the
> > > "Type" to "HSQL Database Engine Standalone" and then setting the URL to
> > > point to my custom dictionary directory. It throws a SQLException that
> > says
> > >
o "HSQL Database Engine Standalone" and then setting the URL to
> > point to my custom dictionary directory. It throws a SQLException that
> says
> > "wrong database file version". Is there some other step I'm missing?
> >
> > - Dave
> >
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