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Posted to user@ctakes.apache.org by Guy Engelhard <gu...@algotec.co.il> on 2016/08/04 13:20:34 UTC
ctakessnorx and the fast pipeline
Hello all,
I'd like to modify some of the dictionary terms in the fast clinical pipeline.
The only reference I found online is the following thread:
http://dev.ctakes.apache.narkive.com/kvWEUaRR/ctakessorx-for-aggregateplaintextfastumlsprocessor-xml
which didn't help too much.
Do you know if there is some more documentation on how to change/build a dictionary for the fast pipeline?
Thanks,
Guy Engelhard
Re: [External] Re: ctakessnorx and the fast pipeline
Posted by nishant kumar <ku...@gmail.com>.
Following is another useful mail related to the dictionary-gui tool:
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201601.mbox/%3CCA+jqmuyBcv-h67bxg=gummpVkE_khOXpSfRvSqx=jK3pzZ7WGA@mail.gmail.com%3E
thanks
Nishant
On Mon, Aug 8, 2016 at 9:59 AM, Geise, Brandon D. <bd...@geisinger.edu>
wrote:
> I’d also recommend checking out the GUI Sean created.
>
>
>
> https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/
>
>
>
> It most likely will make the process a little easier.
>
>
>
> Thanks,
>
> Brandon
>
>
>
> *From:* Jessica Glover [mailto:glover.jessica.m@gmail.com]
> *Sent:* Friday, August 05, 2016 4:27 PM
> *To:* user@ctakes.apache.org
> *Subject:* [External] Re: ctakessnorx and the fast pipeline
>
>
>
> I found this to be a helpful thread when I used Sean Finan's dictionary
> tool in the cTakes sandbox to create my own dictionary:
>
> http://ctakes.markmail.org/search/?q=fast+dictionary+update#query:fast%
> 20dictionary%20update+page:1+mid:qubgmr65aagpu4z7+state:results
> <https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fctakes.markmail.org%2fsearch%2f%3fq%3dfast%2bdictionary%2bupdate%23query%3afast%2520dictionary%2520update%2bpage%3a1%2bmid%3aqubgmr65aagpu4z7%2bstate%3aresults&data=01%7c01%7cbdgeise%40geisinger.edu%7cdb8fefb5101045bfc8e608d3bd6eea95%7c37d46c567c664402a16055c2313b910d%7c0&sdata=ozDAy%2b77dCj8N4me6iRhE1uqiYlbmt7HYvUa4ET9wDM%3d>
>
>
>
> Before you use the dictionary tool, you will need to create a subset of
> the UMLS Metathesaurus using the Metamorphosys tool, which you can read
> about here:
>
> http://www.ncbi.nlm.nih.gov/books/NBK9683/
> <https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.ncbi.nlm.nih.gov%2fbooks%2fNBK9683%2f&data=01%7c01%7cbdgeise%40geisinger.edu%7cdb8fefb5101045bfc8e608d3bd6eea95%7c37d46c567c664402a16055c2313b910d%7c0&sdata=FKEybPx0ofdV8wNzmzdfpb5doYen9%2b4ryay7UpaXJnc%3d>
>
>
>
> Hopefully that will give you a good starting point.
>
>
>
> Best,
>
> Jessica
>
>
>
>
>
>
>
> On Thu, Aug 4, 2016 at 9:20 AM, Guy Engelhard <gu...@algotec.co.il> wrote:
>
> Hello all,
>
>
>
> I'd like to modify some of the dictionary terms in the fast clinical
> pipeline.
>
>
>
> The only reference I found online is the following thread:
>
>
>
> http://dev.ctakes.apache.narkive.com/kvWEUaRR/ctakessorx-for-
> aggregateplaintextfastumlsprocessor-xml
> <https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fdev.ctakes.apache.narkive.com%2fkvWEUaRR%2fctakessorx-for-aggregateplaintextfastumlsprocessor-xml&data=01%7c01%7cbdgeise%40geisinger.edu%7cdb8fefb5101045bfc8e608d3bd6eea95%7c37d46c567c664402a16055c2313b910d%7c0&sdata=IO0SxMAXU%2bJsRTiVGcM1WVwm3PQFyqCZonJ4KermssQ%3d>
>
>
>
> which didn't help too much.
>
>
>
> Do you know if there is some more documentation on how to change/build a
> dictionary for the fast pipeline?
>
>
>
> Thanks,
>
>
>
> Guy Engelhard
>
>
>
> ------------------------------
>
> IMPORTANT WARNING: The information in this message (and the documents
> attached to it, if any) is confidential and may be legally privileged. It
> is intended solely for the addressee. Access to this message by anyone else
> is unauthorized. If you are not the intended recipient, any disclosure,
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> reliance on it is prohibited and may be unlawful. If you have received this
> message in error, please delete all electronic copies of this message (and
> the documents attached to it, if any), destroy any hard copies you may have
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> Geisinger Health System utilizes an encryption process to safeguard
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RE: [External] Re: ctakessnorx and the fast pipeline
Posted by "Geise, Brandon D." <bd...@geisinger.edu>.
I’d also recommend checking out the GUI Sean created.
https://svn.apache.org/repos/asf/ctakes/sandbox/dictionary-gui/
It most likely will make the process a little easier.
Thanks,
Brandon
From: Jessica Glover [mailto:glover.jessica.m@gmail.com]
Sent: Friday, August 05, 2016 4:27 PM
To: user@ctakes.apache.org
Subject: [External] Re: ctakessnorx and the fast pipeline
I found this to be a helpful thread when I used Sean Finan's dictionary tool in the cTakes sandbox to create my own dictionary:
http://ctakes.markmail.org/search/?q=fast+dictionary+update#query:fast%20dictionary%20update+page:1+mid:qubgmr65aagpu4z7+state:results<https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fctakes.markmail.org%2fsearch%2f%3fq%3dfast%2bdictionary%2bupdate%23query%3afast%2520dictionary%2520update%2bpage%3a1%2bmid%3aqubgmr65aagpu4z7%2bstate%3aresults&data=01%7c01%7cbdgeise%40geisinger.edu%7cdb8fefb5101045bfc8e608d3bd6eea95%7c37d46c567c664402a16055c2313b910d%7c0&sdata=ozDAy%2b77dCj8N4me6iRhE1uqiYlbmt7HYvUa4ET9wDM%3d>
Before you use the dictionary tool, you will need to create a subset of the UMLS Metathesaurus using the Metamorphosys tool, which you can read about here:
http://www.ncbi.nlm.nih.gov/books/NBK9683/<https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fwww.ncbi.nlm.nih.gov%2fbooks%2fNBK9683%2f&data=01%7c01%7cbdgeise%40geisinger.edu%7cdb8fefb5101045bfc8e608d3bd6eea95%7c37d46c567c664402a16055c2313b910d%7c0&sdata=FKEybPx0ofdV8wNzmzdfpb5doYen9%2b4ryay7UpaXJnc%3d>
Hopefully that will give you a good starting point.
Best,
Jessica
On Thu, Aug 4, 2016 at 9:20 AM, Guy Engelhard <gu...@algotec.co.il>> wrote:
Hello all,
I'd like to modify some of the dictionary terms in the fast clinical pipeline.
The only reference I found online is the following thread:
http://dev.ctakes.apache.narkive.com/kvWEUaRR/ctakessorx-for-aggregateplaintextfastumlsprocessor-xml<https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fdev.ctakes.apache.narkive.com%2fkvWEUaRR%2fctakessorx-for-aggregateplaintextfastumlsprocessor-xml&data=01%7c01%7cbdgeise%40geisinger.edu%7cdb8fefb5101045bfc8e608d3bd6eea95%7c37d46c567c664402a16055c2313b910d%7c0&sdata=IO0SxMAXU%2bJsRTiVGcM1WVwm3PQFyqCZonJ4KermssQ%3d>
which didn't help too much.
Do you know if there is some more documentation on how to change/build a dictionary for the fast pipeline?
Thanks,
Guy Engelhard
IMPORTANT WARNING: The information in this message (and the documents attached to it, if any) is confidential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken, or omitted to be taken, in reliance on it is prohibited and may be unlawful. If you have received this message in error, please delete all electronic copies of this message (and the documents attached to it, if any), destroy any hard copies you may have created and notify me immediately by replying to this email. Thank you.
Geisinger Health System utilizes an encryption process to safeguard Protected Health Information and other confidential data contained in external e-mail messages. If email is encrypted, the recipient will receive an e-mail instructing them to sign on to the Geisinger Health System Secure E-mail Message Center to retrieve the encrypted e-mail.
Re: ctakessnorx and the fast pipeline
Posted by Jessica Glover <gl...@gmail.com>.
I found this to be a helpful thread when I used Sean Finan's dictionary
tool in the cTakes sandbox to create my own dictionary:
http://ctakes.markmail.org/search/?q=fast+dictionary+update#query:fast%20dictionary%20update+page:1+mid:qubgmr65aagpu4z7+state:results
Before you use the dictionary tool, you will need to create a subset of the
UMLS Metathesaurus using the Metamorphosys tool, which you can read about
here:
http://www.ncbi.nlm.nih.gov/books/NBK9683/
Hopefully that will give you a good starting point.
Best,
Jessica
On Thu, Aug 4, 2016 at 9:20 AM, Guy Engelhard <gu...@algotec.co.il> wrote:
> Hello all,
>
>
>
> I'd like to modify some of the dictionary terms in the fast clinical
> pipeline.
>
>
>
> The only reference I found online is the following thread:
>
>
>
>
> http://dev.ctakes.apache.narkive.com/kvWEUaRR/ctakessorx-for-aggregateplaintextfastumlsprocessor-xml
>
>
>
> which didn't help too much.
>
>
>
> Do you know if there is some more documentation on how to change/build a
> dictionary for the fast pipeline?
>
>
>
> Thanks,
>
>
>
> Guy Engelhard
>