Hi,
I downloaded Latest umls version, and I want to know how to make ctakes
work with icd10 and icd9.
Thanks
Hi Alaa,
You need to create a resource off the terminology/ontology you want to use (in
this case ICD9 or ICD10). Then run that resource with cTAKES for the fast
dictionary lookup. There is cTAKES code and some documentation on how to create
that resource. By default, cTAKES runs with a resource
Hi Alaa,
The -shortest- answer is that you'll need to run the dictionary creation tool.
There are instructions in older devlist threads. By default the dictionary
creation tool does add icd9 and icd10 tables to the dictionary. The problem is
that in Umls 2011AB those codes weren't very well
This seems like a pretty common request and with such an old version of
UMLS database shipped with cTAKES it's only going to get worse. I've been
wanting to build a dictionary using the latest UMLS release (as well as a
custom database), so would be happy to write up the steps as I go through
it. T
Not to perpetuate the instructions again but I sent these out not long ago when
I was going through the process and Sean was helping me.
1. Change /data/default/CtakesSources.txt from "SNOMEDCT" to
"SNOMEDCT_US"
2. Copy ctakesumls.properties and ctakesumls.script from memdbtempla
Yeah, I'm actually building a 2015AB version this very moment. I am going to
do a little testing and then I'll check it into sourceforge. When I'm done
I'll email the link.
Sean
-Original Message-
From: David Kincaid [mailto:kincaid.d...@gmail.com]
Sent: Tuesday, December 08, 2015 12
Hi Reena,
If you search for "ProcedureMention" in the attached output xml, you
should be able to find the Procedures (plus the FSArray of the
associated Concepts) that were extracted...
Or am I missing something...
--Pei
On Mon, Dec 7, 2015 at 12:40 AM, Reena Duggal
wrote:
> Sorry, I attached the
Hi Dave,
If you happen to still have the instructions,
I think it would be great to share what you have on the wiki as it seems to be
a common request (let me know if you need write access).
—Pei
> On Dec 8, 2015, at 12:47 PM, David Kincaid wrote:
>
> This seems like a pretty common request a
Hi Brandon, thanks for finding and forwarding the instructions!
I have checked in two new hsqldb dictionaries, both from the 2015AB version of
the UMLS. They both have codes for snomedct_us, rxnorm, icd9cm and icd10pcs -
as well as the usual cui, tui, preferred term mappings.
One uses cuis fil
The recent discussion over dictionary building, and someone pointing out
it has come up several times, made me think that maybe we should use the
blog space that apache provides. It could be used for write-ups of
things that are not quite as formal as "documentation" but would benefit
from being wr
I like the blog approach.
I think it will help direct the creation of various guide-type documentation
going forward.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com
> On Dec 8, 2015, at 4:41 PM, Miller, Timot
Thanks, Sean! It's great that cTAKES may soon have an up to date database
out of the box. Hopefully it will cut down on the need for many to build
their own DB's. Thank you much for doing that.
Unfortunately, I still will need to build a custom one for us. I work in
veterinary medicine so I need t
That is a great idea! I'd be happy to help provide some content as someone
who has been trying to use cTAKES inside other projects. As I mentioned
previously I am working in veterinary medicine which has just enough
peculiarities to make cTAKES out of the box a challenge (although it is
much better
Hi David,
For step 1 the file may have been updated. At the time I wrote the instructions
only SNOMED was listed in the file.
For step 2 yes, this is a new directory location where the new dictionary will
be created.
Yes you need to build or use the one Sean built and has in the repo.
Sorry t
+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 has been trying to use cT
Hi Dave,
I'm always happy to see interest in our stuff!
>Step 1
I built the tool to be able to build a dictionary using anything in the umls -
snomed, icd9, hpo, etc. so using the veterinary extension shouldn't be a
problem. You just add it to the CtakesSources file (or create an alternate
fi
Fantastic idea
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Tuesday, December 08, 2015 4:41 PM
To: dev@ctakes.apache.org
Subject: ctakes blog
The recent discussion over dictionary building, and someone pointing out it has
come up several t
Thank you very very much Finan,
I am still very nooob to ctakes so please bare with me.
1- Could you please post detailed instructions on how you built the
dictionaries ? or give as much as you can examples on the steps ?
2- what did you upload exactly, I only see a script and properties files
wh
Hi Alaa,
I have a slightly updated version of the dictionary tool - only a couple of
changes but I should check them in nonetheless after I've cleaned up a bit.
I followed the process as emailed by Brandon Geise around 12:51 today. My
command parameters were:
[DictionaryCreator2]
-umls C:\S
Hopefully of use a large number of UMLS concepts are publicly
availability to download without UMLS license for sources in MedGen, which
represents 300k+ concepts, including many concepts and relationships in
SNOMED-CT, MESH, NCI Metathausurus (MTH), etc.
You can download UMLS dictionaries fo
I'd be interested in contributing to making the dictionary tool more user
friendly with a GUI.
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, December 08, 2015 6:12 PM
To: dev@ctakes.apache.org
Subject: RE: ctakes with icd10
I would definitely be happy to work with you!
I've sent some questions to your personal email to prevent devlist spamming.
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Tuesday, December 08, 2015 10:36 PM
To: dev@ctakes.apache.org
Subject: RE: ctakes
Brandon,
That sounds great!
Please open a Jira ticket for any contributions (anyone should be able
to create a Jira account). There are some legal items built into the
ASF Jira attachments for accepting contributions/donations.
It will also credit the contributors with the merit appropriately.
Any
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