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Posted to dev@ctakes.apache.org by Peter Abramowitsch <pa...@gmail.com> on 2020/07/22 21:15:58 UTC
obtaining the UMLS set for the dictionary creator
I've been trying to discover what directory the dictionary creator wants to
see for "UMLS Installation" Although I have the dictionary and lvg
folders, inside ctakes-4.0-resources-bin.zip I don't see any folder that
the dictionary creator is happy with.
When I look for RRF files in my running installation, the only ones I see
are in the ytex folder and they're tiny. Of course the Snomed a-b folder
is there,
I remember downloading the UMLS back 2014 and creating a dictionary then, I
cannot find a link to the umls install I need for the dictionary creator
now?
Can you help?
I've tried every folder from here to the top of the
ctakes-4.0-resources-bin tree.
[image: image.png]
Re: obtaining the UMLS set for the dictionary creator
Posted by Peter Abramowitsch <pa...@gmail.com>.
Thanks Ghandi
I really appreciate the details.
P.
On Wed, Jul 22, 2020 at 10:18 PM gandhi rajan <ga...@gmail.com>
wrote:
> Hi Peter,
>
> To add more info, step by step info on UMLS installation is available in
> the link -
>
> http://blog.appliedinformaticsinc.com/getting-started-with-metamorphosys-the-umls-installation-tool/
>
> Once installed, refer -
> https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
> and Select a *UMLS installation* directory as
> <umls_root_dir>/<umls_download_version>/META (in my case
> umls_root_dir\2020AA\META).
>
> After dictionary creation, the SQL scripts and custom dictionary XML will
> be available under
> <ctakes_root_dir>\resources\org\apache\ctakes\dictionary\lookup\fast
> folder.
>
> Hope it helps.
>
> On Thu, Jul 23, 2020 at 3:16 AM Peter Abramowitsch <
> pabramowitsch@gmail.com>
> wrote:
>
> > Thank you. That's helpful. The last time I did this years ago, the tool
> > wasn't available and I just remember downloading some huge files. It's
> > only mentioned in passing in two Ctakes Wiki pages - and not in
> association
> > with the dictionary creator. whereas the resources file, which is
> > mentioned there has just the pre-built fast lookup.
> >
> >
> >
> > Peter
> >
> > On Wed, Jul 22, 2020 at 2:39 PM Thomas W Loehfelm
> > <tw...@ucdavis.edu.invalid> wrote:
> >
> > > If you have downloaded and created a local UMLS installation using the
> > > MetamorphoSys tool you should end up with a directory structure
> something
> > > like:
> > > ../../umls/2020AA/META/{all of the various .RRF files}
> > >
> > > In that case, you want to point the DictionaryCreator tool to the
> 2020AA
> > > directory, i.e. the one that contains the META directory.
> > >
> > > From: Peter Abramowitsch <pa...@gmail.com>
> > > Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> > > Date: Wednesday, July 22, 2020 at 2:17 PM
> > > To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> > > Subject: obtaining the UMLS set for the dictionary creator
> > >
> > > I've been trying to discover what directory the dictionary creator
> wants
> > > to see for "UMLS Installation" Although I have the dictionary and
> > lvg
> > > folders, inside ctakes-4.0-resources-bin.zip I don't see any folder
> that
> > > the dictionary creator is happy with.
> > >
> > > When I look for RRF files in my running installation, the only ones I
> > see
> > > are in the ytex folder and they're tiny. Of course the Snomed a-b
> > folder
> > > is there,
> > >
> > > I remember downloading the UMLS back 2014 and creating a dictionary
> then,
> > > I cannot find a link to the umls install I need for the dictionary
> > creator
> > > now?
> > >
> > > Can you help?
> > >
> > > I've tried every folder from here to the top of the
> > > ctakes-4.0-resources-bin tree.
> > >
> > > [cid:ii_kcxv5co80]
> > > **CONFIDENTIALITY NOTICE** This e-mail communication and any
> attachments
> > > are for the sole use of the intended recipient and may contain
> > information
> > > that is confidential and privileged under state and federal privacy
> laws.
> > > If you received this e-mail in error, be aware that any unauthorized
> use,
> > > disclosure, copying, or distribution is strictly prohibited. If you
> > > received this e-mail in error, please contact the sender immediately
> and
> > > destroy/delete all copies of this message.
> > >
> >
>
>
> --
> Regards,
> Gandhi
>
> "The best way to find urself is to lose urself in the service of others
> !!!"
>
Re: obtaining the UMLS set for the dictionary creator
Posted by gandhi rajan <ga...@gmail.com>.
Hi Peter,
To add more info, step by step info on UMLS installation is available in
the link -
http://blog.appliedinformaticsinc.com/getting-started-with-metamorphosys-the-umls-installation-tool/
Once installed, refer -
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
and Select a *UMLS installation* directory as
<umls_root_dir>/<umls_download_version>/META (in my case
umls_root_dir\2020AA\META).
After dictionary creation, the SQL scripts and custom dictionary XML will
be available under
<ctakes_root_dir>\resources\org\apache\ctakes\dictionary\lookup\fast folder.
Hope it helps.
On Thu, Jul 23, 2020 at 3:16 AM Peter Abramowitsch <pa...@gmail.com>
wrote:
> Thank you. That's helpful. The last time I did this years ago, the tool
> wasn't available and I just remember downloading some huge files. It's
> only mentioned in passing in two Ctakes Wiki pages - and not in association
> with the dictionary creator. whereas the resources file, which is
> mentioned there has just the pre-built fast lookup.
>
>
>
> Peter
>
> On Wed, Jul 22, 2020 at 2:39 PM Thomas W Loehfelm
> <tw...@ucdavis.edu.invalid> wrote:
>
> > If you have downloaded and created a local UMLS installation using the
> > MetamorphoSys tool you should end up with a directory structure something
> > like:
> > ../../umls/2020AA/META/{all of the various .RRF files}
> >
> > In that case, you want to point the DictionaryCreator tool to the 2020AA
> > directory, i.e. the one that contains the META directory.
> >
> > From: Peter Abramowitsch <pa...@gmail.com>
> > Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> > Date: Wednesday, July 22, 2020 at 2:17 PM
> > To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> > Subject: obtaining the UMLS set for the dictionary creator
> >
> > I've been trying to discover what directory the dictionary creator wants
> > to see for "UMLS Installation" Although I have the dictionary and
> lvg
> > folders, inside ctakes-4.0-resources-bin.zip I don't see any folder that
> > the dictionary creator is happy with.
> >
> > When I look for RRF files in my running installation, the only ones I
> see
> > are in the ytex folder and they're tiny. Of course the Snomed a-b
> folder
> > is there,
> >
> > I remember downloading the UMLS back 2014 and creating a dictionary then,
> > I cannot find a link to the umls install I need for the dictionary
> creator
> > now?
> >
> > Can you help?
> >
> > I've tried every folder from here to the top of the
> > ctakes-4.0-resources-bin tree.
> >
> > [cid:ii_kcxv5co80]
> > **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments
> > are for the sole use of the intended recipient and may contain
> information
> > that is confidential and privileged under state and federal privacy laws.
> > If you received this e-mail in error, be aware that any unauthorized use,
> > disclosure, copying, or distribution is strictly prohibited. If you
> > received this e-mail in error, please contact the sender immediately and
> > destroy/delete all copies of this message.
> >
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
Re: obtaining the UMLS set for the dictionary creator
Posted by Peter Abramowitsch <pa...@gmail.com>.
Thank you. That's helpful. The last time I did this years ago, the tool
wasn't available and I just remember downloading some huge files. It's
only mentioned in passing in two Ctakes Wiki pages - and not in association
with the dictionary creator. whereas the resources file, which is
mentioned there has just the pre-built fast lookup.
Peter
On Wed, Jul 22, 2020 at 2:39 PM Thomas W Loehfelm
<tw...@ucdavis.edu.invalid> wrote:
> If you have downloaded and created a local UMLS installation using the
> MetamorphoSys tool you should end up with a directory structure something
> like:
> ../../umls/2020AA/META/{all of the various .RRF files}
>
> In that case, you want to point the DictionaryCreator tool to the 2020AA
> directory, i.e. the one that contains the META directory.
>
> From: Peter Abramowitsch <pa...@gmail.com>
> Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> Date: Wednesday, July 22, 2020 at 2:17 PM
> To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> Subject: obtaining the UMLS set for the dictionary creator
>
> I've been trying to discover what directory the dictionary creator wants
> to see for "UMLS Installation" Although I have the dictionary and lvg
> folders, inside ctakes-4.0-resources-bin.zip I don't see any folder that
> the dictionary creator is happy with.
>
> When I look for RRF files in my running installation, the only ones I see
> are in the ytex folder and they're tiny. Of course the Snomed a-b folder
> is there,
>
> I remember downloading the UMLS back 2014 and creating a dictionary then,
> I cannot find a link to the umls install I need for the dictionary creator
> now?
>
> Can you help?
>
> I've tried every folder from here to the top of the
> ctakes-4.0-resources-bin tree.
>
> [cid:ii_kcxv5co80]
> **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments
> are for the sole use of the intended recipient and may contain information
> that is confidential and privileged under state and federal privacy laws.
> If you received this e-mail in error, be aware that any unauthorized use,
> disclosure, copying, or distribution is strictly prohibited. If you
> received this e-mail in error, please contact the sender immediately and
> destroy/delete all copies of this message.
>
Re: obtaining the UMLS set for the dictionary creator
Posted by Thomas W Loehfelm <tw...@ucdavis.edu.INVALID>.
If you have downloaded and created a local UMLS installation using the MetamorphoSys tool you should end up with a directory structure something like:
../../umls/2020AA/META/{all of the various .RRF files}
In that case, you want to point the DictionaryCreator tool to the 2020AA directory, i.e. the one that contains the META directory.
From: Peter Abramowitsch <pa...@gmail.com>
Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
Date: Wednesday, July 22, 2020 at 2:17 PM
To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
Subject: obtaining the UMLS set for the dictionary creator
I've been trying to discover what directory the dictionary creator wants to see for "UMLS Installation" Although I have the dictionary and lvg folders, inside ctakes-4.0-resources-bin.zip I don't see any folder that the dictionary creator is happy with.
When I look for RRF files in my running installation, the only ones I see are in the ytex folder and they're tiny. Of course the Snomed a-b folder is there,
I remember downloading the UMLS back 2014 and creating a dictionary then, I cannot find a link to the umls install I need for the dictionary creator now?
Can you help?
I've tried every folder from here to the top of the ctakes-4.0-resources-bin tree.
[cid:ii_kcxv5co80]
**CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message.