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Posted to dev@ctakes.apache.org by "Dunlop, Joyce (HP)" <Jo...@va.gov> on 2017/01/17 16:24:44 UTC
New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Developer+Install+Guide.
Merge the version-matching resources ZIP file from http://sourceforge.net/projects/ctakesresources/files/ into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.2.1.1-bin.zip/download> is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES
Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.
Sean F,
We don't currently have a particular interest but trying to gather information for the VA to make their short/long term plans related to CTAKES.
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 12:22 PM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
Thank you for the information on your background and what is being done for/by the VA. That is very interesting and I am very curious to find out what happens after your analyses. Any contribution back to the open source is welcome!
I am in the process of moving the dictionary builder gui into trunk from sandbox. Other than that I am not aware of anything that is moving over from sandbox. Are you interested in any particular project?
Is anybody else out there working on moving something from sandbox to trunk?
Thanks,
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 1:13 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Hi Sean F,
Thanks for the information.
A little background on me and my Group. We have been contracted by the Veteran's administration to get CTAKES/YTEX running within the VA Network.
Our efforts will include:
-Run HP Fortify source code analyzer against the software to bring it into VA's security compliance.
-Evaluating and bring YTEX into 508 Compliance.
-Integrate LEO into the database connections.
The hope would be to release a sanitized version of CTAKE back to the open source community once these activities are complete. Releasing back to open source take some time and has to go through the VA's processes.
We had to start with 3.2.2 because it was a stable release so potentially integrating any changes we make back into the next release may take some effort.
I did notice several packages in the sandbox version of the code. Is there any plans to bring any of those new packages into the trunk?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 11:54 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
> 3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Good question.
One person has volunteered to be a release manager and we at the Boston Children's Hospital nlp group are trying to get some additional hands on the task. There are still outstanding bugs. Ctakes-core is undergoing some changes and should be tested before release. I think that the state is good, but in my opinion the whole app needs to have some end-to-end testing before a major release. At a recent hackathon, 50% of those present could not by themselves get ctakes installed and running even with written instructions. In my mind a release that is not usable is not a release at all, so I think that we need to devote a little effort to usability. Again, that is just my opinion. I have put in time over the past few months to work on making ctakes easier for newcomers and non-developers. As you noticed, a fair amount of online documentation is stale, and it would be great if people volunteered to update it before a release. After that there are just the matters of updating the main website links, publicizing the release, release notes, and a parade with balloons.
It think that everybody out there would be happy if there was a new official, stable and useable release. I also think that we can get one of good quality together within the next 3 months - more quickly if there are volunteers from the community.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 12:32 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Thanks Sean,
3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 10:57 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES [SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Thanks Tim!
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 2:05 PM
To: dev@ctakes.apache.org
Subject: Re: New to CTAKES [SUSPICIOUS] [SUSPICIOUS]
There are new sentence detector and coref modules in sandbox but I've
just graduated the code into the existing ctakes-core and ctakes-
coreference modules once it's ready.
Tim
On Tue, 2017-01-17 at 18:22 +0000, Finan, Sean wrote:
> Hi Joyce,
>
> Thank you for the information on your background and what is being
> done for/by the VA. That is very interesting and I am very curious
> to find out what happens after your analyses. Any contribution back
> to the open source is welcome!
>
> I am in the process of moving the dictionary builder gui into trunk
> from sandbox. Other than that I am not aware of anything that is
> moving over from sandbox. Are you interested in any particular
> project?
>
> Is anybody else out there working on moving something from sandbox to
> trunk?
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 1:13 PM
> To: dev@ctakes.apache.org
> Subject: RE: New to CTAKES
>
> Hi Sean F,
>
> Thanks for the information.
>
> A little background on me and my Group. We have been contracted by
> the Veteran's administration to get CTAKES/YTEX running within the VA
> Network.
>
> Our efforts will include:
>
> -Run HP Fortify source code analyzer against the software to bring it
> into VA's security compliance.
> -Evaluating and bring YTEX into 508 Compliance.
> -Integrate LEO into the database connections.
>
> The hope would be to release a sanitized version of CTAKE back to
> the open source community once these activities are
> complete. Releasing back to open source take some time and has to go
> through the VA's processes.
>
> We had to start with 3.2.2 because it was a stable release so
> potentially integrating any changes we make back into the next
> release may take some effort.
>
> I did notice several packages in the sandbox version of the code. Is
> there any plans to bring any of those new packages into the trunk?
>
> Thanks,
> Joyce
>
>
>
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Tuesday, January 17, 2017 11:54 AM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES
>
> >
> > 3.2.3 is still considered a snapshot - do you have any feeling
> > when/if it will be released?
> Good question.
>
> One person has volunteered to be a release manager and we at the
> Boston Children's Hospital nlp group are trying to get some
> additional hands on the task. There are still outstanding
> bugs. Ctakes-core is undergoing some changes and should be tested
> before release. I think that the state is good, but in my opinion
> the whole app needs to have some end-to-end testing before a major
> release. At a recent hackathon, 50% of those present could not by
> themselves get ctakes installed and running even with written
> instructions. In my mind a release that is not usable is not a
> release at all, so I think that we need to devote a little effort to
> usability. Again, that is just my opinion. I have put in time over
> the past few months to work on making ctakes easier for newcomers and
> non-developers. As you noticed, a fair amount of online
> documentation is stale, and it would be great if people volunteered
> to update it before a release. After that there are just the matters
> of updating the main website links, publicizing the release, release
> notes, and a parade with balloons.
>
> It think that everybody out there would be happy if there was a new
> official, stable and useable release. I also think that we can get
> one of good quality together within the next 3 months - more quickly
> if there are volunteers from the community.
>
> Sean
>
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 12:32 PM
> To: dev@ctakes.apache.org
> Subject: RE: New to CTAKES
>
> Thanks Sean,
>
> 3.2.3 is still considered a snapshot - do you have any feeling
> when/if it will be released?
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Tuesday, January 17, 2017 10:57 AM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES
>
> Hi Joyce,
>
> If you are building from source then you should not need to manually
> download the resources. Maven should be doing it for you. Well,
> that is the behavior of 3.2.3 ... I honestly cannot remember what
> 3.2.2 did ...
>
> Otherwise, I think that if the latest was the 3.2.1.1 then that is
> probably the most appropriate for the 3.2.2 release if you want all
> of the resources.
>
> As for building and deploying ytex, I don't have any advice. Perhaps
> some ytex power-user out there can help.
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 11:25 AM
> To: dev@ctakes.apache.org
> Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
> Subject: New to CTAKES
>
> Good Morning,
>
> I am trying to set up a development environment using the source
> release of 3.2.2.
>
> Reading though the documentation on
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org
> _confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-
> 2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67
> GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJx
> xrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
>
> Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=BGxHriTJNPK1gRxPEKQBu7PGq9Gp4vawfMNTqZc4etI&s=bZG6uh8ZKRIKdQdjIvYHpiMHM-OSxMv8l3S80nNNrZU&e=
> .proofpoint.com/v2/url?u=http-
> 3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goW
> BT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0b
> cpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-
> yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your
> ctakes-dictionary-lookup-res project.
>
> ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2> /url?u=https-
> 3A__sourceforge.net_projects_ctakesresources_files_ctakes-
> 2Dresources-2D3.2.1.1-
> 2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCopp
> xeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6
> Zf7uY5l9LJxxrRiiE-
> yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is
> available for download. Is there a 3.2.2 version of the resources?
>
> After reading some of the posts from the email box, and reading the
> documentation on the site above. It looks like the documentation may
> be somewhat dated and not fulling integrated for YTEX.
>
> Would you have any recommendations in advance on how to set up a
> build process for deployment and YTEX database from scratch?
>
> Thanks,
> Joyce
>
>
>
>
>
Re: New to CTAKES [SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
There are new sentence detector and coref modules in sandbox but I've
just graduated the code into the existing ctakes-core and ctakes-
coreference modules once it's ready.
Tim
On Tue, 2017-01-17 at 18:22 +0000, Finan, Sean wrote:
> Hi Joyce,
>
> Thank you for the information on your background and what is being
> done for/by the VA. That is very interesting and I am very curious
> to find out what happens after your analyses. Any contribution back
> to the open source is welcome!
>
> I am in the process of moving the dictionary builder gui into trunk
> from sandbox. Other than that I am not aware of anything that is
> moving over from sandbox. Are you interested in any particular
> project?
>
> Is anybody else out there working on moving something from sandbox to
> trunk?
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 1:13 PM
> To: dev@ctakes.apache.org
> Subject: RE: New to CTAKES
>
> Hi Sean F,
>
> Thanks for the information.
>
> A little background on me and my Group. We have been contracted by
> the Veteran's administration to get CTAKES/YTEX running within the VA
> Network.
>
> Our efforts will include:
>
> -Run HP Fortify source code analyzer against the software to bring it
> into VA's security compliance.
> -Evaluating and bring YTEX into 508 Compliance.
> -Integrate LEO into the database connections.
>
> The hope would be to release a sanitized version of CTAKE back to
> the open source community once these activities are
> complete. Releasing back to open source take some time and has to go
> through the VA's processes.
>
> We had to start with 3.2.2 because it was a stable release so
> potentially integrating any changes we make back into the next
> release may take some effort.
>
> I did notice several packages in the sandbox version of the code. Is
> there any plans to bring any of those new packages into the trunk?
>
> Thanks,
> Joyce
>
>
>
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Tuesday, January 17, 2017 11:54 AM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES
>
> >
> > 3.2.3 is still considered a snapshot - do you have any feeling
> > when/if it will be released?
> Good question.
>
> One person has volunteered to be a release manager and we at the
> Boston Children's Hospital nlp group are trying to get some
> additional hands on the task. There are still outstanding
> bugs. Ctakes-core is undergoing some changes and should be tested
> before release. I think that the state is good, but in my opinion
> the whole app needs to have some end-to-end testing before a major
> release. At a recent hackathon, 50% of those present could not by
> themselves get ctakes installed and running even with written
> instructions. In my mind a release that is not usable is not a
> release at all, so I think that we need to devote a little effort to
> usability. Again, that is just my opinion. I have put in time over
> the past few months to work on making ctakes easier for newcomers and
> non-developers. As you noticed, a fair amount of online
> documentation is stale, and it would be great if people volunteered
> to update it before a release. After that there are just the matters
> of updating the main website links, publicizing the release, release
> notes, and a parade with balloons.
>
> It think that everybody out there would be happy if there was a new
> official, stable and useable release. I also think that we can get
> one of good quality together within the next 3 months - more quickly
> if there are volunteers from the community.
>
> Sean
>
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 12:32 PM
> To: dev@ctakes.apache.org
> Subject: RE: New to CTAKES
>
> Thanks Sean,
>
> 3.2.3 is still considered a snapshot - do you have any feeling
> when/if it will be released?
>
> Thanks,
> Joyce
>
> -----Original Message-----
> From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
> Sent: Tuesday, January 17, 2017 10:57 AM
> To: dev@ctakes.apache.org
> Subject: [EXTERNAL] RE: New to CTAKES
>
> Hi Joyce,
>
> If you are building from source then you should not need to manually
> download the resources. Maven should be doing it for you. Well,
> that is the behavior of 3.2.3 ... I honestly cannot remember what
> 3.2.2 did ...
>
> Otherwise, I think that if the latest was the 3.2.1.1 then that is
> probably the most appropriate for the 3.2.2 release if you want all
> of the resources.
>
> As for building and deploying ytex, I don't have any advice. Perhaps
> some ytex power-user out there can help.
>
> Sean
>
> -----Original Message-----
> From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
> Sent: Tuesday, January 17, 2017 11:25 AM
> To: dev@ctakes.apache.org
> Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
> Subject: New to CTAKES
>
> Good Morning,
>
> I am trying to set up a development environment using the source
> release of 3.2.2.
>
> Reading though the documentation on
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org
> _confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-
> 2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67
> GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJx
> xrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
>
> Merge the version-matching resources ZIP file from https://urldefense
> .proofpoint.com/v2/url?u=http-
> 3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goW
> BT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0b
> cpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-
> yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your
> ctakes-dictionary-lookup-res project.
>
> ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2
> /url?u=https-
> 3A__sourceforge.net_projects_ctakesresources_files_ctakes-
> 2Dresources-2D3.2.1.1-
> 2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCopp
> xeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6
> Zf7uY5l9LJxxrRiiE-
> yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is
> available for download. Is there a 3.2.2 version of the resources?
>
> After reading some of the posts from the email box, and reading the
> documentation on the site above. It looks like the documentation may
> be somewhat dated and not fulling integrated for YTEX.
>
> Would you have any recommendations in advance on how to set up a
> build process for deployment and YTEX database from scratch?
>
> Thanks,
> Joyce
>
>
>
>
>
RE: New to CTAKES
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Joyce,
Thank you for the information on your background and what is being done for/by the VA. That is very interesting and I am very curious to find out what happens after your analyses. Any contribution back to the open source is welcome!
I am in the process of moving the dictionary builder gui into trunk from sandbox. Other than that I am not aware of anything that is moving over from sandbox. Are you interested in any particular project?
Is anybody else out there working on moving something from sandbox to trunk?
Thanks,
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 1:13 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Hi Sean F,
Thanks for the information.
A little background on me and my Group. We have been contracted by the Veteran's administration to get CTAKES/YTEX running within the VA Network.
Our efforts will include:
-Run HP Fortify source code analyzer against the software to bring it into VA's security compliance.
-Evaluating and bring YTEX into 508 Compliance.
-Integrate LEO into the database connections.
The hope would be to release a sanitized version of CTAKE back to the open source community once these activities are complete. Releasing back to open source take some time and has to go through the VA's processes.
We had to start with 3.2.2 because it was a stable release so potentially integrating any changes we make back into the next release may take some effort.
I did notice several packages in the sandbox version of the code. Is there any plans to bring any of those new packages into the trunk?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 11:54 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
> 3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Good question.
One person has volunteered to be a release manager and we at the Boston Children's Hospital nlp group are trying to get some additional hands on the task. There are still outstanding bugs. Ctakes-core is undergoing some changes and should be tested before release. I think that the state is good, but in my opinion the whole app needs to have some end-to-end testing before a major release. At a recent hackathon, 50% of those present could not by themselves get ctakes installed and running even with written instructions. In my mind a release that is not usable is not a release at all, so I think that we need to devote a little effort to usability. Again, that is just my opinion. I have put in time over the past few months to work on making ctakes easier for newcomers and non-developers. As you noticed, a fair amount of online documentation is stale, and it would be great if people volunteered to update it before a release. After that there are just the matters of updating the main website links, publicizing the release, release notes, and a parade with balloons.
It think that everybody out there would be happy if there was a new official, stable and useable release. I also think that we can get one of good quality together within the next 3 months - more quickly if there are volunteers from the community.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 12:32 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Thanks Sean,
3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 10:57 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES
Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.
Hi Sean F,
Thanks for the information.
A little background on me and my Group. We have been contracted by the Veteran's administration to get CTAKES/YTEX running within the VA Network.
Our efforts will include:
-Run HP Fortify source code analyzer against the software to bring it into VA's security compliance.
-Evaluating and bring YTEX into 508 Compliance.
-Integrate LEO into the database connections.
The hope would be to release a sanitized version of CTAKE back to the open source community once these activities are complete. Releasing back to open source take some time and has to go through the VA's processes.
We had to start with 3.2.2 because it was a stable release so potentially integrating any changes we make back into the next release may take some effort.
I did notice several packages in the sandbox version of the code. Is there any plans to bring any of those new packages into the trunk?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 11:54 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
> 3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Good question.
One person has volunteered to be a release manager and we at the Boston Children's Hospital nlp group are trying to get some additional hands on the task. There are still outstanding bugs. Ctakes-core is undergoing some changes and should be tested before release. I think that the state is good, but in my opinion the whole app needs to have some end-to-end testing before a major release. At a recent hackathon, 50% of those present could not by themselves get ctakes installed and running even with written instructions. In my mind a release that is not usable is not a release at all, so I think that we need to devote a little effort to usability. Again, that is just my opinion. I have put in time over the past few months to work on making ctakes easier for newcomers and non-developers. As you noticed, a fair amount of online documentation is stale, and it would be great if people volunteered to update it before a release. After that there are just the matters of updating the main website links, publicizing the release, release notes, and a parade with balloons.
It think that everybody out there would be happy if there was a new official, stable and useable release. I also think that we can get one of good quality together within the next 3 months - more quickly if there are volunteers from the community.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 12:32 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Thanks Sean,
3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 10:57 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES [SUSPICIOUS]
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
As Sean mentioned, we the NLP lab at Boston Children's Hospital/Harvard Medical School will be dedicating significant effort in the next several months (=FTE) to make a solid release happen asap. We expect the release within 3 months. As Sean mentioned help from the broader cTAKES community is welcome.
Thank you!
--Guergana
Guergana Savova, PhD, FACMI
Associate Professor
PI Natural Language Processing Lab
Boston Children's Hospital and Harvard Medical School
300 Longwood Avenue
Mailstop: BCH3092
Enders 144.1
Boston, MA 02115
Tel: (617) 919-2972
Fax: (617) 730-0817
Guergana.Savova@childrens.harvard.edu
Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
ctakes.apache.org
thyme.healthnlp.org
cancer.healthnlp.org
share.healthnlp.org
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 12:54 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES [SUSPICIOUS]
> 3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Good question.
One person has volunteered to be a release manager and we at the Boston Children's Hospital nlp group are trying to get some additional hands on the task. There are still outstanding bugs. Ctakes-core is undergoing some changes and should be tested before release. I think that the state is good, but in my opinion the whole app needs to have some end-to-end testing before a major release. At a recent hackathon, 50% of those present could not by themselves get ctakes installed and running even with written instructions. In my mind a release that is not usable is not a release at all, so I think that we need to devote a little effort to usability. Again, that is just my opinion. I have put in time over the past few months to work on making ctakes easier for newcomers and non-developers. As you noticed, a fair amount of online documentation is stale, and it would be great if people volunteered to update it before a release. After that there are just the matters of updating the main website links, publicizing the release, release notes, and a parade with balloons.
It think that everybody out there would be happy if there was a new official, stable and useable release. I also think that we can get one of good quality together within the next 3 months - more quickly if there are volunteers from the community.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 12:32 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Thanks Sean,
3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 10:57 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
> 3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Good question.
One person has volunteered to be a release manager and we at the Boston Children's Hospital nlp group are trying to get some additional hands on the task. There are still outstanding bugs. Ctakes-core is undergoing some changes and should be tested before release. I think that the state is good, but in my opinion the whole app needs to have some end-to-end testing before a major release. At a recent hackathon, 50% of those present could not by themselves get ctakes installed and running even with written instructions. In my mind a release that is not usable is not a release at all, so I think that we need to devote a little effort to usability. Again, that is just my opinion. I have put in time over the past few months to work on making ctakes easier for newcomers and non-developers. As you noticed, a fair amount of online documentation is stale, and it would be great if people volunteered to update it before a release. After that there are just the matters of updating the main website links, publicizing the release, release notes, and a parade with balloons.
It think that everybody out there would be happy if there was a new official, stable and useable release. I also think that we can get one of good quality together within the next 3 months - more quickly if there are volunteers from the community.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 12:32 PM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Thanks Sean,
3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 10:57 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES
Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.
Thanks Sean,
3.2.3 is still considered a snapshot - do you have any feeling when/if it will be released?
Thanks,
Joyce
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 10:57 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES
Posted by "Dunlop, Joyce (HP)" <Jo...@va.gov>.
Sean M,
I will try to work through the process this tomorrow.
Thanks!
Joyce
-----Original Message-----
From: Mullane, Sean *HS [mailto:SPM9R@hscmail.mcc.virginia.edu]
Sent: Tuesday, January 17, 2017 11:10 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Joyce,
This may help, here are some notes I put together when installing YTEX in our Windows/SQL Server test environment. I didn't build from source here, this is just installation (including UMLS). I'm working on writing up these instructions more thoroughly so if you use this please let me know if you find any points of improvement.
Requirements and steps to set up YTEX
These notes refer to the installation instructions at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
1. They suggest installing UMLS in our database
Follow instructions here to install UMLS: https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
-http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is useful when installing from .zip file. The mmsys.zip file needs to be unzipped to access the run64.bat file but also needs to be present as a .zip file for the run64.bat file to read from.
2. Create a database user and schema for use with YTEX 3. Load UMLS into database
-Needed to create ytex.properties file from examples files in the developer/source version of cTAKES
-Needed to change path in ctakes.profile to match version name of CTAKES_HOME directory
-Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to C:\Program Files\Java\jre_Version\bin
-Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
-Need to change table definitions as follows to install UMLS-2016AB:
MRCONSO.CODE varchar(75) -- was varchar(50)
MRDEF.DEF varchar(max) -- was varchar(4000)
MRSAB.VSAB varchar(24) -- was varchar(20)
MRSAT.ATN varchar(64) -- was varchar(50)
MRSAT.ATV varchar(max) -- was varchar(4000) 3. Install cTAKES "as usual"
4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation.
-I believe this step is deprecated - skip to step 6 5. Unzip YTEX Resources (Optional - UTS login required)
-I believe this step is deprecated - skip to step 6
-may be needed for concept graphs and dictionary lookup table for NER 6. Fix the path references in shell script to match your environment 7. Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and specify database connection parameters.
8. Execute the setup script
-Need to use Java 7 - Java 8 errors out
-If SQL errors encountered, appenders can be added to log4j.xml to collect SQL queries
Sean
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 11:57 AM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
Joyce,
This may help, here are some notes I put together when installing YTEX in our Windows/SQL Server test environment. I didn't build from source here, this is just installation (including UMLS). I'm working on writing up these instructions more thoroughly so if you use this please let me know if you find any points of improvement.
Requirements and steps to set up YTEX
These notes refer to the installation instructions at https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
1. They suggest installing UMLS in our database
Follow instructions here to install UMLS: https://cwiki.apache.org/confluence/display/CTAKES/UMLS+MS+SQL+Server+Installation
-http://groups.csail.mit.edu/medg/projects/text/Load_UMLS_mysql.html is useful when installing from .zip file. The mmsys.zip file needs to be unzipped to access the run64.bat file but also needs to be present as a .zip file for the run64.bat file to read from.
2. Create a database user and schema for use with YTEX
3. Load UMLS into database
-Needed to create ytex.properties file from examples files in the developer/source version of cTAKES
-Needed to change path in ctakes.profile to match version name of CTAKES_HOME directory
-Needed to add sqljdbc4.jar to CTAKES_HOME/lib and sqljdbc_auth.dll to C:\Program Files\Java\jre_Version\bin
-Needed to open port 1433 for TCP/IP traffic and clear dynamic ports
-Need to change table definitions as follows to install UMLS-2016AB:
MRCONSO.CODE varchar(75) -- was varchar(50)
MRDEF.DEF varchar(max) -- was varchar(4000)
MRSAB.VSAB varchar(24) -- was varchar(20)
MRSAT.ATN varchar(64) -- was varchar(50)
MRSAT.ATV varchar(max) -- was varchar(4000)
3. Install cTAKES "as usual"
4. Download and unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip 'over' your installation.
-I believe this step is deprecated - skip to step 6
5. Unzip YTEX Resources (Optional - UTS login required)
-I believe this step is deprecated - skip to step 6
-may be needed for concept graphs and dictionary lookup table for NER
6. Fix the path references in shell script to match your environment
7. Create CTAKES_HOME\resources\org\apache\ctakes\ytex\ytex.properties and specify database connection parameters.
8. Execute the setup script
-Need to use Java 7 - Java 8 errors out
-If SQL errors encountered, appenders can be added to log4j.xml to collect SQL queries
Sean
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 11:57 AM
To: dev@ctakes.apache.org
Subject: RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce
RE: New to CTAKES
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Joyce,
If you are building from source then you should not need to manually download the resources. Maven should be doing it for you. Well, that is the behavior of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is probably the most appropriate for the 3.2.2 release if you want all of the resources.
As for building and deploying ytex, I don't have any advice. Perhaps some ytex power-user out there can help.
Sean
-----Original Message-----
From: Dunlop, Joyce (HP) [mailto:Joyce.Dunlop@va.gov]
Sent: Tuesday, January 17, 2017 11:25 AM
To: dev@ctakes.apache.org
Cc: Dorner, Andrew J. (PSI); Rustrian, Armando (Liberty ITS)
Subject: New to CTAKES
Good Morning,
I am trying to set up a development environment using the source release of 3.2.2.
Reading though the documentation on
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B3.2-2BDeveloper-2BInstall-2BGuide&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=iqpkHc0kT5mucNnxYyc1mczXXlbmSVJlX-8dxeJvp2o&e= .
Merge the version-matching resources ZIP file from https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=wPUG8d9qpl_kQBPP5xI9y84mwMEXfaB2cdbkHvWaa0Y&e= into your ctakes-dictionary-lookup-res project.
ctakes-resources-3.2.1.1-bin.zip<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D3.2.1.1-2Dbin.zip_download&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yBXENVQKpWjVraf6Zf7uY5l9LJxxrRiiE-yjyFID6d8&s=pErHE2p1qFyPeMACLDvshPiTpNZXM847MgGESOtvyuU&e= > is available for download. Is there a 3.2.2 version of the resources?
After reading some of the posts from the email box, and reading the documentation on the site above. It looks like the documentation may be somewhat dated and not fulling integrated for YTEX.
Would you have any recommendations in advance on how to set up a build process for deployment and YTEX database from scratch?
Thanks,
Joyce