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Posted to dev@ctakes.apache.org by "Coarr, Matt" <mc...@mitre.org> on 2013/11/15 03:36:06 UTC
using umls dictionary lookup offline?
What would I need to do to run ctakes offline? In particular, I believe that means what do I need to do to get the full dictionary lookup to work?
Do I need to build my own UMLS dictionary database and use a custom dictionary class?
I looked around on the wiki (in the ctakes 3.0 and 3.1 developer guides and the ctakes 3.0 component guide).
I know way back when we used to have this before we simplified things by pre-packaging the UMLS dictionary and doing online validation of the UMLS username and password.
Thanks!
Matt
RE: using umls dictionary lookup offline?
Posted by "Lingren, Todd" <To...@cchmc.org>.
FWIW, MetaMap does the same.
Todd Lingren
Biomedical Informatics
Cincinnati Children's Hospital
Todd.Lingren@cchmc.org
513-803-9032
-----Original Message-----
From: amcmurry [mailto:mcmurry.andy@gmail.com]
Sent: Friday, November 15, 2013 10:51 AM
To: dev@ctakes.apache.org
Subject: Re: using umls dictionary lookup offline?
! NOTEWORTHY !
In the iDASH download you supply your UMLS credentials, they check your cred, and give you the whole NLP stack LICENSED and all.
This includes cTAKES.
Interesting, right?
On Nov 15, 2013, at 5:50 AM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
> Hi Matt,
> The license validation is ultimately the responsibility of the user.
> So if you ensure you have the license, technically, what you can do is just write a Annotator that just uses those resources directly :).
> --Pei
>
>> -----Original Message-----
>> From: Coarr, Matt [mailto:mcoarr@mitre.org]
>> Sent: Thursday, November 14, 2013 9:37 PM
>> To: dev@ctakes.apache.org
>> Subject: using umls dictionary lookup offline?
>>
>> What would I need to do to run ctakes offline? In particular, I
>> believe that means what do I need to do to get the full dictionary lookup to work?
>>
>> Do I need to build my own UMLS dictionary database and use a custom
>> dictionary class?
>>
>> I looked around on the wiki (in the ctakes 3.0 and 3.1 developer
>> guides and the ctakes 3.0 component guide).
>>
>> I know way back when we used to have this before we simplified things
>> by pre-packaging the UMLS dictionary and doing online validation of
>> the UMLS username and password.
>>
>> Thanks!
>> Matt
>>
>
Re: using umls dictionary lookup offline?
Posted by amcmurry <mc...@gmail.com>.
! NOTEWORTHY !
In the iDASH download you supply your UMLS credentials, they check your cred, and give you the whole NLP stack LICENSED and all.
This includes cTAKES.
Interesting, right?
On Nov 15, 2013, at 5:50 AM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
> Hi Matt,
> The license validation is ultimately the responsibility of the user.
> So if you ensure you have the license, technically, what you can do is just write a Annotator that just uses those resources directly :).
> --Pei
>
>> -----Original Message-----
>> From: Coarr, Matt [mailto:mcoarr@mitre.org]
>> Sent: Thursday, November 14, 2013 9:37 PM
>> To: dev@ctakes.apache.org
>> Subject: using umls dictionary lookup offline?
>>
>> What would I need to do to run ctakes offline? In particular, I believe that
>> means what do I need to do to get the full dictionary lookup to work?
>>
>> Do I need to build my own UMLS dictionary database and use a custom
>> dictionary class?
>>
>> I looked around on the wiki (in the ctakes 3.0 and 3.1 developer guides and
>> the ctakes 3.0 component guide).
>>
>> I know way back when we used to have this before we simplified things by
>> pre-packaging the UMLS dictionary and doing online validation of the UMLS
>> username and password.
>>
>> Thanks!
>> Matt
>>
>
RE: using umls dictionary lookup offline?
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
That actually sounds like a good idea.
The code that performs the UMLS check is already in cTAKES... perhaps we just need a place to host/distribution of the resources (simple webapp)...
I wonder if we can just converge and point to a single place for all of their models/resourcing needs...
Richard- I'm just thinking of your idea of a single place to download various models, do you think it's worth thinking about also hosting certain protected resources such as UMLS there as well? (perhaps some place a bit more advanced that Maven Central).
> -----Original Message-----
> From: vijay garla [mailto:vngarla@gmail.com]
> Sent: Monday, November 18, 2013 11:05 AM
> To: dev@ctakes.apache.org
> Subject: Re: using umls dictionary lookup offline?
>
> No need to write any new annotator, just point
> org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator at the
> UMLS HSQL DB.
>
> The UMLS password check is a very weak chastity belt. For ytex, we make
> umls resources available via a UTS password protected website - to get the
> resources the user has to enter their UTS username/password which
> ensures that the user has accepted the UMLS licenses. I think making ctakes
> resources available via a similar method would be more elegant.
>
> -vj
>
>
> On Fri, Nov 15, 2013 at 8:50 AM, Chen, Pei
> <Pe...@childrens.harvard.edu>wrote:
>
> > Hi Matt,
> > The license validation is ultimately the responsibility of the user.
> > So if you ensure you have the license, technically, what you can do is
> > just write a Annotator that just uses those resources directly :).
> > --Pei
> >
> > > -----Original Message-----
> > > From: Coarr, Matt [mailto:mcoarr@mitre.org]
> > > Sent: Thursday, November 14, 2013 9:37 PM
> > > To: dev@ctakes.apache.org
> > > Subject: using umls dictionary lookup offline?
> > >
> > > What would I need to do to run ctakes offline? In particular, I
> > > believe
> > that
> > > means what do I need to do to get the full dictionary lookup to work?
> > >
> > > Do I need to build my own UMLS dictionary database and use a custom
> > > dictionary class?
> > >
> > > I looked around on the wiki (in the ctakes 3.0 and 3.1 developer
> > > guides
> > and
> > > the ctakes 3.0 component guide).
> > >
> > > I know way back when we used to have this before we simplified
> > > things by pre-packaging the UMLS dictionary and doing online
> > > validation of the UMLS username and password.
> > >
> > > Thanks!
> > > Matt
> > >
> >
> >
Re: using umls dictionary lookup offline?
Posted by vijay garla <vn...@gmail.com>.
No need to write any new annotator, just point
org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator at the
UMLS HSQL DB.
The UMLS password check is a very weak chastity belt. For ytex, we make
umls resources available via a UTS password protected website - to get the
resources the user has to enter their UTS username/password which ensures
that the user has accepted the UMLS licenses. I think making ctakes
resources available via a similar method would be more elegant.
-vj
On Fri, Nov 15, 2013 at 8:50 AM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> Hi Matt,
> The license validation is ultimately the responsibility of the user.
> So if you ensure you have the license, technically, what you can do is
> just write a Annotator that just uses those resources directly :).
> --Pei
>
> > -----Original Message-----
> > From: Coarr, Matt [mailto:mcoarr@mitre.org]
> > Sent: Thursday, November 14, 2013 9:37 PM
> > To: dev@ctakes.apache.org
> > Subject: using umls dictionary lookup offline?
> >
> > What would I need to do to run ctakes offline? In particular, I believe
> that
> > means what do I need to do to get the full dictionary lookup to work?
> >
> > Do I need to build my own UMLS dictionary database and use a custom
> > dictionary class?
> >
> > I looked around on the wiki (in the ctakes 3.0 and 3.1 developer guides
> and
> > the ctakes 3.0 component guide).
> >
> > I know way back when we used to have this before we simplified things by
> > pre-packaging the UMLS dictionary and doing online validation of the UMLS
> > username and password.
> >
> > Thanks!
> > Matt
> >
>
>
RE: using umls dictionary lookup offline?
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Matt,
The license validation is ultimately the responsibility of the user.
So if you ensure you have the license, technically, what you can do is just write a Annotator that just uses those resources directly :).
--Pei
> -----Original Message-----
> From: Coarr, Matt [mailto:mcoarr@mitre.org]
> Sent: Thursday, November 14, 2013 9:37 PM
> To: dev@ctakes.apache.org
> Subject: using umls dictionary lookup offline?
>
> What would I need to do to run ctakes offline? In particular, I believe that
> means what do I need to do to get the full dictionary lookup to work?
>
> Do I need to build my own UMLS dictionary database and use a custom
> dictionary class?
>
> I looked around on the wiki (in the ctakes 3.0 and 3.1 developer guides and
> the ctakes 3.0 component guide).
>
> I know way back when we used to have this before we simplified things by
> pre-packaging the UMLS dictionary and doing online validation of the UMLS
> username and password.
>
> Thanks!
> Matt
>