Re: Creating a new annotator

[britt fitch]

Did you declare the new Age type in TypeSystem.xml?
You may want to extend one of the existing types like EntityMention or 
IdentifiedAnnotation.

Cheers,

Britt


Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com

> On Sep 18, 2015, at 11:46 PM, Christopher Baechle  wrote:
> 
> I created a new annotator for finding socio-demographic information
> from a clinical note. It works within eclipse, but fails when I run it
> from the packaged distribution created from mvn install.
> 
> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
> "org.apache.ctakes.sociodemo.Age" used in Java code,  but was not
> declared in the XML type descriptor.
> 
> Age is an Annotation. I didn't follow the normal convention of adding
> it to org.apache.ctakes.typesystem and put it in my package
> org.apache.ctakes.sociodemo.
> 
> I added my descriptor xml file to
> AggregatePlaintextFastUMLSProcessor.xml. I think it might be a
> classpath issue (the jvm unable to find my descriptor file). I added
> the full absolute path to runctakesCVD.sh but it still persists.
> 
> Any suggestions?



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Re: Creating a new annotator

[Christopher Baechle]

That was it! Thanks.

On Sat, Sep 19, 2015 at 8:00 AM, britt fitch <
britt.fi...@wiredinformatics.com> wrote:

> Did you declare the new Age type in TypeSystem.xml?
> You may want to extend one of the existing types like EntityMention or
> IdentifiedAnnotation.
>
> Cheers,
>
> Britt
>
> Britt Fitch
> Wired Informatics
> 265 Franklin St Ste 1702
> Boston, MA 02110
> http://wiredinformatics.com
> britt.fi...@wiredinformatics.com
>
> On Sep 18, 2015, at 11:46 PM, Christopher Baechle 
> wrote:
>
> I created a new annotator for finding socio-demographic information
> from a clinical note. It works within eclipse, but fails when I run it
> from the packaged distribution created from mvn install.
>
> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
> "org.apache.ctakes.sociodemo.Age" used in Java code,  but was not
> declared in the XML type descriptor.
>
> Age is an Annotation. I didn't follow the normal convention of adding
> it to org.apache.ctakes.typesystem and put it in my package
> org.apache.ctakes.sociodemo.
>
> I added my descriptor xml file to
> AggregatePlaintextFastUMLSProcessor.xml. I think it might be a
> classpath issue (the jvm unable to find my descriptor file). I added
> the full absolute path to runctakesCVD.sh but it still persists.
>
> Any suggestions?
>
>
>

Re: [cancer-informatics] Fwd: BD2K Coordination Center Solicits Hackathon Proposals

[Mattmann, Chris A (3980)]

Hey Folks,

If anyone wants to discuss how JPL can contribute to a BD2K
proposal or if someone is already leading it, I would definitely
be interested in contributing. We have been combining Tika, cTAKES,
and other software (Spark, OODT) into a solution we call “Shangridocs”
which could be quite compelling here.

Please feel free to contact me off-line and would love to discuss.

Cheers,
Chris

++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168-527
Email: chris.a.mattm...@nasa.gov
WWW:  http://sunset.usc.edu/~mattmann/
++
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
++





-Original Message-
From: andy mcmurry 
Reply-To: "u...@ctakes.apache.org" 
Date: Friday, September 18, 2015 at 4:24 PM
To: "dev@ctakes.apache.org" 
Cc: "u...@ctakes.apache.org" 
Subject: Re: [cancer-informatics] Fwd: BD2K Coordination Center Solicits
Hackathon Proposals

>+1 , I support the idea of cTAKES as an intermediate step for other
>annotation sources, data "mash up".
>Phenotypes -- Genes, etc.
>
>
>On Thu, Sep 17, 2015 at 2:52 PM, Wilson, Brian
> wrote:
>
>
>> > Food for thought :)
>
>> >
>> > The Big Data to Knowledge Coordination Center (BD2KCC) is announcing
>> > a call for  hackathon event proposals related to biomedical big data
>> > science. The BD2KCC is part of the National Institutes of Health
>> > (NIH)’s Big Data to Knowledge (BD2K) program, which is committed to
>> > fostering consortium activities and collaborations among the
>> > nationwide BD2K investigator teams. The current request for
>> > applications aims to advance the mission of BD2K by inviting
>> > proposals to host public hackathon events that will harness broad
>> > expertise for the development and application of biomedical big data
>> > software tools. Applications for the first round of funding are due
>> > October 15th, 2015. More information about this opportunity can be
>> > found at: 
>http://bd2kcc.org/files/hackathons.pdf
>.
>>
>>
>>
>
>The information in this e-mail is intended only for the person to whom it
>is addressed. If you believe this e-mail was sent to you in error and the
>e-mail contains patient information, please contact the Tufts Medical
>Center HIPAA Hotline at
>(617) 636-4422 . If the e-mail was sent to you
>in error but does not contain patient information, please contact the
>sender and properly dispose of the e-mail.
>
>
>
>
>

Re: [cancer-informatics] Fwd: BD2K Coordination Center Solicits Hackathon Proposals

[andy mcmurry]

Chris: sounds interesting. could you share some of your clinical use cases ?

On Sep 19, 2015 9:27 AM, "Mattmann, Chris A (3980)" <
chris.a.mattm...@jpl.nasa.gov> wrote:
>
> Hey Folks,
>
> If anyone wants to discuss how JPL can contribute to a BD2K
> proposal or if someone is already leading it, I would definitely
> be interested in contributing. We have been combining Tika, cTAKES,
> and other software (Spark, OODT) into a solution we call “Shangridocs”
> which could be quite compelling here.
>
> Please feel free to contact me off-line and would love to discuss.
>
> Cheers,
> Chris
>
> ++
> Chris Mattmann, Ph.D.
> Chief Architect
> Instrument Software and Science Data Systems Section (398)
> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
> Office: 168-519, Mailstop: 168-527
> Email: chris.a.mattm...@nasa.gov
> WWW:  http://sunset.usc.edu/~mattmann/
> ++
> Adjunct Associate Professor, Computer Science Department
> University of Southern California, Los Angeles, CA 90089 USA
> ++
>
>
>
>
>
> -Original Message-
> From: andy mcmurry 
> Reply-To: "u...@ctakes.apache.org" 
> Date: Friday, September 18, 2015 at 4:24 PM
> To: "dev@ctakes.apache.org" 
> Cc: "u...@ctakes.apache.org" 
> Subject: Re: [cancer-informatics] Fwd: BD2K Coordination Center Solicits
> Hackathon Proposals
>
> >+1 , I support the idea of cTAKES as an intermediate step for other
> >annotation sources, data "mash up".
> >Phenotypes -- Genes, etc.
> >
> >
> >On Thu, Sep 17, 2015 at 2:52 PM, Wilson, Brian
> > wrote:
> >
> >
> >> > Food for thought :)
> >
> >> >
> >> > The Big Data to Knowledge Coordination Center (BD2KCC) is announcing
> >> > a call for  hackathon event proposals related to biomedical big data
> >> > science. The BD2KCC is part of the National Institutes of Health
> >> > (NIH)’s Big Data to Knowledge (BD2K) program, which is committed to
> >> > fostering consortium activities and collaborations among the
> >> > nationwide BD2K investigator teams. The current request for
> >> > applications aims to advance the mission of BD2K by inviting
> >> > proposals to host public hackathon events that will harness broad
> >> > expertise for the development and application of biomedical big data
> >> > software tools. Applications for the first round of funding are due
> >> > October 15th, 2015. More information about this opportunity can be
> >> > found at:
> >http://bd2kcc.org/files/hackathons.pdf
> >.
> >>
> >>
> >>
> >
> >The information in this e-mail is intended only for the person to whom it
> >is addressed. If you believe this e-mail was sent to you in error and the
> >e-mail contains patient information, please contact the Tufts Medical
> >Center HIPAA Hotline at
> >(617) 636-4422 . If the e-mail was sent to you
> >in error but does not contain patient information, please contact the
> >sender and properly dispose of the e-mail.
> >
> >
> >
> >
> >
>