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Posted to user@ctakes.apache.org by Maha Zohbi <ma...@gmail.com> on 2014/05/02 01:53:55 UTC
cTAKES API documentation
Hi,
We are looking to developing an application that processes unstructured
medical data and feeds it into a decision support system. To do that we
will use cTAKES. We downloaded the binary and followed the user guide.
However, I couldn't find any API documentation.
Can anyone point me to API documentation for cTAKES or a samples guide to
use the API?
Thanks
RE: cTAKES API documentation
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Instead of using the AggregateUMLS engine, use AggregateTemplateFiller.xml (under ctakes-template-filler)
That engines does UMLS dictionary lookup and relation extraction etc and then runs the TemplateFillerAnnotator.
Hope that helps
-- James
From: Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com]
Sent: Friday, May 02, 2014 10:21 AM
To: user@ctakes.apache.org
Subject: Re: cTAKES API documentation
Timothy,
To create CEMs I understand I will need the template filler API. which API to use. Also there is no associated documentation.
I know to annotate UMLS concepts I have to use AggegrateUMLS engine. Now should I save the output in xml and run the template filler to get CEMS.
Please guide
On Fri, May 2, 2014 at 8:44 PM, Miller, Timothy <Ti...@childrens.harvard.edu>> wrote:
Another resource that may be more useful for many use cases is the type
system documentation. I seem to have lost that link -- can anyone please
chime in with it?
On 05/02/2014 11:05 AM, Masanz, James J. wrote:
> Try
>
> http://ctakes.apache.org/apidocs/3.1.1/
>
> -- James
>
> -----Original Message-----
> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu<ma...@cs.wisc.edu>]
> Sent: Thursday, May 01, 2014 7:41 PM
> To: user@ctakes.apache.org<ma...@ctakes.apache.org>
> Cc: Maha Zohbi
> Subject: Re: cTAKES API documentation
>
> Yes, same question. I have been looking for API or documentation for
> long. Could some one help guide to it?
>
> Thanks,
> Xiayuan
>
> On 2014-05-01 18:53, Maha Zohbi wrote:
>> Hi,
>>
>> We are looking to developing an application that processes
>> unstructured medical data and feeds it into a decision support system.
>> To do that we will use cTAKES. We downloaded the binary and followed
>> the user guide. However, I couldn't find any API documentation.
>> Can anyone point me to API documentation for cTAKES or a samples
>> guide to use the API?
>>
>> Thanks
--
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu<ma...@childrens.harvard.edu>
617-919-1223
Re: cTAKES API documentation
Posted by Anirban Chakraborti <ch...@googlemail.com>.
Timothy,
To create CEMs I understand I will need the template filler API. which API
to use. Also there is no associated documentation.
I know to annotate UMLS concepts I have to use AggegrateUMLS engine. Now
should I save the output in xml and run the template filler to get CEMS.
Please guide
On Fri, May 2, 2014 at 8:44 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> Another resource that may be more useful for many use cases is the type
> system documentation. I seem to have lost that link -- can anyone please
> chime in with it?
>
>
>
> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
> > Try
> >
> > http://ctakes.apache.org/apidocs/3.1.1/
> >
> > -- James
> >
> > -----Original Message-----
> > From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
> > Sent: Thursday, May 01, 2014 7:41 PM
> > To: user@ctakes.apache.org
> > Cc: Maha Zohbi
> > Subject: Re: cTAKES API documentation
> >
> > Yes, same question. I have been looking for API or documentation for
> > long. Could some one help guide to it?
> >
> > Thanks,
> > Xiayuan
> >
> > On 2014-05-01 18:53, Maha Zohbi wrote:
> >> Hi,
> >>
> >> We are looking to developing an application that processes
> >> unstructured medical data and feeds it into a decision support system.
> >> To do that we will use cTAKES. We downloaded the binary and followed
> >> the user guide. However, I couldn't find any API documentation.
> >> Can anyone point me to API documentation for cTAKES or a samples
> >> guide to use the API?
> >>
> >> Thanks
>
> --
> Tim Miller
> Instructor
> Boston Children's Hospital and Harvard Medical School
> timothy.miller@childrens.harvard.edu
> 617-919-1223
>
>
Re: cTAKES API documentation
Posted by N M <ma...@gmail.com>.
it seems to me that we have willing contributors, but no driver for this
project. Any ideas?
-NM
On Thu, May 8, 2014 at 8:17 PM, Maha Zohbi <ma...@gmail.com> wrote:
> Thanks all for your help!
>
>
> On Wed, May 7, 2014 at 7:00 AM, N M <ma...@gmail.com> wrote:
>
>> Hi,
>>
>> Documentation which I was hoping to find as a user (hopefully eventually
>> developer) of cTAKES, was a detailed description of each component (or
>> analysis engine) and their interplay. As I've been looking at the cTAKES
>> source code, I've been creating a chart for each pipeline that I've
>> analyzed, hoping to essentially create a more useful component library than
>> the one available at
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Component+Use+Guide(a "developer version" of this, if you will).
>>
>> I've attached a pdf example of one of my personal note charts I've been
>> working on, this one is specific to the UMLS plaintext aggregate AE. My
>> idea is to have some sort of diagram for each pipeline that I can refer to,
>> so that when I need to customize things in the future, I have a pretty good
>> idea of where to go. I think it is important to chart inputs and output
>> types especially.
>>
>> Has anyone written a UIMA library to automatically document these kinds
>> of things for UIMA components? running something akin to one would save a
>> lot of time and effort, and would be much more maintainable than manually
>> created charts. (of course, the inputs and outputs would have to be noted
>> in the xml files, which doesn't seem to be the case for many of the AE's).
>>
>> Looking at the previous discussions (notably the one regarding lvg
>> entries), it seems to me that having a chart or other type of documentation
>> which lists what types come out of and go into each component would go a
>> long ways.
>>
>> Does anyone know if anything similar exists?
>>
>> Thanks.
>>
>>
>>
>>
>> On Fri, May 2, 2014 at 2:17 PM, ravi garg <ra...@gmail.com> wrote:
>>
>>> Hi Xiayuan,
>>>
>>> I hope this [1] will be of help to you.
>>>
>>> [1]
>>> https://github.com/ravigarg27/phenotips/blob/master/components/ctakes-service/src/main/java/edu/toronto/cs/phenotips/ctakes/AbstractScriptService.java
>>>
>>> Regards,
>>> Ravi
>>>
>>>
>>> On Fri, May 2, 2014 at 10:07 PM, Miller, Timothy <
>>> Timothy.Miller@childrens.harvard.edu> wrote:
>>>
>>>> James posted the links to the API docs earlier, but I suspect you may
>>>> find examples more helpful.
>>>>
>>>> If you look at the classes under
>>>> /ctakes-clinical-pipeline/org.apache.ctakes.clinicalpipeline.runtime,
>>>> you will see how to instantiate the default pipelines from within
>>>> UimaFit using the xml descriptors. You can override
>>>> BagOfAnnotationsGenerator with your own extractInformation() method and
>>>> do whatever you like for each annotation, or you can just copy the
>>>> layout to do something you like.
>>>>
>>>> Alternatively, if you want to build your own pipelines programatically,
>>>> I would look at some of the pipelines in the ctakes-temporal project:
>>>>
>>>> /ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
>>>> if you aren't up to date on trunk (i.e. you are working off of a
>>>> release), then look at the most recent version in svn:
>>>>
>>>> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup
>>>>
>>>> Finally, there is work-in-progress to define factory methods for getting
>>>> commonly used pipelines, not ready for primetime but may give you some
>>>> more examples of how pipelines can be put together:
>>>>
>>>> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?view=markup
>>>>
>>>> Hope this helps.
>>>>
>>>> Tim
>>>>
>>>> On 05/02/2014 12:16 PM, Xiayuan Huang wrote:
>>>> > Actually I am looking for some API documentation like how to use and
>>>> > code with ctakes pipelines. Can anyone share the experience how do you
>>>> > write codes with some pipelines, (maybe in JAVA or else).
>>>> >
>>>> > Thanks,
>>>> > Xiayuan
>>>> >
>>>> >
>>>> > On 2014-05-02 10:55, Miller, Timothy wrote:
>>>> >> Yes Pei, thanks, though now that I see it I'm not as sure that it
>>>> >> will be useful to Maha and Xiayuan.
>>>> >> Tim
>>>> >>
>>>> >> On 05/02/2014 11:17 AM, Pei Chen wrote:
>>>> >>
>>>> >>> Tim,
>>>> >>> Do you mean:
>>>> >>>
>>>> >>
>>>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>>> >>> [3]
>>>> >>>
>>>> >>> ?
>>>> >>>
>>>> >>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
>>>> >>> <Ti...@childrens.harvard.edu> wrote:
>>>> >>>
>>>> >>>> Another resource that may be more useful for many use cases is the
>>>> >>>> type
>>>> >>>> system documentation. I seem to have lost that link -- can anyone
>>>> >>>> please
>>>> >>>> chime in with it?
>>>> >>>>
>>>> >>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
>>>> >>>>> Try
>>>> >>>>>
>>>> >>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
>>>> >>>>>
>>>> >>>>> -- James
>>>> >>>>>
>>>> >>>>> -----Original Message-----
>>>> >>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
>>>> >>>>> Sent: Thursday, May 01, 2014 7:41 PM
>>>> >>>>> To: user@ctakes.apache.org
>>>> >>>>> Cc: Maha Zohbi
>>>> >>>>> Subject: Re: cTAKES API documentation
>>>> >>>>>
>>>> >>>>> Yes, same question. I have been looking for API or
>>>> >>>> documentation for
>>>> >>>>> long. Could some one help guide to it?
>>>> >>>>>
>>>> >>>>> Thanks,
>>>> >>>>> Xiayuan
>>>> >>>>>
>>>> >>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
>>>> >>>>>> Hi,
>>>> >>>>>>
>>>> >>>>>> We are looking to developing an application that processes
>>>> >>>>>> unstructured medical data and feeds it into a decision support
>>>> >>>> system.
>>>> >>>>>> To do that we will use cTAKES. We downloaded the binary and
>>>> >>>> followed
>>>> >>>>>> the user guide. However, I couldn't find any API
>>>> >>>> documentation.
>>>> >>>>>> Can anyone point me to API documentation for cTAKES or a
>>>> >>>> samples
>>>> >>>>>> guide to use the API?
>>>> >>>>>>
>>>> >>>>>> Thanks
>>>> >>>> --
>>>> >>>> Tim Miller
>>>> >>>> Instructor
>>>> >>>> Boston Children's Hospital and Harvard Medical School
>>>> >>>> timothy.miller@childrens.harvard.edu
>>>> >>>> 617-919-1223 [2]
>>>> >> --
>>>> >> Tim Miller
>>>> >> Instructor
>>>> >> Boston Children's Hospital and Harvard Medical School
>>>> >> timothy.miller@childrens.harvard.edu
>>>> >> 617-919-1223
>>>> >>
>>>> >>
>>>> >> Links:
>>>> >> ------
>>>> >> [1] http://ctakes.apache.org/apidocs/3.1.1/
>>>> >> [2] tel:617-919-1223
>>>> >> [3]
>>>> >>
>>>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>>>
>>>> --
>>>> Tim Miller
>>>> Instructor
>>>> Boston Children's Hospital and Harvard Medical School
>>>> timothy.miller@childrens.harvard.edu
>>>> 617-919-1223
>>>>
>>>>
>>>
>>>
>>> --
>>> Ravi Garg
>>> 4th Year
>>> MSc (hons) Biological Sciences
>>> B.E (hons) Computer Science and Engineering
>>> BITS Pilani KK Birla Goa Campus
>>>
>>
>>
>
Re: cTAKES API documentation
Posted by Maha Zohbi <ma...@gmail.com>.
Thanks all for your help!
On Wed, May 7, 2014 at 7:00 AM, N M <ma...@gmail.com> wrote:
> Hi,
>
> Documentation which I was hoping to find as a user (hopefully eventually
> developer) of cTAKES, was a detailed description of each component (or
> analysis engine) and their interplay. As I've been looking at the cTAKES
> source code, I've been creating a chart for each pipeline that I've
> analyzed, hoping to essentially create a more useful component library than
> the one available at
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Component+Use+Guide(a "developer version" of this, if you will).
>
> I've attached a pdf example of one of my personal note charts I've been
> working on, this one is specific to the UMLS plaintext aggregate AE. My
> idea is to have some sort of diagram for each pipeline that I can refer to,
> so that when I need to customize things in the future, I have a pretty good
> idea of where to go. I think it is important to chart inputs and output
> types especially.
>
> Has anyone written a UIMA library to automatically document these kinds of
> things for UIMA components? running something akin to one would save a lot
> of time and effort, and would be much more maintainable than manually
> created charts. (of course, the inputs and outputs would have to be noted
> in the xml files, which doesn't seem to be the case for many of the AE's).
>
> Looking at the previous discussions (notably the one regarding lvg
> entries), it seems to me that having a chart or other type of documentation
> which lists what types come out of and go into each component would go a
> long ways.
>
> Does anyone know if anything similar exists?
>
> Thanks.
>
>
>
>
> On Fri, May 2, 2014 at 2:17 PM, ravi garg <ra...@gmail.com> wrote:
>
>> Hi Xiayuan,
>>
>> I hope this [1] will be of help to you.
>>
>> [1]
>> https://github.com/ravigarg27/phenotips/blob/master/components/ctakes-service/src/main/java/edu/toronto/cs/phenotips/ctakes/AbstractScriptService.java
>>
>> Regards,
>> Ravi
>>
>>
>> On Fri, May 2, 2014 at 10:07 PM, Miller, Timothy <
>> Timothy.Miller@childrens.harvard.edu> wrote:
>>
>>> James posted the links to the API docs earlier, but I suspect you may
>>> find examples more helpful.
>>>
>>> If you look at the classes under
>>> /ctakes-clinical-pipeline/org.apache.ctakes.clinicalpipeline.runtime,
>>> you will see how to instantiate the default pipelines from within
>>> UimaFit using the xml descriptors. You can override
>>> BagOfAnnotationsGenerator with your own extractInformation() method and
>>> do whatever you like for each annotation, or you can just copy the
>>> layout to do something you like.
>>>
>>> Alternatively, if you want to build your own pipelines programatically,
>>> I would look at some of the pipelines in the ctakes-temporal project:
>>>
>>> /ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
>>> if you aren't up to date on trunk (i.e. you are working off of a
>>> release), then look at the most recent version in svn:
>>>
>>> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup
>>>
>>> Finally, there is work-in-progress to define factory methods for getting
>>> commonly used pipelines, not ready for primetime but may give you some
>>> more examples of how pipelines can be put together:
>>>
>>> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?view=markup
>>>
>>> Hope this helps.
>>>
>>> Tim
>>>
>>> On 05/02/2014 12:16 PM, Xiayuan Huang wrote:
>>> > Actually I am looking for some API documentation like how to use and
>>> > code with ctakes pipelines. Can anyone share the experience how do you
>>> > write codes with some pipelines, (maybe in JAVA or else).
>>> >
>>> > Thanks,
>>> > Xiayuan
>>> >
>>> >
>>> > On 2014-05-02 10:55, Miller, Timothy wrote:
>>> >> Yes Pei, thanks, though now that I see it I'm not as sure that it
>>> >> will be useful to Maha and Xiayuan.
>>> >> Tim
>>> >>
>>> >> On 05/02/2014 11:17 AM, Pei Chen wrote:
>>> >>
>>> >>> Tim,
>>> >>> Do you mean:
>>> >>>
>>> >>
>>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>> >>> [3]
>>> >>>
>>> >>> ?
>>> >>>
>>> >>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
>>> >>> <Ti...@childrens.harvard.edu> wrote:
>>> >>>
>>> >>>> Another resource that may be more useful for many use cases is the
>>> >>>> type
>>> >>>> system documentation. I seem to have lost that link -- can anyone
>>> >>>> please
>>> >>>> chime in with it?
>>> >>>>
>>> >>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
>>> >>>>> Try
>>> >>>>>
>>> >>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
>>> >>>>>
>>> >>>>> -- James
>>> >>>>>
>>> >>>>> -----Original Message-----
>>> >>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
>>> >>>>> Sent: Thursday, May 01, 2014 7:41 PM
>>> >>>>> To: user@ctakes.apache.org
>>> >>>>> Cc: Maha Zohbi
>>> >>>>> Subject: Re: cTAKES API documentation
>>> >>>>>
>>> >>>>> Yes, same question. I have been looking for API or
>>> >>>> documentation for
>>> >>>>> long. Could some one help guide to it?
>>> >>>>>
>>> >>>>> Thanks,
>>> >>>>> Xiayuan
>>> >>>>>
>>> >>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
>>> >>>>>> Hi,
>>> >>>>>>
>>> >>>>>> We are looking to developing an application that processes
>>> >>>>>> unstructured medical data and feeds it into a decision support
>>> >>>> system.
>>> >>>>>> To do that we will use cTAKES. We downloaded the binary and
>>> >>>> followed
>>> >>>>>> the user guide. However, I couldn't find any API
>>> >>>> documentation.
>>> >>>>>> Can anyone point me to API documentation for cTAKES or a
>>> >>>> samples
>>> >>>>>> guide to use the API?
>>> >>>>>>
>>> >>>>>> Thanks
>>> >>>> --
>>> >>>> Tim Miller
>>> >>>> Instructor
>>> >>>> Boston Children's Hospital and Harvard Medical School
>>> >>>> timothy.miller@childrens.harvard.edu
>>> >>>> 617-919-1223 [2]
>>> >> --
>>> >> Tim Miller
>>> >> Instructor
>>> >> Boston Children's Hospital and Harvard Medical School
>>> >> timothy.miller@childrens.harvard.edu
>>> >> 617-919-1223
>>> >>
>>> >>
>>> >> Links:
>>> >> ------
>>> >> [1] http://ctakes.apache.org/apidocs/3.1.1/
>>> >> [2] tel:617-919-1223
>>> >> [3]
>>> >>
>>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>>
>>> --
>>> Tim Miller
>>> Instructor
>>> Boston Children's Hospital and Harvard Medical School
>>> timothy.miller@childrens.harvard.edu
>>> 617-919-1223
>>>
>>>
>>
>>
>> --
>> Ravi Garg
>> 4th Year
>> MSc (hons) Biological Sciences
>> B.E (hons) Computer Science and Engineering
>> BITS Pilani KK Birla Goa Campus
>>
>
>
Re: cTAKES API documentation
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Sorry for the delayed response, but this is really great. A few follow-up points:
1) There was a figure on the website that showed the standard pipeline flow, but not the detailed inputs and outputs.
2) I believe that UIMA xml descriptors are intended to contain this information, but I'm not sure how mandatory it is, and how well that actually is done in current implementations.
3) UIMAFit has annotations that can specify much of this information. See, for example the Dependency Parser AE:
/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE.java
which has TypeCapability annotations specifying its inputs. I believe outputs can be specified as well.
Thanks for sharing this document -- wonder if there is a good place to put it if others might find it useful?
Tim
On 05/06/2014 05:35 PM, N M wrote:
Hi,
Documentation which I was hoping to find as a user (hopefully eventually developer) of cTAKES, was a detailed description of each component (or analysis engine) and their interplay. As I've been looking at the cTAKES source code, I've been creating a chart for each pipeline that I've analyzed, hoping to essentially create a more useful component library than the one available at https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Component+Use+Guide (a "developer version" of this, if you will).
I've attached a pdf example of one of my personal note charts I've been working on, this one is specific to the UMLS plaintext aggregate AE. My idea is to have some sort of diagram for each pipeline that I can refer to, so that when I need to customize things in the future, I have a pretty good idea of where to go. I think it is important to chart inputs and output types especially.
Has anyone written a UIMA library to automatically document these kinds of things for UIMA components? running something akin to one would save a lot of time and effort, and would be much more maintainable than manually created charts. (of course, the inputs and outputs would have to be noted in the xml files, which doesn't seem to be the case for many of the AE's).
Looking at the previous discussions (notably the one regarding lvg entries), it seems to me that having a chart or other type of documentation which lists what types come out of and go into each component would go a long ways.
Does anyone know if anything similar exists?
Thanks.
On Fri, May 2, 2014 at 2:17 PM, ravi garg <ra...@gmail.com>> wrote:
Hi Xiayuan,
I hope this [1] will be of help to you.
[1] https://github.com/ravigarg27/phenotips/blob/master/components/ctakes-service/src/main/java/edu/toronto/cs/phenotips/ctakes/AbstractScriptService.java
Regards,
Ravi
On Fri, May 2, 2014 at 10:07 PM, Miller, Timothy <Ti...@childrens.harvard.edu>> wrote:
James posted the links to the API docs earlier, but I suspect you may
find examples more helpful.
If you look at the classes under
/ctakes-clinical-pipeline/org.apache.ctakes.clinicalpipeline.runtime,
you will see how to instantiate the default pipelines from within
UimaFit using the xml descriptors. You can override
BagOfAnnotationsGenerator with your own extractInformation() method and
do whatever you like for each annotation, or you can just copy the
layout to do something you like.
Alternatively, if you want to build your own pipelines programatically,
I would look at some of the pipelines in the ctakes-temporal project:
/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
if you aren't up to date on trunk (i.e. you are working off of a
release), then look at the most recent version in svn:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup
Finally, there is work-in-progress to define factory methods for getting
commonly used pipelines, not ready for primetime but may give you some
more examples of how pipelines can be put together:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?view=markup
Hope this helps.
Tim
On 05/02/2014 12:16 PM, Xiayuan Huang wrote:
> Actually I am looking for some API documentation like how to use and
> code with ctakes pipelines. Can anyone share the experience how do you
> write codes with some pipelines, (maybe in JAVA or else).
>
> Thanks,
> Xiayuan
>
>
> On 2014-05-02 10:55, Miller, Timothy wrote:
>> Yes Pei, thanks, though now that I see it I'm not as sure that it
>> will be useful to Maha and Xiayuan.
>> Tim
>>
>> On 05/02/2014 11:17 AM, Pei Chen wrote:
>>
>>> Tim,
>>> Do you mean:
>>>
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>> [3]
>>>
>>> ?
>>>
>>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
>>> <Ti...@childrens.harvard.edu>> wrote:
>>>
>>>> Another resource that may be more useful for many use cases is the
>>>> type
>>>> system documentation. I seem to have lost that link -- can anyone
>>>> please
>>>> chime in with it?
>>>>
>>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
>>>>> Try
>>>>>
>>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
>>>>>
>>>>> -- James
>>>>>
>>>>> -----Original Message-----
>>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu<ma...@cs.wisc.edu>]
>>>>> Sent: Thursday, May 01, 2014 7:41 PM
>>>>> To: user@ctakes.apache.org<ma...@ctakes.apache.org>
>>>>> Cc: Maha Zohbi
>>>>> Subject: Re: cTAKES API documentation
>>>>>
>>>>> Yes, same question. I have been looking for API or
>>>> documentation for
>>>>> long. Could some one help guide to it?
>>>>>
>>>>> Thanks,
>>>>> Xiayuan
>>>>>
>>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
>>>>>> Hi,
>>>>>>
>>>>>> We are looking to developing an application that processes
>>>>>> unstructured medical data and feeds it into a decision support
>>>> system.
>>>>>> To do that we will use cTAKES. We downloaded the binary and
>>>> followed
>>>>>> the user guide. However, I couldn't find any API
>>>> documentation.
>>>>>> Can anyone point me to API documentation for cTAKES or a
>>>> samples
>>>>>> guide to use the API?
>>>>>>
>>>>>> Thanks
>>>> --
>>>> Tim Miller
>>>> Instructor
>>>> Boston Children's Hospital and Harvard Medical School
>>>> timothy.miller@childrens.harvard.edu<ma...@childrens.harvard.edu>
>>>> 617-919-1223<tel:617-919-1223> [2]
>> --
>> Tim Miller
>> Instructor
>> Boston Children's Hospital and Harvard Medical School
>> timothy.miller@childrens.harvard.edu<ma...@childrens.harvard.edu>
>> 617-919-1223<tel:617-919-1223>
>>
>>
>> Links:
>> ------
>> [1] http://ctakes.apache.org/apidocs/3.1.1/
>> [2] tel:617-919-1223<tel:617-919-1223>
>> [3]
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
--
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu<ma...@childrens.harvard.edu>
617-919-1223<tel:617-919-1223>
--
Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus
--
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu<ma...@childrens.harvard.edu>
617-919-1223
Re: cTAKES API documentation
Posted by N M <ma...@gmail.com>.
Hi,
Documentation which I was hoping to find as a user (hopefully eventually
developer) of cTAKES, was a detailed description of each component (or
analysis engine) and their interplay. As I've been looking at the cTAKES
source code, I've been creating a chart for each pipeline that I've
analyzed, hoping to essentially create a more useful component library than
the one available at
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Component+Use+Guide(a
"developer version" of this, if you will).
I've attached a pdf example of one of my personal note charts I've been
working on, this one is specific to the UMLS plaintext aggregate AE. My
idea is to have some sort of diagram for each pipeline that I can refer to,
so that when I need to customize things in the future, I have a pretty good
idea of where to go. I think it is important to chart inputs and output
types especially.
Has anyone written a UIMA library to automatically document these kinds of
things for UIMA components? running something akin to one would save a lot
of time and effort, and would be much more maintainable than manually
created charts. (of course, the inputs and outputs would have to be noted
in the xml files, which doesn't seem to be the case for many of the AE's).
Looking at the previous discussions (notably the one regarding lvg
entries), it seems to me that having a chart or other type of documentation
which lists what types come out of and go into each component would go a
long ways.
Does anyone know if anything similar exists?
Thanks.
On Fri, May 2, 2014 at 2:17 PM, ravi garg <ra...@gmail.com> wrote:
> Hi Xiayuan,
>
> I hope this [1] will be of help to you.
>
> [1]
> https://github.com/ravigarg27/phenotips/blob/master/components/ctakes-service/src/main/java/edu/toronto/cs/phenotips/ctakes/AbstractScriptService.java
>
> Regards,
> Ravi
>
>
> On Fri, May 2, 2014 at 10:07 PM, Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
>> James posted the links to the API docs earlier, but I suspect you may
>> find examples more helpful.
>>
>> If you look at the classes under
>> /ctakes-clinical-pipeline/org.apache.ctakes.clinicalpipeline.runtime,
>> you will see how to instantiate the default pipelines from within
>> UimaFit using the xml descriptors. You can override
>> BagOfAnnotationsGenerator with your own extractInformation() method and
>> do whatever you like for each annotation, or you can just copy the
>> layout to do something you like.
>>
>> Alternatively, if you want to build your own pipelines programatically,
>> I would look at some of the pipelines in the ctakes-temporal project:
>>
>> /ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
>> if you aren't up to date on trunk (i.e. you are working off of a
>> release), then look at the most recent version in svn:
>>
>> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup
>>
>> Finally, there is work-in-progress to define factory methods for getting
>> commonly used pipelines, not ready for primetime but may give you some
>> more examples of how pipelines can be put together:
>>
>> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?view=markup
>>
>> Hope this helps.
>>
>> Tim
>>
>> On 05/02/2014 12:16 PM, Xiayuan Huang wrote:
>> > Actually I am looking for some API documentation like how to use and
>> > code with ctakes pipelines. Can anyone share the experience how do you
>> > write codes with some pipelines, (maybe in JAVA or else).
>> >
>> > Thanks,
>> > Xiayuan
>> >
>> >
>> > On 2014-05-02 10:55, Miller, Timothy wrote:
>> >> Yes Pei, thanks, though now that I see it I'm not as sure that it
>> >> will be useful to Maha and Xiayuan.
>> >> Tim
>> >>
>> >> On 05/02/2014 11:17 AM, Pei Chen wrote:
>> >>
>> >>> Tim,
>> >>> Do you mean:
>> >>>
>> >>
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>> >>> [3]
>> >>>
>> >>> ?
>> >>>
>> >>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
>> >>> <Ti...@childrens.harvard.edu> wrote:
>> >>>
>> >>>> Another resource that may be more useful for many use cases is the
>> >>>> type
>> >>>> system documentation. I seem to have lost that link -- can anyone
>> >>>> please
>> >>>> chime in with it?
>> >>>>
>> >>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
>> >>>>> Try
>> >>>>>
>> >>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
>> >>>>>
>> >>>>> -- James
>> >>>>>
>> >>>>> -----Original Message-----
>> >>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
>> >>>>> Sent: Thursday, May 01, 2014 7:41 PM
>> >>>>> To: user@ctakes.apache.org
>> >>>>> Cc: Maha Zohbi
>> >>>>> Subject: Re: cTAKES API documentation
>> >>>>>
>> >>>>> Yes, same question. I have been looking for API or
>> >>>> documentation for
>> >>>>> long. Could some one help guide to it?
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Xiayuan
>> >>>>>
>> >>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
>> >>>>>> Hi,
>> >>>>>>
>> >>>>>> We are looking to developing an application that processes
>> >>>>>> unstructured medical data and feeds it into a decision support
>> >>>> system.
>> >>>>>> To do that we will use cTAKES. We downloaded the binary and
>> >>>> followed
>> >>>>>> the user guide. However, I couldn't find any API
>> >>>> documentation.
>> >>>>>> Can anyone point me to API documentation for cTAKES or a
>> >>>> samples
>> >>>>>> guide to use the API?
>> >>>>>>
>> >>>>>> Thanks
>> >>>> --
>> >>>> Tim Miller
>> >>>> Instructor
>> >>>> Boston Children's Hospital and Harvard Medical School
>> >>>> timothy.miller@childrens.harvard.edu
>> >>>> 617-919-1223 [2]
>> >> --
>> >> Tim Miller
>> >> Instructor
>> >> Boston Children's Hospital and Harvard Medical School
>> >> timothy.miller@childrens.harvard.edu
>> >> 617-919-1223
>> >>
>> >>
>> >> Links:
>> >> ------
>> >> [1] http://ctakes.apache.org/apidocs/3.1.1/
>> >> [2] tel:617-919-1223
>> >> [3]
>> >>
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>
>> --
>> Tim Miller
>> Instructor
>> Boston Children's Hospital and Harvard Medical School
>> timothy.miller@childrens.harvard.edu
>> 617-919-1223
>>
>>
>
>
> --
> Ravi Garg
> 4th Year
> MSc (hons) Biological Sciences
> B.E (hons) Computer Science and Engineering
> BITS Pilani KK Birla Goa Campus
>
Re: cTAKES API documentation
Posted by ravi garg <ra...@gmail.com>.
Hi Xiayuan,
I hope this [1] will be of help to you.
[1]
https://github.com/ravigarg27/phenotips/blob/master/components/ctakes-service/src/main/java/edu/toronto/cs/phenotips/ctakes/AbstractScriptService.java
Regards,
Ravi
On Fri, May 2, 2014 at 10:07 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> James posted the links to the API docs earlier, but I suspect you may
> find examples more helpful.
>
> If you look at the classes under
> /ctakes-clinical-pipeline/org.apache.ctakes.clinicalpipeline.runtime,
> you will see how to instantiate the default pipelines from within
> UimaFit using the xml descriptors. You can override
> BagOfAnnotationsGenerator with your own extractInformation() method and
> do whatever you like for each annotation, or you can just copy the
> layout to do something you like.
>
> Alternatively, if you want to build your own pipelines programatically,
> I would look at some of the pipelines in the ctakes-temporal project:
>
> /ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
> if you aren't up to date on trunk (i.e. you are working off of a
> release), then look at the most recent version in svn:
>
> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup
>
> Finally, there is work-in-progress to define factory methods for getting
> commonly used pipelines, not ready for primetime but may give you some
> more examples of how pipelines can be put together:
>
> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?view=markup
>
> Hope this helps.
>
> Tim
>
> On 05/02/2014 12:16 PM, Xiayuan Huang wrote:
> > Actually I am looking for some API documentation like how to use and
> > code with ctakes pipelines. Can anyone share the experience how do you
> > write codes with some pipelines, (maybe in JAVA or else).
> >
> > Thanks,
> > Xiayuan
> >
> >
> > On 2014-05-02 10:55, Miller, Timothy wrote:
> >> Yes Pei, thanks, though now that I see it I'm not as sure that it
> >> will be useful to Maha and Xiayuan.
> >> Tim
> >>
> >> On 05/02/2014 11:17 AM, Pei Chen wrote:
> >>
> >>> Tim,
> >>> Do you mean:
> >>>
> >>
> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
> >>> [3]
> >>>
> >>> ?
> >>>
> >>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
> >>> <Ti...@childrens.harvard.edu> wrote:
> >>>
> >>>> Another resource that may be more useful for many use cases is the
> >>>> type
> >>>> system documentation. I seem to have lost that link -- can anyone
> >>>> please
> >>>> chime in with it?
> >>>>
> >>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
> >>>>> Try
> >>>>>
> >>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
> >>>>>
> >>>>> -- James
> >>>>>
> >>>>> -----Original Message-----
> >>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
> >>>>> Sent: Thursday, May 01, 2014 7:41 PM
> >>>>> To: user@ctakes.apache.org
> >>>>> Cc: Maha Zohbi
> >>>>> Subject: Re: cTAKES API documentation
> >>>>>
> >>>>> Yes, same question. I have been looking for API or
> >>>> documentation for
> >>>>> long. Could some one help guide to it?
> >>>>>
> >>>>> Thanks,
> >>>>> Xiayuan
> >>>>>
> >>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
> >>>>>> Hi,
> >>>>>>
> >>>>>> We are looking to developing an application that processes
> >>>>>> unstructured medical data and feeds it into a decision support
> >>>> system.
> >>>>>> To do that we will use cTAKES. We downloaded the binary and
> >>>> followed
> >>>>>> the user guide. However, I couldn't find any API
> >>>> documentation.
> >>>>>> Can anyone point me to API documentation for cTAKES or a
> >>>> samples
> >>>>>> guide to use the API?
> >>>>>>
> >>>>>> Thanks
> >>>> --
> >>>> Tim Miller
> >>>> Instructor
> >>>> Boston Children's Hospital and Harvard Medical School
> >>>> timothy.miller@childrens.harvard.edu
> >>>> 617-919-1223 [2]
> >> --
> >> Tim Miller
> >> Instructor
> >> Boston Children's Hospital and Harvard Medical School
> >> timothy.miller@childrens.harvard.edu
> >> 617-919-1223
> >>
> >>
> >> Links:
> >> ------
> >> [1] http://ctakes.apache.org/apidocs/3.1.1/
> >> [2] tel:617-919-1223
> >> [3]
> >>
> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>
> --
> Tim Miller
> Instructor
> Boston Children's Hospital and Harvard Medical School
> timothy.miller@childrens.harvard.edu
> 617-919-1223
>
>
--
Ravi Garg
4th Year
MSc (hons) Biological Sciences
B.E (hons) Computer Science and Engineering
BITS Pilani KK Birla Goa Campus
Re: cTAKES API documentation
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
James posted the links to the API docs earlier, but I suspect you may
find examples more helpful.
If you look at the classes under
/ctakes-clinical-pipeline/org.apache.ctakes.clinicalpipeline.runtime,
you will see how to instantiate the default pipelines from within
UimaFit using the xml descriptors. You can override
BagOfAnnotationsGenerator with your own extractInformation() method and
do whatever you like for each annotation, or you can just copy the
layout to do something you like.
Alternatively, if you want to build your own pipelines programatically,
I would look at some of the pipelines in the ctakes-temporal project:
/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
if you aren't up to date on trunk (i.e. you are working off of a
release), then look at the most recent version in svn:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup
Finally, there is work-in-progress to define factory methods for getting
commonly used pipelines, not ready for primetime but may give you some
more examples of how pipelines can be put together:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?view=markup
Hope this helps.
Tim
On 05/02/2014 12:16 PM, Xiayuan Huang wrote:
> Actually I am looking for some API documentation like how to use and
> code with ctakes pipelines. Can anyone share the experience how do you
> write codes with some pipelines, (maybe in JAVA or else).
>
> Thanks,
> Xiayuan
>
>
> On 2014-05-02 10:55, Miller, Timothy wrote:
>> Yes Pei, thanks, though now that I see it I'm not as sure that it
>> will be useful to Maha and Xiayuan.
>> Tim
>>
>> On 05/02/2014 11:17 AM, Pei Chen wrote:
>>
>>> Tim,
>>> Do you mean:
>>>
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>>> [3]
>>>
>>> ?
>>>
>>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
>>> <Ti...@childrens.harvard.edu> wrote:
>>>
>>>> Another resource that may be more useful for many use cases is the
>>>> type
>>>> system documentation. I seem to have lost that link -- can anyone
>>>> please
>>>> chime in with it?
>>>>
>>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
>>>>> Try
>>>>>
>>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
>>>>>
>>>>> -- James
>>>>>
>>>>> -----Original Message-----
>>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
>>>>> Sent: Thursday, May 01, 2014 7:41 PM
>>>>> To: user@ctakes.apache.org
>>>>> Cc: Maha Zohbi
>>>>> Subject: Re: cTAKES API documentation
>>>>>
>>>>> Yes, same question. I have been looking for API or
>>>> documentation for
>>>>> long. Could some one help guide to it?
>>>>>
>>>>> Thanks,
>>>>> Xiayuan
>>>>>
>>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
>>>>>> Hi,
>>>>>>
>>>>>> We are looking to developing an application that processes
>>>>>> unstructured medical data and feeds it into a decision support
>>>> system.
>>>>>> To do that we will use cTAKES. We downloaded the binary and
>>>> followed
>>>>>> the user guide. However, I couldn't find any API
>>>> documentation.
>>>>>> Can anyone point me to API documentation for cTAKES or a
>>>> samples
>>>>>> guide to use the API?
>>>>>>
>>>>>> Thanks
>>>> --
>>>> Tim Miller
>>>> Instructor
>>>> Boston Children's Hospital and Harvard Medical School
>>>> timothy.miller@childrens.harvard.edu
>>>> 617-919-1223 [2]
>> --
>> Tim Miller
>> Instructor
>> Boston Children's Hospital and Harvard Medical School
>> timothy.miller@childrens.harvard.edu
>> 617-919-1223
>>
>>
>> Links:
>> ------
>> [1] http://ctakes.apache.org/apidocs/3.1.1/
>> [2] tel:617-919-1223
>> [3]
>> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
--
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu
617-919-1223
Re: cTAKES API documentation
Posted by Xiayuan Huang <hu...@cs.wisc.edu>.
Actually I am looking for some API documentation like how to use and
code with ctakes pipelines. Can anyone share the experience how do you
write codes with some pipelines, (maybe in JAVA or else).
Thanks,
Xiayuan
On 2014-05-02 10:55, Miller, Timothy wrote:
> Yes Pei, thanks, though now that I see it I'm not as sure that it
> will be useful to Maha and Xiayuan.
> Tim
>
> On 05/02/2014 11:17 AM, Pei Chen wrote:
>
>> Tim,
>> Do you mean:
>>
> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
>> [3]
>>
>> ?
>>
>> On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy
>> <Ti...@childrens.harvard.edu> wrote:
>>
>>> Another resource that may be more useful for many use cases is the
>>> type
>>> system documentation. I seem to have lost that link -- can anyone
>>> please
>>> chime in with it?
>>>
>>> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
>>>> Try
>>>>
>>>> http://ctakes.apache.org/apidocs/3.1.1/ [1]
>>>>
>>>> -- James
>>>>
>>>> -----Original Message-----
>>>> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
>>>> Sent: Thursday, May 01, 2014 7:41 PM
>>>> To: user@ctakes.apache.org
>>>> Cc: Maha Zohbi
>>>> Subject: Re: cTAKES API documentation
>>>>
>>>> Yes, same question. I have been looking for API or
>>> documentation for
>>>> long. Could some one help guide to it?
>>>>
>>>> Thanks,
>>>> Xiayuan
>>>>
>>>> On 2014-05-01 18:53, Maha Zohbi wrote:
>>>>> Hi,
>>>>>
>>>>> We are looking to developing an application that processes
>>>>> unstructured medical data and feeds it into a decision support
>>> system.
>>>>> To do that we will use cTAKES. We downloaded the binary and
>>> followed
>>>>> the user guide. However, I couldn't find any API
>>> documentation.
>>>>> Can anyone point me to API documentation for cTAKES or a
>>> samples
>>>>> guide to use the API?
>>>>>
>>>>> Thanks
>>>
>>> --
>>> Tim Miller
>>> Instructor
>>> Boston Children's Hospital and Harvard Medical School
>>> timothy.miller@childrens.harvard.edu
>>> 617-919-1223 [2]
>
> --
> Tim Miller
> Instructor
> Boston Children's Hospital and Harvard Medical School
> timothy.miller@childrens.harvard.edu
> 617-919-1223
>
>
> Links:
> ------
> [1] http://ctakes.apache.org/apidocs/3.1.1/
> [2] tel:617-919-1223
> [3]
> https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
Re: cTAKES API documentation
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Yes Pei, thanks, though now that I see it I'm not as sure that it will be useful to Maha and Xiayuan.
Tim
On 05/02/2014 11:17 AM, Pei Chen wrote:
Tim,
Do you mean:
https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
?
On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy <Ti...@childrens.harvard.edu>> wrote:
Another resource that may be more useful for many use cases is the type
system documentation. I seem to have lost that link -- can anyone please
chime in with it?
On 05/02/2014 11:05 AM, Masanz, James J. wrote:
> Try
>
> http://ctakes.apache.org/apidocs/3.1.1/
>
> -- James
>
> -----Original Message-----
> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu<ma...@cs.wisc.edu>]
> Sent: Thursday, May 01, 2014 7:41 PM
> To: user@ctakes.apache.org<ma...@ctakes.apache.org>
> Cc: Maha Zohbi
> Subject: Re: cTAKES API documentation
>
> Yes, same question. I have been looking for API or documentation for
> long. Could some one help guide to it?
>
> Thanks,
> Xiayuan
>
> On 2014-05-01 18:53, Maha Zohbi wrote:
>> Hi,
>>
>> We are looking to developing an application that processes
>> unstructured medical data and feeds it into a decision support system.
>> To do that we will use cTAKES. We downloaded the binary and followed
>> the user guide. However, I couldn't find any API documentation.
>> Can anyone point me to API documentation for cTAKES or a samples
>> guide to use the API?
>>
>> Thanks
--
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu<ma...@childrens.harvard.edu>
617-919-1223<tel:617-919-1223>
--
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu<ma...@childrens.harvard.edu>
617-919-1223
Re: cTAKES API documentation
Posted by Pei Chen <ch...@apache.org>.
Tim,
Do you mean:
https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.1.1/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
?
On Fri, May 2, 2014 at 11:14 AM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> Another resource that may be more useful for many use cases is the type
> system documentation. I seem to have lost that link -- can anyone please
> chime in with it?
>
>
>
> On 05/02/2014 11:05 AM, Masanz, James J. wrote:
> > Try
> >
> > http://ctakes.apache.org/apidocs/3.1.1/
> >
> > -- James
> >
> > -----Original Message-----
> > From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
> > Sent: Thursday, May 01, 2014 7:41 PM
> > To: user@ctakes.apache.org
> > Cc: Maha Zohbi
> > Subject: Re: cTAKES API documentation
> >
> > Yes, same question. I have been looking for API or documentation for
> > long. Could some one help guide to it?
> >
> > Thanks,
> > Xiayuan
> >
> > On 2014-05-01 18:53, Maha Zohbi wrote:
> >> Hi,
> >>
> >> We are looking to developing an application that processes
> >> unstructured medical data and feeds it into a decision support system.
> >> To do that we will use cTAKES. We downloaded the binary and followed
> >> the user guide. However, I couldn't find any API documentation.
> >> Can anyone point me to API documentation for cTAKES or a samples
> >> guide to use the API?
> >>
> >> Thanks
>
> --
> Tim Miller
> Instructor
> Boston Children's Hospital and Harvard Medical School
> timothy.miller@childrens.harvard.edu
> 617-919-1223
>
>
Re: cTAKES API documentation
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Another resource that may be more useful for many use cases is the type
system documentation. I seem to have lost that link -- can anyone please
chime in with it?
On 05/02/2014 11:05 AM, Masanz, James J. wrote:
> Try
>
> http://ctakes.apache.org/apidocs/3.1.1/
>
> -- James
>
> -----Original Message-----
> From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
> Sent: Thursday, May 01, 2014 7:41 PM
> To: user@ctakes.apache.org
> Cc: Maha Zohbi
> Subject: Re: cTAKES API documentation
>
> Yes, same question. I have been looking for API or documentation for
> long. Could some one help guide to it?
>
> Thanks,
> Xiayuan
>
> On 2014-05-01 18:53, Maha Zohbi wrote:
>> Hi,
>>
>> We are looking to developing an application that processes
>> unstructured medical data and feeds it into a decision support system.
>> To do that we will use cTAKES. We downloaded the binary and followed
>> the user guide. However, I couldn't find any API documentation.
>> Can anyone point me to API documentation for cTAKES or a samples
>> guide to use the API?
>>
>> Thanks
--
Tim Miller
Instructor
Boston Children's Hospital and Harvard Medical School
timothy.miller@childrens.harvard.edu
617-919-1223
RE: cTAKES API documentation
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Try
http://ctakes.apache.org/apidocs/3.1.1/
-- James
-----Original Message-----
From: Xiayuan Huang [mailto:huangxy@cs.wisc.edu]
Sent: Thursday, May 01, 2014 7:41 PM
To: user@ctakes.apache.org
Cc: Maha Zohbi
Subject: Re: cTAKES API documentation
Yes, same question. I have been looking for API or documentation for
long. Could some one help guide to it?
Thanks,
Xiayuan
On 2014-05-01 18:53, Maha Zohbi wrote:
> Hi,
>
> We are looking to developing an application that processes
> unstructured medical data and feeds it into a decision support system.
> To do that we will use cTAKES. We downloaded the binary and followed
> the user guide. However, I couldn't find any API documentation.
> Can anyone point me to API documentation for cTAKES or a samples
> guide to use the API?
>
> Thanks
Re: cTAKES API documentation
Posted by Xiayuan Huang <hu...@cs.wisc.edu>.
Yes, same question. I have been looking for API or documentation for
long. Could some one help guide to it?
Thanks,
Xiayuan
On 2014-05-01 18:53, Maha Zohbi wrote:
> Hi,
>
> We are looking to developing an application that processes
> unstructured medical data and feeds it into a decision support system.
> To do that we will use cTAKES. We downloaded the binary and followed
> the user guide. However, I couldn't find any API documentation.
> Can anyone point me to API documentation for cTAKES or a samples
> guide to use the API?
>
> Thanks