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From N M <maveric...@gmail.com>
Subject Re: cTAKES API documentation
Date Mon, 12 May 2014 14:07:07 GMT
a pdf is probably not the best format to contain this information, since
updates are a hassle. I think this could be something that would be useful
on the wiki, as versioning and history are much easier to control. I don't
think it would be unreasonable to propose a working group to create
something like this?

@James: thanks for providing the slides. they are a different "view" of the
types, and important as well... I wonder if there would be some way to
cross-reference a pipeline diagram (such as in the pdf) with a type
inheritance diagram? One way I could see this working in a wiki setting
would be to link the name of a type on a pipeline diagram page to its
location on a type hierarchy tree page.

@Tim:
2) this depends on the pipeline. Some of the newer pipelines are slightly
better at this, though even then the information is somewhat incomplete.
Older pipelines (for example smoking) seem to be missing this information
completely.

3) you're right that any UIMAfit components have the type annotations
specified. Those cases really helped when I was creating my notes. It
didn't seem to me that outputs were specified. it would be nice if a
UIMAfit library/parser existed that could draw out this information. Though
incomplete, it would help create a "fill-in-the-blank" initial structure,
which could then be manually amended.

Is there any overall interest in making documentation like this more
complete and available? I don't have the resources to do all of this
myself, but if there are others who would like to pitch in, I'd gladly take
part in the project.

-NM


On Wed, May 7, 2014 at 4:00 PM, Masanz, James J. <Masanz.James@mayo.edu>wrote:

>  The slides I was referring to are:
>
>
> https://wiki.nci.nih.gov/download/attachments/63996717/CTAKES_type_system_v1.0.5.ppt
>
>
>
> The slides took the approach of highlighting the type system, not the
> annotators, showing which types of annotations were created and attributes
> filled in by each annotator, but without explicitly naming the annotator in
> the slide
>
>
>
> *From:* Masanz, James J.
> *Sent:* Wednesday, May 07, 2014 2:47 PM
> *To:* 'user@ctakes.apache.org'
> *Subject:* RE: cTAKES API documentation
>
>
>
> There were slides created for the very first release of cTAKES that showed
> something along these lines. I don’t see it online anymore, but it’s
> outdated anyway. I’ll look for a copy and post them somewhere.
>
>
>
> I like the PDF but I’d suggest keeping the format as simple as possible to
> make it easy to make updates.
>
>
>
> Also, I suggest either removing or adding a footnote for those attributes
> that aren’t set by a given annotator.  For example, the output of Tokenizer
> Annotator is shown to be BaseToken, but because some attributes of
> BaseToken are listed, someone might wrongly infer that the Tokenizer sets
> the values of those attributes, when some of them are actually set by later
> annotators.
>
>
>
> It would also be good to list which release of cTAKES it applies to.
>
>
>
> -- James
>
>
>
> *From:* N M [mailto:mavericnlp@gmail.com <mavericnlp@gmail.com>]
> *Sent:* Tuesday, May 06, 2014 4:01 PM
> *To:* user@ctakes.apache.org
>
> *Subject:* Re: cTAKES API documentation
>
>
>
> 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 <ravigarg27@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
> >>> <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/ [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
>
>
>

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