Documentation

[John Green <jo...@gmail.com>]

Hi all, Happy Holidays!

I have a week off, then 6 weeks of insanity, then Ill finally be regularly
free to try and help out, not that anyone is holding their breath or
anything. When February roles around and I really start applying myself to
some development corner of cTakes, is there anything I can do in the
meantime that is pressing slop-work? Anything that I can leverage my
clinical experience with to helping ctakes? Other than committing some more
notes. Or maybe menial coding that is pressing? Like I've said before, Im
no computer scientist (only aspiring), but I can definitely knock out some
grunt-work coding.

In the meantime, this week, Im still trying to get a real working
understanding of all the moving parts in cTakes, both from a user side
(building annotators, pipelines, dictionaries, etc) and a development side.
I dont want to trouble anyone with individual questions before I've tackled
all the literature/code documentation; however, what --is-- all the
literature? The documentation, beyond installing the software, seems to be
very spread out. Am I missing something obvious? Or is it just, "dig in and
read a billion different posts from 2008-till present" time (including all
the UIMA documentation/Lucene documentation etc)?

As is the patent phrase in moments like these: forgive me if this has been
asked before.

John Green

Re: Documentation

[John Green <jo...@gmail.com>]

For sure! I read everyone of the emails on this list everyday!

JG


On Fri, Dec 20, 2013 at 4:22 PM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:

> Hi John,
> In addition to the documentation, you may want to follow some of the
> Groovy discussion (plus any other active topics on the dev list..).
> The Groovy scripts may be an easy way to get started with some programming
> experience and one can easily start poking at the code to see what the
> components are doing.
> Just an idea...
>
> > -----Original Message-----
> > From: John Green [mailto:john.travis.green@gmail.com]
> > Sent: Friday, December 20, 2013 4:15 PM
> > To: dev@ctakes.apache.org
> > Subject: Documentation
> >
> > Hi all, Happy Holidays!
> >
> > I have a week off, then 6 weeks of insanity, then Ill finally be
> regularly free to
> > try and help out, not that anyone is holding their breath or anything.
> When
> > February roles around and I really start applying myself to some
> > development corner of cTakes, is there anything I can do in the meantime
> > that is pressing slop-work? Anything that I can leverage my clinical
> > experience with to helping ctakes? Other than committing some more notes.
> > Or maybe menial coding that is pressing? Like I've said before, Im no
> > computer scientist (only aspiring), but I can definitely knock out some
> grunt-
> > work coding.
> >
> > In the meantime, this week, Im still trying to get a real working
> > understanding of all the moving parts in cTakes, both from a user side
> > (building annotators, pipelines, dictionaries, etc) and a development
> side.
> > I dont want to trouble anyone with individual questions before I've
> tackled all
> > the literature/code documentation; however, what --is-- all the
> literature?
> > The documentation, beyond installing the software, seems to be very
> spread
> > out. Am I missing something obvious? Or is it just, "dig in and read a
> billion
> > different posts from 2008-till present" time (including all the UIMA
> > documentation/Lucene documentation etc)?
> >
> > As is the patent phrase in moments like these: forgive me if this has
> been
> > asked before.
> >
> > John Green
>

RE: Documentation

["Chen, Pei" <Pe...@childrens.harvard.edu>]

Hi John,
In addition to the documentation, you may want to follow some of the Groovy discussion (plus any other active topics on the dev list..).  
The Groovy scripts may be an easy way to get started with some programming experience and one can easily start poking at the code to see what the components are doing.  
Just an idea...

> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com]
> Sent: Friday, December 20, 2013 4:15 PM
> To: dev@ctakes.apache.org
> Subject: Documentation
> 
> Hi all, Happy Holidays!
> 
> I have a week off, then 6 weeks of insanity, then Ill finally be regularly free to
> try and help out, not that anyone is holding their breath or anything. When
> February roles around and I really start applying myself to some
> development corner of cTakes, is there anything I can do in the meantime
> that is pressing slop-work? Anything that I can leverage my clinical
> experience with to helping ctakes? Other than committing some more notes.
> Or maybe menial coding that is pressing? Like I've said before, Im no
> computer scientist (only aspiring), but I can definitely knock out some grunt-
> work coding.
> 
> In the meantime, this week, Im still trying to get a real working
> understanding of all the moving parts in cTakes, both from a user side
> (building annotators, pipelines, dictionaries, etc) and a development side.
> I dont want to trouble anyone with individual questions before I've tackled all
> the literature/code documentation; however, what --is-- all the literature?
> The documentation, beyond installing the software, seems to be very spread
> out. Am I missing something obvious? Or is it just, "dig in and read a billion
> different posts from 2008-till present" time (including all the UIMA
> documentation/Lucene documentation etc)?
> 
> As is the patent phrase in moments like these: forgive me if this has been
> asked before.
> 
> John Green

Re: Documentation

[John Green <jo...@gmail.com>]

James, thank you for such a comprehensive reply! I sincerely appreciate the
effort.

I was being slightly tongue-in-cheek in regards to "diving into old posts",
but thank you for the affirmation that I'm probably right on track. Im
finding the UIMA documentation profoundly helpful along with cherry-picked
old messages on the cTakes boards.

Thank you for pointing me at 3 useful issues to tackle. I'm going to take a
hard look at those 3 issues around Feb 3rd, when my latest series of exams
are over.

Regards groovy, I'm not familiar with it, but Ill take a brief look also in
February. This week I had off was spent almost entirely reading UIMA
documentation and a lot of the papers around cTakes.

The documentation is also something I am very interested in helping with,
especially since I'm going through it all right now as a new
user/developer. I will make this a high priority Feb 3rd as well.

Again, thank you for pointing me in a couple of directions where I can be
most helpful. I look forward to this set of exams being done with so I can
get to it. Reading all of the cTakes literature and its associated article
references was very exciting.

Sincerely,
JG


On Mon, Dec 23, 2013 at 11:41 AM, Masanz, James J. <Ma...@mayo.edu>wrote:

> Hi John,
>
> As far as documentation, I doubt you are missing anything
>
> It all really starts from
> http://ctakes.apache.org/
> but with most of it on the confluence wiki
> https://cwiki.apache.org/confluence/display/CTAKES/
>
> And then yes there are bits and pieces spread across old posts.
>
> As far as code, you might try taking a look at any of these
> https://issues.apache.org/jira/i#browse/CTAKES-217
> https://issues.apache.org/jira/i#browse/CTAKES-155
> https://issues.apache.org/jira/i#browse/CTAKES-66
>
> Or any other JIRA issue that doesn't have an assignee.
> Or if you see an open issue with an assignee that looks interesting, you
> could also ask if someone is in the middle of a fix or not.
>
> I also plan to post or checkin some a groovy script for running the
> AggregatePlaintextUMLSProcessor today or tomorrow. The version I am working
> on doesn't do the dynamic downloading of the required components - I am
> taking the tactic of assuming the user downloaded a cTAKES binary and the
> separately downloadable resources.
>
> I think it would be great if you could try it out, and perhaps extend so
> there is a way to run an example of each component to give people an idea
> of what each component can do, as has been discussed on the dev@ mailing
> list.
>
> Another task might be to point out where you think the documentation is
> most scattered and maybe we can address that.
>
> -- James
>
> -----Original Message-----
> From: dev-return-2334-Masanz.James=mayo.edu@ctakes.apache.org [mailto:
> dev-return-2334-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of
> John Green
> Sent: Friday, December 20, 2013 3:15 PM
> To: dev@ctakes.apache.org
> Subject: Documentation
>
> Hi all, Happy Holidays!
>
> I have a week off, then 6 weeks of insanity, then Ill finally be regularly
> free to try and help out, not that anyone is holding their breath or
> anything. When February roles around and I really start applying myself to
> some development corner of cTakes, is there anything I can do in the
> meantime that is pressing slop-work? Anything that I can leverage my
> clinical experience with to helping ctakes? Other than committing some more
> notes. Or maybe menial coding that is pressing? Like I've said before, Im
> no computer scientist (only aspiring), but I can definitely knock out some
> grunt-work coding.
>
> In the meantime, this week, Im still trying to get a real working
> understanding of all the moving parts in cTakes, both from a user side
> (building annotators, pipelines, dictionaries, etc) and a development side.
> I dont want to trouble anyone with individual questions before I've tackled
> all the literature/code documentation; however, what --is-- all the
> literature? The documentation, beyond installing the software, seems to be
> very spread out. Am I missing something obvious? Or is it just, "dig in and
> read a billion different posts from 2008-till present" time (including all
> the UIMA documentation/Lucene documentation etc)?
>
> As is the patent phrase in moments like these: forgive me if this has been
> asked before.
>
> John Green
>

RE: Documentation

["Masanz, James J." <Ma...@mayo.edu>]

Hi John,

As far as documentation, I doubt you are missing anything

It all really starts from 
http://ctakes.apache.org/
but with most of it on the confluence wiki
https://cwiki.apache.org/confluence/display/CTAKES/

And then yes there are bits and pieces spread across old posts.

As far as code, you might try taking a look at any of these
https://issues.apache.org/jira/i#browse/CTAKES-217
https://issues.apache.org/jira/i#browse/CTAKES-155
https://issues.apache.org/jira/i#browse/CTAKES-66

Or any other JIRA issue that doesn't have an assignee.
Or if you see an open issue with an assignee that looks interesting, you could also ask if someone is in the middle of a fix or not.

I also plan to post or checkin some a groovy script for running the AggregatePlaintextUMLSProcessor today or tomorrow. The version I am working on doesn't do the dynamic downloading of the required components - I am taking the tactic of assuming the user downloaded a cTAKES binary and the separately downloadable resources. 

I think it would be great if you could try it out, and perhaps extend so there is a way to run an example of each component to give people an idea of what each component can do, as has been discussed on the dev@ mailing list.

Another task might be to point out where you think the documentation is most scattered and maybe we can address that.

-- James

-----Original Message-----
From: dev-return-2334-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-2334-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of John Green
Sent: Friday, December 20, 2013 3:15 PM
To: dev@ctakes.apache.org
Subject: Documentation

Hi all, Happy Holidays!

I have a week off, then 6 weeks of insanity, then Ill finally be regularly
free to try and help out, not that anyone is holding their breath or
anything. When February roles around and I really start applying myself to
some development corner of cTakes, is there anything I can do in the
meantime that is pressing slop-work? Anything that I can leverage my
clinical experience with to helping ctakes? Other than committing some more
notes. Or maybe menial coding that is pressing? Like I've said before, Im
no computer scientist (only aspiring), but I can definitely knock out some
grunt-work coding.

In the meantime, this week, Im still trying to get a real working
understanding of all the moving parts in cTakes, both from a user side
(building annotators, pipelines, dictionaries, etc) and a development side.
I dont want to trouble anyone with individual questions before I've tackled
all the literature/code documentation; however, what --is-- all the
literature? The documentation, beyond installing the software, seems to be
very spread out. Am I missing something obvious? Or is it just, "dig in and
read a billion different posts from 2008-till present" time (including all
the UIMA documentation/Lucene documentation etc)?

As is the patent phrase in moments like these: forgive me if this has been
asked before.

John Green