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Posted to dev@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2015/12/08 22:41:23 UTC
ctakes blog
The recent discussion over dictionary building, and someone pointing out
it has come up several times, made me think that maybe we should use the
blog space that apache provides. It could be used for write-ups of
things that are not quite as formal as "documentation" but would benefit
from being written down somewhere that is easier to search and link to
than a mailing list.
Any thoughts?
Tim
Re: ctakes blog
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Sounds like there is enough interest. I will request a blog and take responsibility for a few posts along with occasionally asking for others to create content (like Andy and David who volunteered :) ).
Tim
________________________________________
From: Finan, Sean <Se...@childrens.harvard.edu>
Sent: Tuesday, December 8, 2015 6:12 PM
To: dev@ctakes.apache.org
Subject: RE: ctakes blog
Fantastic idea
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Tuesday, December 08, 2015 4:41 PM
To: dev@ctakes.apache.org
Subject: ctakes blog
The recent discussion over dictionary building, and someone pointing out it has come up several times, made me think that maybe we should use the blog space that apache provides. It could be used for write-ups of things that are not quite as formal as "documentation" but would benefit from being written down somewhere that is easier to search and link to than a mailing list.
Any thoughts?
Tim
RE: ctakes blog
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Fantastic idea
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Tuesday, December 08, 2015 4:41 PM
To: dev@ctakes.apache.org
Subject: ctakes blog
The recent discussion over dictionary building, and someone pointing out it has come up several times, made me think that maybe we should use the blog space that apache provides. It could be used for write-ups of things that are not quite as formal as "documentation" but would benefit from being written down somewhere that is easier to search and link to than a mailing list.
Any thoughts?
Tim
Re: ctakes blog
Posted by andy mcmurry <mc...@gmail.com>.
Hopefully of use .... a large number of UMLS concepts are publicly
availability to download without UMLS license for sources in MedGen, which
represents 300k+ concepts, including many concepts and relationships in
SNOMED-CT, MESH, NCI Metathausurus (MTH), etc.
You can download UMLS dictionaries for medgen here from NLM (no login)
<ftp://ftp.ncbi.nlm.nih.gov/pub/medgen/>
For custom dictionaries, you can use Bash to download and build many
concepts in UMLS related dictionaries:
https://bitbucket.org/invitae/medgen-mysql
#concepts for each UMLS Semantic Type (STY) referenced by MedGen
+-------------------------------------------+--------+
| STY | cnt |
+-------------------------------------------+--------+
| Pharmacologic Substance | 102511 |
| Finding | 90413 |
| Organic Chemical | 81329 |
| Disease or Syndrome | 47223 |
| Neoplastic Process | 16151 |
| Amino Acid, Peptide, or Protein | 9383 |
| Congenital Abnormality | 6536 |
| Pathologic Function | 5655 |
| Steroid | 3919 |
| Sign or Symptom | 2909 |
| ... | ... |
On Tue, Dec 8, 2015 at 2:19 PM, andy mcmurry <mc...@gmail.com> wrote:
> +1 I would be happy to write about the experience of creating the medgen
> (medical genetics) database, especially useful for cancer and cardio
> On Dec 8, 2015 2:04 PM, "David Kincaid" <ki...@gmail.com> wrote:
>
>> That is a great idea! I'd be happy to help provide some content as someone
>> who has been trying to use cTAKES inside other projects. As I mentioned
>> previously I am working in veterinary medicine which has just enough
>> peculiarities to make cTAKES out of the box a challenge (although it is
>> much better now than it was a couple years ago, so kudos to those of you
>> who have been making it better). I also can't stand Eclipse, happily left
>> Subversion behind years ago and prefer to work in Clojure as much as
>> possible.
>>
>> - Dave
>>
>> On Tue, Dec 8, 2015 at 3:41 PM, Miller, Timothy <
>> Timothy.Miller@childrens.harvard.edu> wrote:
>>
>> > The recent discussion over dictionary building, and someone pointing out
>> > it has come up several times, made me think that maybe we should use the
>> > blog space that apache provides. It could be used for write-ups of
>> > things that are not quite as formal as "documentation" but would benefit
>> > from being written down somewhere that is easier to search and link to
>> > than a mailing list.
>> > Any thoughts?
>> > Tim
>> >
>> >
>>
>
--
Andy McMurry, PhD
Chief Technical Officer
http://GetMedal.com
Re: ctakes blog
Posted by andy mcmurry <mc...@gmail.com>.
+1 I would be happy to write about the experience of creating the medgen
(medical genetics) database, especially useful for cancer and cardio
On Dec 8, 2015 2:04 PM, "David Kincaid" <ki...@gmail.com> wrote:
> That is a great idea! I'd be happy to help provide some content as someone
> who has been trying to use cTAKES inside other projects. As I mentioned
> previously I am working in veterinary medicine which has just enough
> peculiarities to make cTAKES out of the box a challenge (although it is
> much better now than it was a couple years ago, so kudos to those of you
> who have been making it better). I also can't stand Eclipse, happily left
> Subversion behind years ago and prefer to work in Clojure as much as
> possible.
>
> - Dave
>
> On Tue, Dec 8, 2015 at 3:41 PM, Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
> > The recent discussion over dictionary building, and someone pointing out
> > it has come up several times, made me think that maybe we should use the
> > blog space that apache provides. It could be used for write-ups of
> > things that are not quite as formal as "documentation" but would benefit
> > from being written down somewhere that is easier to search and link to
> > than a mailing list.
> > Any thoughts?
> > Tim
> >
> >
>
Re: ctakes blog
Posted by David Kincaid <ki...@gmail.com>.
That is a great idea! I'd be happy to help provide some content as someone
who has been trying to use cTAKES inside other projects. As I mentioned
previously I am working in veterinary medicine which has just enough
peculiarities to make cTAKES out of the box a challenge (although it is
much better now than it was a couple years ago, so kudos to those of you
who have been making it better). I also can't stand Eclipse, happily left
Subversion behind years ago and prefer to work in Clojure as much as
possible.
- Dave
On Tue, Dec 8, 2015 at 3:41 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:
> The recent discussion over dictionary building, and someone pointing out
> it has come up several times, made me think that maybe we should use the
> blog space that apache provides. It could be used for write-ups of
> things that are not quite as formal as "documentation" but would benefit
> from being written down somewhere that is easier to search and link to
> than a mailing list.
> Any thoughts?
> Tim
>
>
Re: ctakes blog
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
So, it turned out we already had one setup for ctakes that wasn't being
used. But I think anyone in the PMC can sign up for access by creating a
JIRA item under the INFRA project asking for blog access to ctakes.
I think a great topic for a blog post would be how to use the dictionary
tool to build a custom dictionary. If anyone wants to volunteer please
sign up as above.
I would like to create one on how to scale with UIMA-AS and maybe one on
how to use ctakes as an API, schedule to be determined.
Tim
On 12/09/2015 11:17 AM, John Travis Green wrote:
> I think there is a lot of opportunity here to document things (e.g. Tutorials like how to setup an annotator; I created a video for example that still needs posted somewhere to this effect) that may not have a formal place on the website but need explaining. Example: given the number of ancillary software (maven, uima, eclipse itself etc) there are some serious barriers to would-be contributers who may not work with all of these technologies on a daily basis, if ever. I think this might engender more community engagement. JG
>
> ---Sent from Boxer | https://urldefense.proofpoint.com/v2/url?u=http-3A__getboxer.com&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=KfDEZkK8LpvsFFY55y4XCt2cUmab3IvXKgPNONjgSIg&s=RLiFd4TZtbdAxdB-ODdjWwQoVjyc8fghIe5-z2h27zI&e=
>
> Excellent idea!
>
> +1
>
> --guergana
>
>
>
> -----Original Message-----
>
> From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
> Sent: Tuesday, December 8, 2015 4:41 PM
>
> To: dev@ctakes.apache.org
>
> Subject: ctakes blog
>
>
>
> The recent discussion over dictionary building, and someone pointing out it has come up several times, made me think that maybe we should use the blog space that apache provides. It could be used for write-ups of things that are not quite as formal as "documentation" but would benefit from being written down somewhere that is easier to search and link to than a mailing list.
>
> Any thoughts?
>
> Tim
>
>
>
>
RE: ctakes blog
Posted by John Travis Green <jo...@gmail.com>.
I think there is a lot of opportunity here to document things (e.g. Tutorials like how to setup an annotator; I created a video for example that still needs posted somewhere to this effect) that may not have a formal place on the website but need explaining. Example: given the number of ancillary software (maven, uima, eclipse itself etc) there are some serious barriers to would-be contributers who may not work with all of these technologies on a daily basis, if ever. I think this might engender more community engagement. JG
---Sent from Boxer | http://getboxer.com
Excellent idea!
+1
--guergana
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Tuesday, December 8, 2015 4:41 PM
To: dev@ctakes.apache.org
Subject: ctakes blog
The recent discussion over dictionary building, and someone pointing out it has come up several times, made me think that maybe we should use the blog space that apache provides. It could be used for write-ups of things that are not quite as formal as "documentation" but would benefit from being written down somewhere that is easier to search and link to than a mailing list.
Any thoughts?
Tim
RE: ctakes blog
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
Excellent idea!
+1
--guergana
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Tuesday, December 8, 2015 4:41 PM
To: dev@ctakes.apache.org
Subject: ctakes blog
The recent discussion over dictionary building, and someone pointing out it has come up several times, made me think that maybe we should use the blog space that apache provides. It could be used for write-ups of things that are not quite as formal as "documentation" but would benefit from being written down somewhere that is easier to search and link to than a mailing list.
Any thoughts?
Tim
Re: ctakes blog
Posted by britt fitch <br...@wiredinformatics.com>.
I like the blog approach.
I think it will help direct the creation of various guide-type documentation going forward.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com
> On Dec 8, 2015, at 4:41 PM, Miller, Timothy <Ti...@childrens.harvard.edu> wrote:
>
> The recent discussion over dictionary building, and someone pointing out
> it has come up several times, made me think that maybe we should use the
> blog space that apache provides. It could be used for write-ups of
> things that are not quite as formal as "documentation" but would benefit
> from being written down somewhere that is easier to search and link to
> than a mailing list.
> Any thoughts?
> Tim
>