Thanks Sean - it is working again with the 5.0.0 models. I'm actually
glad you did not roll in my updates yet, as I found another subtle bug
in the creation of the concept graphs and I have implemented 4 more of
the kernel metrics which we are investigating based on the paper from
Sanchez and Batet:
https://www.sciencedirect.com/science/article/pii/S1532046411000645
I am adding in the Dice, Ochiai, Simpson and Braun-Blanquet methods
shown in Table 3. I discovered some of the path metrics were being
inflated due to invalid max-depth calculations in the original concept
graph creation due to the root concept not being set to a depth of zero
which I have fixed and now all appears to be working. I will cancel
those PR's and update later today.
Thanks,
Jeff
On 1/26/24 15:30, Finan, Sean wrote:
This is open for other responses, but I would probably use:
Savova, G. K. et al. Mayo clinical Text Analysis and Knowledge Extraction
System (cTAKES): architecture, component evaluation and applications. J. Am.
Med. Inform. Assoc. JAMIA 17, 507–513 (2010).
You can also point to the github repo if appropriate.
Sean
________________________________
From: Jeffery Painter <j...@jivecast.com>
Sent: Friday, January 26, 2024 1:19 PM
To: dev@ctakes.apache.org <dev@ctakes.apache.org>
Subject: Re: Build issues today [EXTERNAL]
* External Email - Caution *
Thanks!
We are preparing an abstract to submit to ICPE in a couple of weeks - is
there a preferred way to reference cTakes in publications?
-
Jeffery
On 1/26/24 12:29, Finan, Sean wrote:
Hi Jeff,
I updated the poms in 5.0.0-SNAPSHOT to use the correct models. There
shouldn't be any problem building.
Sean
________________________________
From: Jeffery Painter <j...@jivecast.com>
Sent: Tuesday, January 23, 2024 11:55 AM
To: dev@ctakes.apache.org <dev@ctakes.apache.org>
Subject: Build issues today [EXTERNAL]
* External Email - Caution *
Just a heads up, getting several build issues due to the fact that the
5.0.0-SNAPSHOT jars for most of the ctakes-??-models.jar seem to have
disappeared from the snapshot repository.
Manually adjusting those to 5.0.1-SNAPSHOT is working for now, but
thought I would let whoever controls the build process know that a fresh
checkout from github is currently broken.
Example:
[ERROR] Failed to execute goal on project ctakes-ytex-uima: Could not
resolve dependencies for project
org.apache.ctakes:ctakes-ytex-uima:jar:5.0.0-SNAPSHOT: The following
artifacts could not be resolved:
org.apache.ctakes:ctakes-dependency-parser-models:jar:5.0.0-SNAPSHOT
(absent):
org.apache.ctakes:ctakes-dependency-parser-models:jar:5.0.0-SNAPSHOT was
not found in
https://urldefense.com/v3/__https://repository.apache.org/content/groups/snapshots/__;!!NZvER7FxgEiBAiR_!rib8DHyV18yZjtkkuXnrMN2QW0rSURWoyL5_Smr6rhyFqr3JaSzUbSIpnLP1QfUSfCeKAE5VksX-Ls64kzyp0Ej7uw$
during a previous attempt. This failure was cached in the local
repository and resolution is not reattempted until the update interval
of apache.snapshots has elapsed or updates are forced -> [Help 1]
Verified that core models have disappeared:
https://urldefense.com/v3/__https://repository.apache.org/content/groups/snapshots/org/apache/ctakes/ctakes-core-models/5.0.0-SNAPSHOT/__;!!NZvER7FxgEiBAiR_!rib8DHyV18yZjtkkuXnrMN2QW0rSURWoyL5_Smr6rhyFqr3JaSzUbSIpnLP1QfUSfCeKAE5VksX-Ls64kzxgwSJHlg$
contains no jars
Thanks,
Jeff
