Hi Jeff, This looks pretty nice. Thank you for the reference - I gave it a skim but will be more thorough in a second run through whenever I get the time.
Sean ________________________________ From: Jeffery Painter <j...@jivecast.com> Sent: Tuesday, January 30, 2024 9:02 AM To: dev@ctakes.apache.org <dev@ctakes.apache.org> Subject: Re: Build issues today [EXTERNAL] * External Email - Caution * 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://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S1532046411000645__;!!NZvER7FxgEiBAiR_!s3995wdWcA05lOS5icNAI7H_mffo2rfYVluIJXerr1bCMEAvc8bYwNToVmeLxyWqHUBW3AC6KWehvAgdRIUcSeoiYg$ 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 >> >> >> >>
