Hi Jeff, That sounds great - I am happy when ctakes beneficial in any way.
As far as simplicity goes, there is an installation tool in 5.0.0-SNAPSHOT: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dockhand/5.0.0-SNAPSHOT/ I have to run some final tests, but I have been thinking of placing it in GitHub as an artifact. The single jar is all that is needed and it is a self-contained executable - as long as java is in the $PATH. It builds an installation with a piper file that can be edited by the user. We are still trying to make standard installation easier, so if you have any suggestions please post them on the ctakes GitHub repo here: https://github.com/apache/ctakes/issues with the label "enhancement". Thank you for all the enhancements and technical information, Sean ________________________________ From: Jeffery Painter <j...@jivecast.com> Sent: Tuesday, January 30, 2024 11:40 AM To: dev@ctakes.apache.org <dev@ctakes.apache.org> Subject: Re: Build issues today [EXTERNAL] * External Email - Caution * Thanks Sean, I think we may end up with a series of pubs out of this work. I just want to emphasize how much more efficient it is to compute these metrics using cTakes than the old Perl UMLS::Similarity module. I don't think anyone realizes the amount of computational time this saves us (days to compute matrices with Perl versus seconds/minutes with cTakes). Hopefully we can shed some light on the benefits (even if it is a bit more complicated to setup and use) :-) - Jeff On 1/30/24 10:59, Finan, Sean wrote: > 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 >>> >>> >>> >>>
