Re: Question about DrugNerAnnotator [EXTERNAL]

g this can offer some advice > you should probably throw up those hands and look for another solution to > extracting drug attributes. > > Definitely less interesting than sunken treasure. > > Sean > > From: Peter Abramowitsch > Sent: Wedne

Re: Question about DrugNerAnnotator [EXTERNAL]

ome point, but it may have been removed. > > ____ > From: Peter Abramowitsch > Sent: Wednesday, December 4, 2024 10:25 AM > To: dev@ctakes.apache.org > Subject: Re: Question about DrugNerAnnotator [EXTERNAL] > > * External Email - Caution * > >

Re: Question about DrugNerAnnotator [EXTERNAL]

ere has > a general solution please share. > https://github.com/apache/uima-uimaj/issues/234 > > > Sean > > > From: Peter Abramowitsch > Sent: Tuesday, December 3, 2024 3:29 PM > To: dev@ctakes.apache.org > Subject: Question about

Question about DrugNerAnnotator

Hi All If anyone has tried using the Drugner in 5.1.0 have they run into this error when its process() method is run. message: JCas type "org.apache.ctakes.drugner.type.FractionStrengthAnnotation" used in Java code, but was not declared in the XML type descriptor The thing is that this attribut

Re: Fw: Please test the cTAKES-6.0.0 candidate for release

Thanks Sean. I haven't had time to test yet, but i may get a chance this week. Peter On Wed, Sep 11, 2024, 06:54 Finan, Sean wrote: > Hi all, > > I have requested a vote on the release by the Apache cTAKES Project > Management Committee (PMC). The vote will end at 5:pm next Monday, > Septembe

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

Hi Gandhi and RIchard, Just pasting the versionRange change into my 5.1.0 root pom in the m2e plugin fixed the lifecycle errors on every project I've been living with, in Eclipse, for a while. Gandhi, if you can find a different solution I'm good with that too. In any case, this change should on

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

Hi Richard... It was a typo on my part. I meant to write: "wasn't" Peter On Fri, Jul 26, 2024 at 9:09 AM Richard Eckart de Castilho wrote: > Hi, > > > On 26. Jul 2024, at 12:42, Peter Abramowitsch > wrote: > > > > The log4j team themselv

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

wonder why "the log4j team themselves say that bundling > property files inside distributed jars is good practice" ? Did they just > mean that it was better than not supplying any and having log4j rely upon > defaults that may change with new log4j versions? I digress. > >

Re: SLF4J instead of Log4J at the API level? [EXTERNAL]

And again on this same topic - log4j, I noticed a new inability to control the logging level of our high-volume ctakes installation and discovered that there are several jars (two 3rd-party new in 5.1.0) that contain a log4j.properties with root logging set to INFO and a console appender on root.

Resending without attachments.,

Shifting this thread back to the main ctakes thread where it belongs... Hi Joel, >From your dump, it looks as if the main concept dictionary is missing. *"No Resource at resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.script"* It's currently configured to run with a s

Re: Remaining Maven errors visible in Eclipse [EXTERNAL]

't know that it is worth doing. Personally, I'd like to put ytex-web in > the attic and refer to ctakes-web-rest as a replacement. Perhaps we can do > that in ctakes 6 ? > > Thanks, > > Sean > > > From: Peter Abramowits

Remaining Maven errors visible in Eclipse

Hi Sean, there are some minor 5.1.0 Maven glitches picked up by Eclipse, one of which I can fix and others not. in ctakes-ytex-web's pom.xml, I changed *ctakes*.version to *parent*.version. I have not checked it in, it case it wasn't the right thing to do, but it made the error go away. org.apa

Mastif Zoner is there now

Hi Sean I did a clean build, also removing the mastif zoner library from my maven cache. It does get into the distribution now. My git branch got a bit confused when I tried to merge the tag into it. But by destroying my branch and using switch -c to create a new one off the 5.1.0 tag it seemed

Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

I'll test it today. Thanks Sean. Peter On Wed, May 1, 2024, 14:05 Finan, Sean wrote: > Hi Peter, > > I think that I have the ctakes-mastif-zoner module behavior as desired. > Let me know if you have any problems with the new candidate. > > Sean > ____

Re: Please test the Apache cTAKES 5.1.0 release candidate

at > java.base/java.lang.reflect.Method.setAccessible(Method.java:193) > [INFO] [java] at > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:177) > [INFO] [java] at > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:172) > [IN

Re: Please test the Apache cTAKES 5.1.0 release candidate

some debug statements rather than asserts would tell you, I think. Peter On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch wrote: > Hi Gandhi > This project is an odd one in the sense that when you tell it to skip the > tests, it still goes through the effort in building up the db envi

Re: Please test the Apache cTAKES 5.1.0 release candidate

l which in turn is trying to invoke the following target in > build.setup.xml: > > depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> > > > > Did you try running this on a fresh setup Peter? > > On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch > w

Re: Please test the Apache cTAKES 5.1.0 release candidate

Hi Gandhi Your error appears to be at this line C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java returned: 1 A test application being run here: AppMain is in charge of loading a temporary mysqldb that is used to test that part of ytex. For me it is working, but if y

Re: Please test the Apache cTAKES 5.1.0 release candidate

ve our own Apart from the missing project I mentioned in the previous email that does need to be fixed, I would give 5.1.0 a plus for release. Peter On Fri, Apr 26, 2024 at 8:41 PM Peter Abramowitsch wrote: > Hi Sean, > > It all compiles, but one of the jars is missing from the distributio

Re: Please test the Apache cTAKES 5.1.0 release candidate

Hi Sean, It all compiles, but one of the jars is missing from the distribution. It's the one I added: ctakes-mastif-zoner which is required if you're going to use the Zone Annotator. It's in the master pom, and in the pom of ctakes-distribution, and the jar got built in its projecte, but it's no

Re: Please test the Apache cTAKES 5.1.0 release candidate

Hi Sean I'll do a runthrough. But looking through the commits, except for label changes, it looks as if most of the last code additions & changes were mine from a couple of months ago. I'm planning to put this release (wrapped in our webservice framework) into production in a month or so. Peter

Changes to the Assertion-Zoner

Hi all. I've merged in an update to the AssertionZoner (for detection of Sections in clinical text). There's a new markdown file in the project ctakes-assertion-zoner describing the changes and how to take advantage of the new features. The update (code graciously permitted by my client UCSF)

Re: Examining Ctakes 5.0 - two sides of the same question [EXTERNAL]

as a dependency. Keep your project code > only in your project repository. If you want to make changes to ctakes in > parallel, you can also create a module in your ctakes source root and put > your non-ctakes code only in that module. Don't check in that module! > - All that said

Examining Ctakes 5.0 - two sides of the same question

The question is: what is our policy if a resource in the ctakes archive depends upon another resource that is not in the archive and may not be available elsewhere. I'm sure there are other examples, but here are two 1. I've done some enhancements to the ZoneAnnotator for note section dete

Re: Compilation Errors and the context.tokenizer [EXTERNAL]

my case. > > But "https://repository.apache.org/content/groups/snapshots/"; is the only > repo where I could find the missing jars the build is looking for. I can > probably work around this problem by referring this link in settings.xml > but will that be feasible is my point? >

Re: Compilation Errors and the context.tokenizer [EXTERNAL]

> > I will do some more research on this tonight, though I welcome people to > beat me to a solution! > > Sean > > ____ > From: Peter Abramowitsch > Sent: Monday, November 27, 2023 7:01 AM > To: dev@ctakes.apache.org > Subject: Re: C

Re: Compilation Errors and the context.tokenizer

t; > any changes to it. My issue still remains the same. The build is trying > > to > > > pull the org.apache.ctakes:ctakes-core:jar:5.0.0-SNAPSHOT jar from the > > > remote maven repo which its not able to find. > > > > > > Complete error trace a

Re: Compilation Errors and the context.tokenizer

> org.apache.ctakes:ctakes-core-models:jar:5.0.0-SNAPSHOT (absent): Cannot > access nexus (https://repo1.maven.org/maven2) in offline mode and the > artifact org.apache.ctakes:ctakes-core-models:jar:5.0.0-SNAPSHOT has not > been downloaded from it before. > > > On Sun, 26

Re: Compilation Errors and the context.tokenizer

at you are finding. Peter On Sun, Nov 26, 2023 at 6:47 PM Peter Abramowitsch wrote: > Nope, that is not the issue. Those version changes are intentional and > necessary. The core pom and the subsidiary poms have been changed to > 5.0.0-SNAPSHOT as well because this is a new release. F

Re: Compilation Errors and the context.tokenizer

; *ctakes-core 5.0.0:* > > > org.apache.ctakes > ctakes-core-models > ${ctakes.models.version} > > > Do u know about the changes Peter by any chance? or only Sean can throw > some light on these changes? > > On Sun, 26 Nov 2023 at 22:54, Peter Abramowitsch > wr

Re: Compilation Errors and the context.tokenizer

pt. This failure was > cached in the local repository and resolution is not reattempted until the > update interval of nexus has elapsed or updates are forced. > > Looks like maven build is expecting "ctakes:ctakes-core-models" in the > maven repository and trying to pull the

Re: Compilation Errors and the context.tokenizer

g a previous attempt. This failure was > cached in the local repository and resolution is not reattempted until the > update interval of nexus has elapsed or updates are forced. > > Looks like maven build is expecting "ctakes:ctakes-core-models" in the > maven repository an

Re: Compilation Errors and the context.tokenizer

Just a curiosity - Ghandi, are you using Eclipse+Maven? If not, do you have another IDE wrapped around Maven ? On Sun, Nov 26, 2023 at 4:43 PM Peter Abramowitsch wrote: > HI Ghandi, > > That's one of the fundamental jars that gets built when you start from the > top. And

Re: Compilation Errors and the context.tokenizer

t of curiosity to check on this issue. But I am hitting on a different > issue in building ctakes-core module. The error is "Could not resolve > dependencies for project org.apache.ctakes:ctakes-core:jar:5.0.0-SNAPSHOT" > > Am I missing something? Where do I get or build > or

Compilation Errors and the context.tokenizer

About package naming and the context tokenizer, I was quite puzzled as to why no one had so far complained about the compilation issues in the Git Archive which I noticed. The issue is that a bunch of the ctakes files refer to a package *org.apache.ctakes.* *contexttokenizer/...* when its conten

Starting to look at 5.0 repo and found this...

Hi all, Looking at the 5.0 repo, there's a compilation error across many projects because what is being imported as *org.apache.ctakes.contexttokenizer.ae.** is actually located in package *org.apache.ctakes.context.tokenizer.ae * and the maven arti

Re: Junk E-Mail Fwd: Initial CTakes analysis

Peter Abramowitsch wrote: > Hi Paul > > 1. The cTakes ecosystem is Java with a some optional Python code. I have > little experience running it in a Windows environment and so perhaps > someone else in the group can give you pointers. My instinct would be to > run it in a

Re: Junk E-Mail Fwd: Initial CTakes analysis

R. Stearns > Advanced Consulting Enterprises, Inc. > 15150 NW 79th Court, > Suite: 206 > Miami Lakes Fl, 33016 > > Voice: (305)623-0360 x107 > Fax: (305)623-4588 > > > From: "Peter Abramowitsch" > Sent: 8/10/23 11

Fwd: Initial CTakes analysis

Hi Paul Out of the box, cTakes would get you part of the way there, but would require several types of customization to meet your requirements. All of these are the kind of customizations that most of us have had to do, so there's nothing new here, but they are not trivial. As I see it they fall

Re: Testing the 5.0 version [EXTERNAL]

u would > like to receive some attention. > > If anybody can, please work with Peter to help keep ctakes a top-notch > application for clinical NLP. > > Cheers, > > Sean > > > From: Peter Abramowitsch > Sent: Monday, Augus

Testing the 5.0 version

Hi Sean, looks like my funding for some experimentation with 5.0 is finally going to happen in a month or so. I'm going to be looking at all the new functionality (I'm back on a branch of 4.0.1 on a custom webservices platform), but is there any particular area of 5.0 that you'd like me to exer

What's new in 5.0 && testing JDK 11

Hi Sean, It looks like I may get some support from my employer to explore 5.0 this summer, and while doing so, also test the jdk11 build, but I have a couple of quick questions. 1. If the system would still require 1.8 to run due to certain dependencies, what would be the advantage of building i

Re: cTAKES running slower with each run

There are many ways to package ctakes, and admittedly ours is unlike the console app and we have our own multithreaded API, but we regularly do millions of documents at a time and haven't seen this issue. The core application with our fairly standard pipeline is up for a month at a time with no d

Re: It is Official! Steps toward a cTAKES 5.0 release. [EXTERNAL]

Hi Sean and all, If you expect the release process to last a couple of months, I can volunteer. At the moment and for the next few weeks I'm really busy. One thing that would really help is to have a list of all the major changes & additions that have happened since the 4.0.0 release. I think

Re: Apache cTAKES is now on GitHub ! [EXTERNAL]

27;t really paying close > attention. Thanks again for the improvements! > > Cheers, > Sean > > > From: Peter Abramowitsch > Sent: Friday, December 30, 2022 11:31 PM > To: dev@ctakes.apache.org > Subject: Re: Apache cTAKES is now on GitHub

Re: Apache cTAKES is now on GitHub !

Thank you Sean - looks like you & others put in a lot of work to make this transition. I'm looking forward to the "toys" you mentioned. Will the repository protocol be the same as it was during the SVN days with designated contributors? Although I didn't receive any feedback, I might check in som

Re: Best practices for documenting NLP versions

Boettiger, An > introduction to Docker for reproducible research, SIGOPS Oper. Syst. Rev. > 49 > (2015) 71–79. doi:10.1145/2723872.2723882. > <https://www.zotero.org/google-docs/?Xd3H9e>" > > > > On Fri, Oct 21, 2022 at 3:15 PM Peter Abramowitsch < > pabramowit...@gmail.

Re: Best practices for documenting NLP versions

Well, obviously, the full range of permutations of all source files and all annotators and pre and post ctakes code would require a huge amount of commit information on thousands of files... and not only ctakes files...recently I made some pretty significant changes to the ZonerCli library which i

Re: Two Questions about OverlapJcasTermAnnotator [EXTERNAL]

d, > but the default settings (window size, etc.) may have been changed since > then. > > Everything in preftext is simple string literal. It is likely that > certain things will not appear in raw text. The UMLS has some interesting > synonym sources. > > Sean > >

Two Questions about OverlapJcasTermAnnotator

Hi Sean (or whoever has some historical knowledge) I'm trying to improve the term annotators for speed and have noticed that the overlap term annotator does not seem to pass even the most rudimentary use cases suggested in the code comments: // things like "blood, urine, sputum cultures" should p

Re: Issue in running developers version of Apache cTakes to process DefaultClinicalPipeline

Hi Ankit, One normally doesn't put the input and output folders in the trunk area, but I just tried it and works fin r 2022 08:15:53 INFO FinishedLogger - Run Start Time: Thu Apr 07 08:14:53 CEST 2022 07 Apr 2022 08:15:53 INFO FinishedLogger - Processing Start Time: Thu Apr 0

Re: doubt

Bavithra, There are many possible encapsulations of cTakes as a service. You are free to create your own, as I have done. But for the team and particularly for the developer of cTakes Web Rest, it would be useful to document in some detail what your experience with it has been. Peter On Tue,

Re: Segment annotation type

Hi Greg I don't bother about segments but have been pretty successful using this to get a document's sections. *add org.mitre.medfacts.uima.ZoneAnnotator SectionRegex=org/mitre/medfacts/uima/section_regex.xml* Have you checked out this annotator? It creates "Heading" types and the config file ab

Fwd: neural negation model in ctakes

-- Forwarded message - From: Peter Abramowitsch Date: Thu, Feb 10, 2022 at 6:41 PM Subject: Re: neural negation model in ctakes To: Hi Tom My changes to negex are checked into the ctakes trunk in sub-project ctakes-ytex-uima Make sure you also pick up the updated resources

Question for Sean et al?

Hi all I've started using the mitre ZoneAnnotator am making some optimizations and necessary changes which prevent it from leaking note text into the log file (horrors!!!) But I have a question. Turns out that back in 2012 someone left raw system.outs in the mastif-zoner code which comes to cT

Re: Ctakes + UMLS dictionary

As distributed, it contains the mappings of cuis to 2015 snomed and rxnorm vocabularies. It does not contain ICD 9 or 10 mappings. But creating a custom dictionary is a normal aspect of any serious installation. This is how you can incorporate more recent versions of the umls and other vocabulari

Re: What URLs does ctakes use

The only one you need for ctakes is https://utslogin.nlm.nih.gov The other one is for accessing the NLM's apis for content - such as the metathesaurus. It is not used by ctakes. peter On Thu, Jan 13, 2022 at 12:11 PM John Doe wrote: > Hello, > > I'm trying to run ctakes in an environment wher

Re: Performance of the cleartk history module [EXTERNAL]

le of your notes? Just curious because I wouldn't have > expected regex to be that much of a bottleneck. > Tim > > > On Tue, 2022-01-04 at 17:36 -0800, Peter Abramowitsch wrote: > > * External Email - Caution * > > > > Thank you for the fulsome and humorous respons

Re: Performance of the cleartk history module [EXTERNAL]

example above, the end delegate is the same. > Hence the processing is the same and repeatable. In my tests on both small > and gargantuan documents the windowed version and the original version > produced the same output. > > Sean > > > > > > > From: Peter Abramowitsch >

Re: Performance of the cleartk history module [EXTERNAL]

, EventMention.class ) > .stream() > .filter( this::isHistory ) > .foreach( e -> e.setHistoryOf( > CONST.NE_HISTORY_OF_PRESENT ) ); > } > } > > It requires a stroll through the monstrous cas array and it certainly > isn't

Re: Performance of the cleartk history module [EXTERNAL]

n Mon, Jan 3, 2022 at 2:26 PM Finan, Sean wrote: > Hi Peter, > > I have noticed this and just added a following engine that recognized text > within event spans. It is a lazy solution, but it fit my needs and > available time. > > Sean > _____

Performance of the cleartk history module

Hi All I've noticed that the HistoryCleartkAnalysisEngine misses many common forms of subject history including the obvious "h/o" prefix.Looking into the distribution, there's a model.jar and what appears to be a weights file containing trigger words: resources/org/apache/ctakes/assertion/mod

Re: empty preferredText [EXTERNAL]

t it on a snowy afternoon this winter. Of course, if > anybody out there in the dev world would like to take a first crack at it > ... > > Sean > > From: Peter Abramowitsch > Sent: Tuesday, December 7, 2021 12:34 PM > To: dev@ctake

Re: empty preferredText [EXTERNAL]

ing oral hydrocortisone.' > > I will see if I can find the older UMLS release lying around. I think the > right workaround for now is your suggestion of using the covered text. > > Tim > > > On Tue, 2021-12-07 at 17:59 +0100, Peter Abramowitsch wrote: > > * Ext

Re: empty preferredText

Hi Tim, Yes, I've definitely encountered it. It happens when the concept has a CUI_TERM which has matched the text, but there is no corresponding entry in the SNOMED or other vocab table mapping CUI to SNOMED. The obvious choice is to use the covered text as a surrogate, but technically it coul

Question about Relation Extractors

Thanks Sean and Tim for the background & code on these annotators & models. Just looking at how the EventTimeRelationAnnotator works, I think the internal representation would be a bit different, but I get the gist of it for sure. Unless I'm using outdated code The "actual data" is captured in

followup question

Hi Sean, I've been doing a bit of reading on propbanks, framesets, etc in relation to what I'm seeing in the CAS when I turn on some of the relation extractors that do work (in contrast to the ones I mentioned before that are missing a model). Is it safe to say that these extractors are mostly

Another question about relationship extractors

Hi (probably Sean), are the default model.jars for the *CausesBringsAboutRelationExtractorAnnotator* and the *ManagesTreatsRelationExtractorAnnotator* not part of the cTakes sources?I looked through the source at all pipers and all unit tests and on the net and I didn't find references to the

Re: Question about use of Time Annotators in 4.0.1 (trunk) [EXTERNAL]

ary relations. > add EventTimeRelationAnnotator > classifierJarPath=/org/apache/ctakes/temporal/ae/eventtime/model.jar > > // Event - Event binary relations. > add EventEventRelationAnnotator > classifierJarPath=/org/apache/ctakes/temporal/ae/eventevent/model.jar > > > T

Question about use of Time Annotators in 4.0.1 (trunk)

I have a couple of questions about the TimeAnnotators forward and backward 1. The BackwardsTimeAnnotator complains that it doesn't know whether it is in training mode when there is no "inTraining" parameter. But when I supply it with the value false, then it complains that it doesn't have a cla

Re: An exception occured while executing the Java class. URI is not hierarchical [EXTERNAL]

Can you elaborate a > bit on where I can find the DependencyParser? > > > On Wed, Aug 18, 2021 at 5:56 PM Peter Abramowitsch < > pabramowit...@gmail.com> > wrote: > > > Hi Benjamin, > > > > If what you're looking for are the lemmas of tokens, just

Re: An exception occured while executing the Java class. URI is not hierarchical [EXTERNAL]

Hi Benjamin, If what you're looking for are the lemmas of tokens, just use the DependencyParser instead of LVG I had another problem with LVG as well, but I think that it might be simply that all the needed resources are not being copied into the right place. This was done without the lvg {

Re: ctakes activity gauge

not give any details on how he > did this. > Would you by any chance know where i can find more information about how to > achieve this? > > Best regards > > On Thu, Jul 29, 2021 at 6:21 PM Peter Abramowitsch < > pabramowit...@gmail.com> > wrote: > > > Hi Ben,

Re: ctakes activity gauge

Hi Ben, I can only speak for myself, but I am using cTakes extensively at two major California Universities in multiple projects. The kind of customizations I am doing are mostly specific to the facility and to the project and therefore wouldn't be for inclusion in the source repository.We hav

Re: UMLS Changes

Hi Dylan, I guess you missed many emails about this. The new regime has been in place since January and changes have been made to the 4.0.0.1 release and on the trunk to accomodate the use of an API key in place of user and password. If you go onto the ctakes Wiki you will get the information

Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]

pAnnotator; > higher precision than the UmlsOverlapLookupAnnotator (which skips a > specified number of tokens regardless of syntax). > > I've been wanting a more general framework to fit this into, and thinking > it might be Ruta. > Thanks for the pointer to TokensRegex;

Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS]

Hi All, yes, the line between "lookup" and rule execution is a little blurry sometimes. Here's some more blurriness. I've done something related, adapting a UIMA tokens regex engine for Ctakes. You create a new type in the TypeSystem. In my case it uses CONLLDEP Annotations as the tokens to

Re: Healthcare Division for Apache

Hi Javi, I'm a long term ctakes user and contributor who has worked in various professional, incubator, and standards-creating environments for healthcare. I like your idea in theory, but I see an on-the-ground issue with a specific health oriented section of Apache - and that is a lack of conten

Re: multi-threads on REST client?

I did a different implementation in my own rest service where I instantiated not only a fresh cas, but fresh pipeline for each threadpool object. It's memory hungry but safe - running for weeks with 35 simultaneous threads & zero errors. I wasn't convinced that all the AEs were thread-safe to le

Re: Issue with dictionary creator? [EXTERNAL]

tated as > such in the first place , e.g. today as an antibiotic which led me to think > it may have had something to do with broken links, even residuals from > efforts to "fix" certain entries perhaps? Our cohort was for heart attack > so not a very broad range of meds were pre

Issue with dictionary creator?

Has anyone seen an issue where a dictionary is created from UMLS sources where there is no entry in PREFTERM for a valid CUI that is present in TUI, CUI_TERMS, and SNOMEDCT_US?. It seems to be happening in certain medication mentions where there is a base drug instance and then various forms. It

Re: 4.0.0.1 patch [EXTERNAL]

#x27;t overwrite with a > copy of 4.0.0.1 > > If you can find the CuiFilterAnnotator file in your previous installation, > just copy it over in a custom jar. After rerunning you may find another > missing class, then another. Such can be the pains of working with custom > alterat

Re: 4.0.0.1 patch [EXTERNAL]

I don't mean to butt in on another conversation, but for the UMLS authentication to work in 4.0.0.1, you would need to replace ctakes-dictionary-lookup-fast jar, the ctakes-dictionary-lookup.jar and for safety's sake the ctakes-core jar too. Peter On Fri, Feb 26, 2021 at 6:01 PM Mullane, Sean *HS

Looking for comparable experiences with mysql

Hi all, As an experiment I extracted my rather large HSQL UMLS dictionary into a local MYSQL instance and ran the equivalent of 3 simultaneous ctakes pipelines with the overlap lookup annotator against it with a set of 1000 notes. Comparing that with the same setup running against the traditional

Re: Identifying dates for identified annotations

Hi Muhammad, Obviously, the first thing to say is that you can only extract information that is available in the note. So if the note doesn't give you enough clues, then there's no magic way to infer dates. Sometimes what you want is already in structured data that is available alongside the no

Re: Dictionary "bad" codes

;s there somewhere... > > [image: image.png] > > I do use the BSV for concepts that are not in the script file at all. > > > I use BSV files for adding both synonyms and concepts. The concept BSV > has its own ; the synonym BSV doesn't. > > > On Mon, Feb 15, 2021

Re: Dictionary "bad" codes

evation myocardial infarction > C1276061|non st elevated myocardial infarction > C1276061|non-st elevated myocardial infarction > C1276061|non st elevated mi > C1276061|non-st elevated mi > > On Mon, Feb 15, 2021 at 10:09 AM Peter Abramowitsch < > pabramowit...@gmail.com> >

Re: Dictionary "bad" codes

Hi Eugenia There may be better ways to do this, but I would insert these as Synonyms in the CUI_TERMS table. The concept is already there: insert this: INSERT INTO CUI_TERMS VALUES(1303258,0,1,'stemi','stemi') the concept is already declared here INSERT INTO PREFTERM VALUES(1303258,'Acute ST seg

Re: authentication issue?

Hi Greg 401 means either not authenticated or there's a problem at the UMLS end - which does happen every now and then. I've already told their guy about it, But at this very instant 19:18 GMT, it is working 10 Feb 2021 20:18:43 INFO UmlsUserApprover - Checking UMLS Account at https://utslogi

Re: error: CRITICAL

Hi Greg I would help you, but unfortunately I'm in italy at the back end of an abysmally slow internet, especially in upload. But still it would be interesting if I could see an example anonymized note that has this FP error problem as I could try it on my version of 4.0.0. The fact that 4.0

Re: Passing SectionsBsv to piper containing BsvRegexSectionizer [EXTERNAL] [SUSPICIOUS]

Hi Tom, I think there is a way to do what you were thinking of. I'm not suggesting it's a better solution. It's just a thought. In Java you can create a new ClassLoader, and with this ClassLoader you can create a second definition of a Class, and from that you can create a new instance of the

Re: performance report [EXTERNAL]

for each specific > > pipeline component. I assume there is a way to enable the performance > > report output available in the GUI version of ctakes at the command line > - > > which is what I'm really interested in. > > > > We're fine with information at a very

Re: performance report [EXTERNAL]

erformance > report output available in the GUI version of ctakes at the command line - > which is what I'm really interested in. > > We're fine with information at a very coarse level, since we're interested > in a particular note type, so the aforementioned report sh

Re: neural negation model in ctakes

Thats great Tim - it sounds very sophisticated! In fact I had made some changes to the Negex Annotator a last fall which I hadn't checked in but was waiting for Sean to test. In a great deal of my own testing I discovered that Negex, which is easily expandable to accommodate new constructions, ha

Re: performance report

Hi Greg, I’ve found that there’s so much difference between note styles that have performance implications and so many interactions between pipeline configurations which affect overall performance, that really the only way to get a sense of performance is either on a vary coarse level, measurin

Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch

til the pre-built archive downloads are available through the website, > you can find them in the release repository. > > > https://repository.apache.org/content/repositories/releases/org/apache/ctakes/ctakes-core/4.0.0.1/ > > > For more information please visit the wiki page on the Ap

Sean... about the UMLS URL

Hi Sean While helping Eugenia, I discover that there's another spot that needs changing which I had forgotten about. I'm happy to help, but you need first to decide how you want it done. When one uses the DictionaryCreator, it, of course, write a Dictionary Descriptor xml file and this will now

Re: Running PiperGui produces authentication error

; Eugenia Monogyiou | NTT Data UK > Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG > > Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com > > > -Original Message- > From: Peter Abramowitsch > Sent: 08 January 2021 18:47 > To: dev@ct

Re: Running PiperGui produces No Analysis Component found for ContextDependentTokenizerAnnotator error

Hi Eugenia Not sure if Sean has changed this part of the code that I had checked in, I'm still using my original check-in. So there may be a small alignment issue if you are using his newer version and my original instructions. Raising the level of log4j to DEBUG, the UmlsUserValidator module sh

Re: Sean... & UMLS

enia Monogyiou | NTT Data UK > Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG > > Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com > > -Original Message- > From: Peter Abramowitsch > Sent: 28 December 2020 09:46 > To: dev@ctakes.apa

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