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

Dictionary, running bin/runPiperSubmitter also works. I don't want to do it for 5.1.0, but I should make names of the class, profile and script match. I will check the wiki instructions and make sure that -exact- details are in there. Sean ____ From: Miller, Tim

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

: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev

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

What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]

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

] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Hi Tim, Thanks for the explanation. I am going to remove the BERTRest classes. Sean From: Miller, Timothy Sent: Wednesday, December 20, 2023 6:25 PM To: dev@ctakes.apache.org Subject: Re: Examining

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

Hi Sean and Peter, I put the BERTRest stuff in, with the intention of finishing it and adding the python code to run the REST server, but just never finished it up. I’m ok with leaving it out for now. (Now that we are on GitHub it would be so much easier to do things like this in branches and

Best practices for documenting NLP versions

We’ve recently been using cTAKES for some internal projects where we make modifications, often using the REST server, combined with an open-source python client that makes the output of the REST server easy to post-process:

Re: Apache cTAKES GitHub mirror is stuck in 2019 [EXTERNAL] [SUSPICIOUS]

My recollection was that we ran into issues in previous attempts at migration with the large file sizes in our repo. Tim On Thu, 2022-06-02 at 20:55 +, Finan, Sean wrote: * External Email - Caution * Thank you Gandhi and Richard. Unless somebody else beats me to it I will perform some

Re: Ctakes + UMLS dictionary [EXTERNAL]

I recently posted an updated 2021AA UMLS file to the ctakes resource sourceforge repo: https://sourceforge.net/projects/ctakesresources/files/ which should be a drop-in replacement for the version included in the last ctakes release. If you extract this new file in the same directory as your

Re: Performance of the cleartk history module [EXTERNAL]

Peter, That sounds really useful! Were you able to benchmark it for runtime on a reasonably sized sample 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 -

Re: empty preferredText [EXTERNAL]

it could be PHI if that matters to you. The other thing is to see if there's an MSH term that maps using the metathesaurus. If so, including MSH in your dictionary as a src AND dest vocab will solve the problem. Peter On Tue, Dec 7, 2021 at 5:45 PM Miller, Timothy < <mailto:timot

empty preferredText

Hello, I'm using the dictionary lookup (through ctakes-web-rest) and trying to read off the preferredText that comes back as a human-readable way to display the CUI. On a very small percentage, there does not seem to be any preferredText. Has anyone else encountered this? Is this a limitation

Re: Another question about relationship extractors [EXTERNAL]

Hi Peter, I guess you're asking why there is annotator code for all the relations but only released models for location_of and degree_of (severity)? The simple reason is those are the only two that we felt were accurate enough to release. We had an annotated training corpus with all the

Re: Loading model - what? [EXTERNAL]

Hi Ben, Those come from the dependency parser and SRL system, and I think are generated from the external library (ClearNLP?) we depend on for those modules. As for the models themselves, the files are in ctakes-dependency-parser-res, but they are binary files that will be difficult to

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

But Sean, isn't what he's asking for essentially already implemented in cTAKES as the custom dictionary? I'm currently using that approach for my covid container: https://github.com/Machine-Learning-for-Medical-Language/ctakes-covid-container Tim From:

multi-threads on REST client?

Just wondering what the logistics of this are. The REST interface has a CAS pool of 10, and when it gets a new request, it grabs a CAS and sends it into a pipeline. So what happens if the REST endpoint is getting hit by tons of different requests at the same time? I'm experimenting with this in

Re: 4.0.0.1 patch [EXTERNAL]

Hi Sean, I can't answer your primary question, but my recollection is that 4.0.0.1 was an absolutely minimalist change to just fix the authentication, so I don't think ytex would've been touched. Tim On Thu, 2021-02-25 at 17:24 +, Mullane, Sean *HS wrote: > * External Email - Caution * > >

Re: Looking for comparable experiences with mysql [EXTERNAL]

Gandhi, Is that code public at all? I made a docker container for the REST server that uses the hsql, but if mysql is even faster and the dictionary building can be containerized that might be a nice next step for better performance of the container. Tim On Thu, 2021-02-25 at 20:33 +0530, gandhi

Re: neural negation model in ctakes [EXTERNAL]

. Or what happens when a series of entities which begins as all being negated has one expressed in a way that stops the negation pattern. These are the weaknesses I addressed in my changes. Regards Peter On Sun, Jan 24, 2021 at 5:08 PM Miller, Timothy < timothy.mil...@childrens.harvard.edu>

neural negation model in ctakes

Hi all, I just checked in a usable proof-of-concept for a neural (RoBERTa-based to be specific) negation classifier. The way it works is a tiny bit of python code (using FastAPI) sets up a REST interface that runs the classifier: ctakes-assertion/src/main/python/negation_rest.py it runs a

Re: Apache cTAKES 4.0.0.1 : UMLS Authentication Patch [EXTERNAL]

Seconded, thanks a lot Sean and Peter for getting this working and turned around so quickly! Tim On Wed, 2021-01-20 at 23:13 +0100, Peter Abramowitsch wrote: > * External Email - Caution * > > > Thanks Sean! > > Peter > > On Wed, Jan 20, 2021 at 4:25 PM Finan, Sean < >

Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

l_isValidUMLSUser-2522_=DwIFAw=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=uRA81eRtCuJYVkMEzd47jQTacPEI0XTrHeDpgKY_Ma0=9SE2vJimnmdqHHlSYjb0EtK6QJ0DDzB7O7PBZQ6ayJI= > > > > > > > > > ___

Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

kes_umls_apikey > > > I think that is what I used ... > > > From: Miller, Timothy > Sent: Tuesday, December 8, 2020 11:52 AM > To: dev@ctakes.apache.org > Subject: Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a > release [EXTERNAL] [SUSPICIOUS] [SUS

Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS]

u able to test out the 4.0.0 umls authentication patch?It > would > be good to know if it and its instructions can be dropped in without > much > further work. > > Peter > > On Tue, Dec 1, 2020 at 3:34 PM Miller, Timothy < > timothy.mil...@childrens.harvard.edu&g

Re: 4.0.0 UMLS Authentication Patch - for Developers - Not a release [EXTERNAL] [SUSPICIOUS]

Peter, I saw the readme attachment, but it sounded from your email like there was a patch attachment too that I didn't see. Did that not come through? Tim On Fri, 2020-11-27 at 18:19 +, Finan, Sean wrote: > * External Email - Caution * > > > ?Thanks Peter, > > > Happy Thanksgiving all >

Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

9zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=QVEto_k7Ovh16r4YjW7Uelv9_lDmvjxRwoI2r7_6qBk=fjMkpO1i2FXprtFbQ-XJ1cvVlSQ8-uz3gSOBojxNMI8= > > I am not sure of anything specifically regarding patches. > I don't know if we need to go through the full proc

Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

CIOUS] > > > > * External Email - Caution * > > > > > > > ctakes-4.0.0-rc3to ctakes-4.0.1 > > > > I think that is certainly one way to do it. > > > > One could checkout the branch > > > > Would the method be: > > 1

Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

main > ctakes web site. On that note, the web site needs to be redone > asap. > > Anyway, cheers to Peter for taking upon himself this update! > We do still have a few things left to do. > Volunteers? > > Sean > > >

Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL]

Peter, I was able to try your changes and get this new authentication mechanism to work in the default pipeline. Peter, Sean, et al, what are the next steps for getting this in to trunk? If you're not comfortable checking in directly maybe you can share the patch for review. Tim On Sun,

Re: cTAKES data flow [EXTERNAL]

With the default pipelines, the only information that leaves your computer is your UMLS credentials, which are used to verify that you are a registered/current UMLS user. Tim On Tue, 2020-10-13 at 15:37 +0530, moinuddeen smrk wrote: > * External Email - Caution * > > > Hi Team, > i am one of

Re: I think I found a bug. [EXTERNAL]

Peter, I think the email server doesn't let images through. Can you post an imgur link maybe? Tim On Sun, 2020-08-30 at 14:35 -0700, Peter Abramowitsch wrote: > * External Email - Caution * > > Hi, > I was getting a StringIndexOutOfBoundsException in > DependencyUtil.doesSubsume(annot1, annot2)

Re: Sentence detector changes [EXTERNAL] [SUSPICIOUS]

Hi Abad, I've been following the thread but don't have much to add on top of what Sean's saying. The BIO version has one major benefit, in that it allows sentences to wrap newlines. But it does seem to break on Mr. and Dr. unfortunately. The solution is to create more training data but it's

Re: Missing Medication Frequency and Allergy attributes from MedicationMention [EXTERNAL]

Hi Honey, I created a module last year for doing some medication attribute extraction, but it is not part of core ctakes yet so you would have to integrate it yourself. It uses the typesystem and most of the regular ctakes pipeline so it shouldn't be that difficult. Check it out here:

Re: how to activate inactive features in cTAKES? [EXTERNAL]

Akram, the typesystem in ctakes was created by a project with the aim of specifying things that are useful, without specifying implementations for them all. There are many items in the data model that there are no ctakes modules to fill. The idea was that when people bring things online there

Re: ML NER for cTakes [EXTERNAL]

Yes, this is still true. I know there are different folks working on ML-based NER but none of it is in main line cTAKES yet. There is some ML in the pre-processing stages, and the outputs of that are used by the dictionary tool, but the lookup itself is done without learning. Tim -Original

Re: Clinical Processor [EXTERNAL]

Can you send an error message that is as complete as possible? It is hard to tell from the information you've given. Thanks Tim -Original Message- From: Sébastien Boussard mailto:%3d%3fiso-8859-1%3fq%3fs%3de9bastien%3f%3d%20boussard%20%3cbouss...@bu.edu%3e>> Reply-to: To:

Re: unicode issues [EXTERNAL]

ying, or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender immediately by replying to this message and please delete it from your computer. On Thu, Jul 18, 2019 at 1:20 PM Miller, Timothy

unicode issues

I'm having a weird issue with unicode characters in one of the sample notes distributed with ctakes. The sentence is: The right breast and axilla were sterilely prepped and draped in the usual standard fashion. First the right 1 o’clock position 5 cm from the nipple was targeted. Local

Re: Accessing the External Resource from the UimaContext without Using XML descriptor [EXTERNAL] [SUSPICIOUS]

Just wanted to make a general comment about this. I've worked on the spelling correction problem a tiny bit and it has all of the difficulties you all describe, and I think it is also slow in a kind of unavoidable way because it's doing quite a bit of extra work on each word. I still would

RE: Convert type system of a component to cTakes typesysem [EXTERNAL]

I don't have much experience with Heideltime, but I think this would be a great addition to ctakes, so if you know Heideltime a bit and you're willing to put in the effort I'm happy to help with your understanding the typesystem. I don't know that there's an easy way of 'converting' other than

Re: Looking for cTakes deployment strategies [EXTERNAL]

Yousof, I have seen this with SentenceDetectorAnnotatorBIO.xml annotator, but with the one you describe, I thought it had a hard-coded rule to break on newlines and split them into sentences. Do you have any log files that you can copy/paste the initialization lines so we can verify which

Re: ctakes-web-rest changes [EXTERNAL]

TERNAL] Date: Sat, 22 Dec 2018 08:40:20 +0530 Thanks Tim. Great work. On Friday, December 21, 2018, Miller, Timothy < timothy.mil...@childrens.harvard.edu<mailto:timothy.mil...@childrens.harvard.edu>> wrote: There is certainly no need to apologize! It's 100x easier for me to ch

Re: uima-as examples [EXTERNAL]

Greg - I've developed a cluster-like architecture that uses Docker-wrapped UIMA-AS components on AWS for scalability. It's a work in progress but it might be helpful: https://github.com/tmills/ctakes-docker Tim -Original Message- From: Greg Silverman

Re: Looking for cTakes deployment strategies [EXTERNAL]

Hi Anusha, I've been working on a project that hasn't merged with ctakes yet, but has a github page: https://github.com/tmills/ctakes-docker it is a work in progress and so documentation is not great, but I've used it to do exactly what you're asking about -- setup a ctakes cluster on AWS to

Re: Question about negation [EXTERNAL]

tes? Also is there a way for me to look into the trained SVM model? Say what are features there and their weights? Best, Yu Pan On Wed, Jan 16, 2019 at 7:58 AM Miller, Timothy mailto:timothy.mil...@childrens.harvard.edu>> wrote: It uses an SVM model. The training data is from a project ca

Re: Question about negation [EXTERNAL]

It uses an SVM model. The training data is from a project called SHARPn, it is notes from Mayo Clinic with a variety of note types and specialties represented. As for the example, is it a real example that someone wrote "Deny hepatitis"? That sounds more like a command than documentation of a

Re: AggregateCdaUmlsprocessor only annotates last section of CDA document [EXTERNAL] [SUSPICIOUS]

Looks like someone fixed that as part of a different issue: https://issues.apache.org/jira/browse/CTAKES-500 Tim -Original Message- From: "Finan, Sean" mailto:%22Finan,%20sean%22%20%3csean.fi...@childrens.harvard.edu%3e>> Reply-to: To: dev@ctakes.apache.org

SemanticCleanupTermConsumer

Sean (and team), I was using PrecisionTermConsumer for my ctakes-web-rest implementation hoping to avoid any overlaps at all, but when I saw some overlaps I noticed the comment: PrecisionTermConsumer will only persist only the longest overlapping span of any semantic group. So with this term

Re: ctakes-web-rest changes [EXTERNAL]

not improvise on the REST module which is more suitable for our business needs due to lack of domain expertise. Regards, Gandhi -Original Message- From: Miller, Timothy Sent: Friday, December 21, 2018 1:54 AM To: dev@ctakes.apache.org Subject: ctakes-web-rest changes Hello all, I've been

Re: Recognising Concept and its Value for text without space [EXTERNAL]

Hi Zakir, I think the problem here is that the default tokenizer will never split up a string like POD10 into ['POD', '10'] since there is no whitespace. The dictionary lookup uses tokens as the unit of analysis, so unless something like POD10 is in the dictionary database you will not get a

test

Please ignore. Tim

Re: Cannot authenticate license on REST API TRACKING:000308016 [EXTERNAL]

Are you providing your password via the xml descriptor file or an environment variable? The only thing I can think of is that there might be some misformatting in the xml, like an extra trailing space/newline in the field where one of the username/password goes. Tim

Re: Parse Medical Research Papers [EXTERNAL]

To get predicate argument structure the best method is probably to use the SRL (Semantic Role Labeling) annotator which is part of the ctakes-dependency-parser module. Check in the desc/ directory in that module for some sample pipelines to see its dependencies. Once you have that running,

Re: issues with line endings [EXTERNAL]

0hBDeU=r9A1Uam0pxgIy7Nzt2833VYY4xaAqQAiSWMRB38-6rU= and see if it helps. Regards, Gandhi -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Saturday, May 05, 2018 2:25 AM To: dev@ctakes.apache.org Subject: issues with line endings I'm trying

issues with line endings

I'm trying to use git-svn to do ctakes development but it has this weird issue where it auto "fixes" line endings (mainly in -ytex* modules) to be LF from CRLF. So it won't let me pull until I've checked in those changes. And because it's automatic I can't clean my local copy (if I try they just

Re: SentenceDetector [EXTERNAL]

The changes were mainly meant to adapt the OpenNLP model to idiosyncrasies of clinical text, but you're right that they have some shortcomings. The newline thing is in the data sources used originally to build the model, there were frequent cases of headings/sentence fragments by themselves on a

Re: consequences of change to typesystem [EXTERNAL]

Yes, that's right. Especially for one-off contributions, it is really helpful to the project if you open up a jira issue and attach the patch to the issue, then one of the committers will check it and commit it. Let us know if you have any questions about that. For people interested in

uima 3

Has some cool looking useful new functionality: https://uima.apache.org/d/uimaj-3.0.0-alpha02/version_3_users_guide.htm l#uv3.overview.new Support for arbitrary Java objects, transportable in the CAS New types: FSHashSet Automatic garbage collection of unreferenced Feature Structures better

Re: Sentence splitter [EXTERNAL]

That sounds bizarre! I can think of two possibilities: a sentence break in the middle of the word (unlikely), or the different sentence splits caused the POS tagger some confusion, and tagged the word aspirin as a forbidden part of speech, like a preposition or something. If you check the token

Re: UmlsUserApprover Error [EXTERNAL]

Is it possible there is some network issue preventing connectivity? New institutional firewall maybe? Otherwise, it looks like somehow your credentials are not getting into the right place. Possible a configuration file had them before and it's been changed out from under you? One thing you can

Re: Fast UMLS dictionary lookup description [EXTERNAL] [SUSPICIOUS]

Didn't you have some slides at some point as well? I don't know if they are suitable for public consumption but I remember it was helpful for me at least. Tim On Fri, 2018-02-23 at 15:34 +, Finan, Sean wrote: > Unfortunately, writing is not my jam.  I wrote about 50% of a paper > and then

Re: using umls dictionary lookup offline [EXTERNAL] [SUSPICIOUS]

Again, not legal advice, but this is my rule of thumb: - If you had to enter your UMLS credentials to download the copy of the UMLS you're using with cTAKES, then you don't need to have the online credentials check. (As Sean said, you are responsible for following licenses in terms of

Re: SubjectClearTkAnalysisEngine not working [EXTERNAL]

ation. > > SUBJECT it belongs to like - > *"Vital Signs", "BP", "Physical Examination", "Family Medical > History", > "Lab Results"* > > Any idea how to achieve this. > > > On Wed, Jan 17, 2018 at 1:05 AM, Miller

Re: Can we build CollectionReader from database [EXTERNAL]

Hi Kishore, Take a look in this directory for many different collection reader options: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cr/ JcdbCollectionReader may work for you. here are the parameters with comments: 59 /** 60 * SQL

Re: Unable to understand the importance of attributes in IdentifiedAnnotations [EXTERNAL]

have a mind to work on this one day, but I think I'll be doing it in my > CAS post processor rather than the annotator itself as the problem really > involves a whole new solution that looks at the semantics of the whole > sentence and not just "history of (x)" For t

Re: Unable to get Confidence score for any entity [EXTERNAL]

These items are created by a dictionary lookup -- not any kind of probabilistic algorithm -- which doesn't set the confidence score. There is nothing really like confidence distinguishing different kinds of found dictionary concepts. Tim From: Ratan

Re: non Medical entity extraction [EXTERNAL]

formation about the “structured > fields” from the notes. Is there a specific module for it.  > > Thanks, > Nitesh > > > > > On Dec 21, 2017, at 4:24 AM, Miller, Timothy <Timothy.Miller@childr > > ens.harvard.edu> wrote: > > > > No, the

Re: non Medical entity extraction [EXTERNAL]

No, there is not that I'm aware of. While that information is often in the note, it is also usually in structured fields where it can be extracted with ~100% accuracy so it's not a high priority for NLP. Thanks Tim On Thu, 2017-12-21 at 09:26 +, abilash.mat...@cognizant.com wrote: > Hi All,

Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

> Thanks again for the detailed feedback. > > Regards, > Gandhi > > > -Original Message- > From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] > Sent: Friday, December 15, 2017 1:25 AM > To: dev@ctakes.apache.org > Subject: Re: cTAKES as REST

Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

great start though, and as far as I know it is > the first publicly available ctakes json writer.  If anybody else out > there already has or knows of another, please share! > > > Cheers all, > Sean > > > -Original Message- > From: Miller, Timothy [mailto:timoth

Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

+, Miller, Timothy wrote: > I am really interested in this too, just waiting until I have a few > free hours to look around. Don't want you to think it's not of > interest. > Tim > > > On Tue, 2017-12-05 at 19:18 +, Finan, Sean wrote: > > > > Hi a

Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]

I am really interested in this too, just waiting until I have a few free hours to look around. Don't want you to think it's not of interest. Tim On Tue, 2017-12-05 at 19:18 +, Finan, Sean wrote: > Hi all, > > I am trying to clear a backlog at work.  I will most likely not be > able to do

Re: polarity tag in output for mention/concept. [EXTERNAL] [SUSPICIOUS]

I'll just point out -- the kind of examples Kathy gave were the bane of our existence while working on the ML-based assertion system. Even though it is obvious what is going on to a human it was hard to encode as a feature in a way that was learnable. But I think most rule-based algorithms will

Re: Contribute to ctakes: it is in your best interests! RE: unknown dependencies [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

   ./ctakes-constituency-parser-res/src/main/resources/org/ > > apache/ctakes/constituency/parser/models/thyme.bin > > > > 15M > > ./ctakes-constituency-parser-res/src/main/resources/org/ > > apache/ctakes/constituency/parser/models/sharpacq-3.1.bin > > >

Re: Contribute to ctakes: it is in your best interests! RE: unknown dependencies [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

people for whom that was > 50% of their job. Why? Because we made a commitment to use that open source > software. > It was a better use of our resources to contribute to it, improve it > and keep its momentum going and prevent it from becoming stale (or > abandoned) while our software c

Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

t; > > > > > Hi Bhagwat, > > > > > > > > > > If you are interested in the default clinical pipeline, you > > > > > can look at the wiki here: > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache. >

Re: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

_cwiki.apache.org_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=ONC114Bki6vY6dmCLn3sPjdNegVyawdkxXvYuBFoonI=oN0sRQQgrlsp8j926ayeysmYTVO2kriknuUjfIjlUq8= > > > confluence/display/CTAKES/Simple+Pipeline+Fabricator+GUI &

Re: cTAKES as REST service [EXTERNAL]

Sounds great, Matthew and Gandhi, thanks for sharing your solution. Tim From: Matthew Vita Sent: Sunday, October 29, 2017 11:59 AM To: dev@ctakes.apache.org Subject: Re: cTAKES as REST service [EXTERNAL] Sean, Ghandi and I have

Re: CAS Visual Debugger - [EXTERNAL]

I've had the same thought, and come to the same conclusions. Tim From: Melvin Ma Sent: Wednesday, October 25, 2017 1:33 PM To: dev@ctakes.apache.org Subject: CAS Visual Debugger - [EXTERNAL] This is more of a question. I am fully

Re: Missing resources for script that extracts markables from a corpus for analysis [EXTERNAL]

HAzxTM3GMiXKrSbnE=jOmot_onPFb31eg689D0ihb5Y4dZTzKcQ40vMCW0Bgk= On Mon, Oct 2, 2017 at 6:46 PM, Miller, Timothy <Timothy.Miller@childrens. harvard.edu> wrote: > Yeah, it might be nice to build a lucene index of all the sample notes in > the ctakes-example modul

Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

of liver lesion > with development of multiple new satellite nodules.  On 29Jul02, the > investigator removed this patient from protocol for progressive > disease and recommended hospice care.  After seeking a second opinion > from two other institutions, this patient was admitted to h

Re: Missing resources for script that extracts markables from a corpus for analysis [EXTERNAL]

d unit test the code? I think this would have the double benefit of the code being tested and showing dev/users how the code is supposed to be used. What do you think? Alex On Mon, Oct 2, 2017 at 9:45 AM, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > Thanks Al

Re: CTAKES-460: coreference Test should not be part of main [EXTERNAL]

Thanks Alex, I've committed this patch. I unfortunately looked at the wrong tab when typing my commit message and committed it with the wrong issue number (459). Tim On Mon, 2017-10-02 at 08:17 -0400, Alexandru Zbarcea wrote: > Hi, > > I have refactor a main class that should have been a UTest.

Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

-Original Message- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Thursday, September 28, 2017 8:21 PM > To: dev@ctakes.apache.org > Cc: Miller, Timothy <timothy.mil...@childrens.harvard.edu> > Subject: RE: Enabling drugner pipeline and identifyin

Re: Missing resources for script that extracts markables from a corpus for analysis [EXTERNAL]

Thanks Alex, This code is for processing a clinical text data corpus stored as a lucene index -- data that cannot be redistributed for privacy reasons. Since it's so related to the coref stuff I thought it should go alongside the coreference module. But maybe it makes more sense as an external

Re: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

ave a look and know your thoughts please? > > Regards, > Gandhi > > > -Original Message----- > From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] > Sent: Thursday, September 28, 2017 8:21 PM > To: dev@ctakes.apache.org > Cc: Miller, Timothy <timothy.m

Re: bitwise operator vs logical operator [EXTERNAL]

Thanks Alexz, I've committed the patch. Tim On Sun, 2017-09-24 at 21:57 -0400, Alexandru Zbarcea wrote: > Hi, > > I have reported and provided patch for: > https://issues.apache.org/jira/browse/CTAKES-456 > > I hope it helps to improve readability at least. > > Is there anything else related

Re: semantic Role mapping [EXTERNAL]

?The image isn't rendering for me -- can you upload to imgur and post a link maybe? Tim From: abilash.mat...@cognizant.com Sent: Friday, September 15, 2017 12:42 AM To: dev@ctakes.apache.org Subject: RE: semantic Role mapping

question about PersonTitleAnnotation class

More specifically: /ctakes-type-system/target/generated-sources/jcasgen/org/apache/ctakes/typesystem/type/textsem/PersonTitleAnnotation.java? Just curious what this type is intended to represent. Is it titles, as in "Dr." or "Mrs."? And is there a type for just representing a person? If

Re: Proposed improvements [EXTERNAL] [SUSPICIOUS]

y I support Hadrian initiative to have better logging since cTakes setup has some quirks which could be faster resolved by better logging. 2017-06-23 17:38 GMT+06:00 Miller, Timothy < timothy.mil...@childrens.harvard.edu>: > Thanks Hadrian, I hadn't heard of OSEHRA but it looks interesting a

Re: Proposed improvements [EXTERNAL]

Thanks Hadrian, I hadn't heard of OSEHRA but it looks interesting and like something where we should be making people aware of cTAKES! svn vs. git -- I'm with you on preferring git, but not by so much that it's worth spending time on an argument if it turns into an argument :). As far as I

Re: negation/uncertainty: pipeline runs very slowly [EXTERNAL]

Sean's feedback. Tim From: Dligach, Dmitriy <ddlig...@luc.edu> Sent: Wednesday, June 21, 2017 9:18 PM To: dev@ctakes.apache.org Cc: Miller, Timothy Subject: Re: negation/uncertainty: pipeline runs very slowly [EXTERNAL] Sean, thanks for your comments. You are right. The slowd

Re: Get the Annotator descriptor file [EXTERNAL]

Thanks for your suggestion. I need a little more help. Can you tell the full procedure on how to build custom dictionary which will include terms defined by me and then how to configure that custom dictionary with the annotator. Thanks, Avanish kumar -Original Message- From: Miller, T

Re: Get the Annotator descriptor file [EXTERNAL]

You should be able to add the dictionary to an AggregateBuilder with DefaultJCasTermAnnotator.java.createAnnotatorDescription() and then get a descriptor with toXml() (or whatever the uimafit method is called). If you've tried that and it's not working then I think we'll need more information

Re: cTAKES 4.0.0 Release

Congrats cTAKES team! This is an important milestone! Tim On Mon, 2017-04-24 at 09:02 -0400, Murali Minnah wrote: > The Apache cTAKES team is pleased to announce the availability of the > 4.0.0 release. > > For the complete release notes, please visit >

Re: Docker

One of those that Oleg found is my github repo which is very early stages: https://github.com/tmills/ctakes-docker it can create 2 docker images, one for a UIMA AS queue server and another that downloads ctakes, installs the dictionary, and starts a basic concept extraction server with a UIMA AS

Re: [VOTE] Release Apache cTAKES 4.0.0 (rc3)

Sorry for the delay, but I finally got around to testing RC3. I did a dictionary download for the bin release following the wiki, a test of the timex annotator, and a test of the coref annotator, and all worked to my satisfaction. My vote is +1. Thanks Tim On Thu, 2017-04-20 at 14:53 -0400,

Re: testing release candidates Re: Release Apache cTAKES 4.0.0 (rc2) [SUSPICIOUS]

tive on documentation. > > > > So, if you find instructions for installation, workflow, etc. > > please > > "test" the instructions.  If there are none then comment on the > > absence. > > However, I think that a paucity of documentation should not hold up &g

Re: testing release candidates Re: Release Apache cTAKES 4.0.0 (rc2)

Thanks all for your hard work. I added some minor instructions to the spreadsheet that are hopefully helpful. I want to test the cvd for standard dictionary lookup with the separate resoureces. Am I meant to be testing documentation as well? As in, something I can follow along and make sure it's

Re: Regarding Negation, Uncertainty Pipes

Thanks for that perspective, Yiming. I contributed to the ClearTK version of the system. At that time we evaluated it for negation [1] and found that it was more generalizable than the rule-based negation detectors like Negex. Since then, we've found on some projects that Negex is easier to

Re: Evaluate cTAKES perfomance

To save you a little trouble, in ctakes-temporal we rely a lot on an outside library called ClearTK that has some evaluation APIs built in that work well with UIMA frameworks and typical NLP tasks. We use the following classes:

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