Re: The 2020 UMLS dictionary and our default SNO_RX

> <-- missing > INSERT INTO CUI_TERMS VALUES(750426,0,5,'elevated white blood cell > count','elevated') > > So back to your recommendation on using MMSYS > > You chose the ACTIVE_SUBSETS option - right? > And on the Sources to Ex

Re: The 2020 UMLS dictionary and our default SNO_RX

g the correct SNOMED code though. > Wouldn't that be a problem for your researchers? > > Peter > > On Wed, Aug 5, 2020 at 5:37 PM Jeffrey Miller wrote: > > > Hi Peter, > > > > If I create a dictionary using UMLS 2020aa with just snomed and rxnorm my > &g

Re: The 2020 UMLS dictionary and our default SNO_RX

Hi Peter, If I create a dictionary using UMLS 2020aa with just snomed and rxnorm my cTAKES dictionary still seems to have a CUI associated with the string 'wbc' that links to the snomed term for Leukocyte (Cell). It is not mapping to a lab result TUI, but rather an anatomical site, but it seems to

Re: RE Tuning custom dictionary recommendations

, I'll say that 'bed' is not a disorder, while > 'BED' > > could be one. > > > > > > > > On Tue, Aug 4, 2020 at 2:12 PM Jeffrey Miller wrote: > > > >> Hi Peter, > >> > >> To your question about sno_rx_16ab I

Re: RE Tuning custom dictionary recommendations

Hi Peter, To your question about sno_rx_16ab I suspect that the CUI is new since 2016, or if it existed in UMLS back then, it was not associated with a term in snomed or rxnorm at that time. To those solutions, if you are able to use the trunk I know Sean said there was a suppression text feature

Re: With custom dictionary - over-eager resolution of acronyms [EXTERNAL]

s got to be wrong or I'm missing > something to say that it only applies (as an acronym) if it's capitalized > > In sno_rx there is neither a CUI 3542022 nor the definition of "soft" as a > solitary word, nor even a mention of ONYCHODYSPLASIA or HYPOTRICHOSIS > &

Re: With custom dictionary - over-eager resolution of acronyms

Sorry, I meant suggest to search for 'soft' in the dictionary file not 'short' grep -i ,\'soft\', *.script On Sat, Aug 1, 2020 at 7:47 PM Jeffrey Miller wrote: > Hi Peter, > > To my knowledge, there isn't any drastic difference in the behavior of

Re: With custom dictionary - over-eager resolution of acronyms

Hi Peter, To my knowledge, there isn't any drastic difference in the behavior of the dictionary gui creator and the way the sno_rx dictionary was created. I originally thought there was, but I realized the difference was that I had not installed all of UMLS to my machine (just the vocabularies I w

Re: Problem trying to load a custom dictionary [EXTERNAL]

if neither of you wants to take the > reins > > Peter > > > > On Fri, Jul 31, 2020 at 7:39 AM Jeffrey Miller wrote: > > > I can help with this as well. I have some documentation that I have > written > > for myself that would probably be useful. I've tr

Re: Clarification regarding NegationFSM [EXTERNAL] [EXTERNAL] [EXTERNAL]

Sean, When I use cTAKES I'd like to be able to refer to the version number for reproducibility. If I run just the latest trunk (to get access to a new feature), it is not easily referenced. How is it decided to make a new cTAKES release? Do you think there will be any future releases or would it b

Re: Problem trying to load a custom dictionary [EXTERNAL]

load a custom dictionary [EXTERNAL] > > > > > > * External Email - Caution * > > > > > > > > > Thanks Jeff > > > > > > That worked! > > > > > > Seems like something that should get fixed in the PiperCreator and in >

Re: Problem trying to load a custom dictionary

Peter, 1) This is loaded by cTAKES, you don't need to manually create the database. 2) I can't see the highlights here, but I think that file should be okay as created by the GUI. 3) I think the parameter name to configure your dictionary location is LookupXml instead of DictionaryDescriptor Jeff

Re: DefaultJCasTermAnnotator behavior with period and semicolon in UMLS terms [EXTERNAL]

st insert above the Dictionary lookup addition > > set windowAnnotations=Section > > or > set windowAnnotations=Paragraph > if you are using a paragraph parser. > > Sean > > > > From: Jeffrey Miller > Sent: Wednesday, February 5

DefaultJCasTermAnnotator behavior with period and semicolon in UMLS terms

Hi, I've noticed that if a term contains a period or a semicolon, as an example, from the sno_rx_16ab dictionary, "antibody ; toxoplasma", that this will not be found if the semicolon is attached to the first word, but will be found if it is either "antibody ; toxoplasma" or "antibody ;toxoplasma"

Re: Manually editing dictionary script file [EXTERNAL]

should be excluded. This is in the trunk version > of ctakes. > If you are comfortable reading java code you can have a look and see if > that is easier for you to use. > > > Sean > > ____ > From: Jeffrey Miller > Sent: Thursday, Janua

Manually editing dictionary script file

Hi, Are there any issues I have to be on the look out for if I want to remove a few synonyms from the CUI_TERMS table in the .script file created by the dictionary creator gui? Is there any concern about corrupting the rare term look up? If there is another way to suppress certain synonyms for a

Re: How does cTAKES work? [EXTERNAL]

Akram, The .xmi format that the ctakes utilities output is a XML serialized version of the JCAS ( https://uima.apache.org/d/uimaj-current/apidocs/org/apache/uima/jcas/JCas.html) which contains all the information that each annotation engine in your cTAKES pipeline extracted. You can either parse t

Re: Relating MeasurementAnnotations to other IdentifiedAnnotations

UOM; > > The last approach was a home-built mechanism using the ConllDependencyNode > collection and the RelationArguments to detect the same connection between > certain typed pairs of Identified annotations. > > Problem is. I've always been in prototyping mode and never had ti

Relating MeasurementAnnotations to other IdentifiedAnnotations

Hi, Is there any configuration or component in cTAKES that can be used to attribute a measurement annotation to another annotation that it applies to? For example, for "2 mm incision" where we relate "2 mm" to "incision"? It looks like there might be a roundabout way to find the head of the span o

Re: Struggling initializing

Sebastien, Just wanted to confirm that you have the sno_rx_16ab.script file in org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/ Jeff On Sat, Aug 10, 2019, 2:16 PM gandhi rajan wrote: > Sorry Sebastien I still don't get what you are trying to do. > > On Saturday, August 10, 2019, Sebastie

Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge [EXTERNAL]

mellitus" and "diabete mellitus" in the umls mrconso file might > have a hint. Perhaps some code thinks that it is fixing a plural term? > > Sean > > From: Jeffrey Miller > Sent: Tuesday, June 18, 2019 10:23 PM > To: dev@ct

Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge [EXTERNAL]

projects requiring larger nets I > have built dictionaries that are horribly inclusive - 2 to 3 times the > sno_rx_16ab. > > Sean > > From: Jeffrey Miller > Sent: Monday, June 17, 2019 4:39 PM > To: dev@ctakes.apache.org > Subject: Re: Differences in dictionary built

Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge [EXTERNAL]

ere, but writing (especially technical) is > > pretty much my least favorite activity. > > > > Sean > > > > > > p.s. > > Please don't wait for it, but I am currently working on new dictionary > > code and plan to introduce that in ctakes. Again, ple

Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge [EXTERNAL]

be nice because the tokenization that occurs when > > creating the dictionaries from the releases make comparisons a bit tricky > > and is not 100% reversible. I would love to hear an answer to your > > quandary. > > > > Remy > > > > On Sat, Jun 15, 20

Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge

ies should work seamlessly. > > > > On Saturday, June 15, 2019, Jeffrey Miller wrote: > > > > > Thanks Remy. Does anyone know if these manually curated > > > modifications/synonyms are tracked anywhere (aside from the dictionary > > > itself) so they can b

Re: Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge

y > > On Fri, Jun 14, 2019 at 1:03 PM Jeffrey Miller wrote: > > > Hi, > > I have created a custom dictionary from the latest UMLS release with > > SNOMEDCT_US and RxNorm and I've noticed it seems to be generating > .script > > file with unexpected differen

Differences in dictionary built with dictionaryBuilder and sno_rx16ab from sourceforge

Hi, I have created a custom dictionary from the latest UMLS release with SNOMEDCT_US and RxNorm and I've noticed it seems to be generating .script file with unexpected differences as compared to the sno_rx_16ab file available as part of the cTAKES release. Specifically, for diabetes, it is missing

Re: MySQL web rest version unstable (with question) and note about official web rest Dockerfile

Hi Matthew, I don't know if you've run into this issue, but one of the problems I had when playing with the service was that the code allowing the HTTP request to switch between Pipelines did not work when using the TS components if different dictionaries were used in each pipeline. I think the NE

Re: RxNorm and Orange book [EXTERNAL]

tic-equivalence-evaluations-orange-book > > Sean > ____ > From: Jeffrey Miller > Sent: Friday, May 10, 2019 9:46 AM > To: dev@ctakes.apache.org > Subject: RxNorm and Orange book [EXTERNAL] > > Hi, > > Does cTAKES 4.0.0 still make use of the Orange Book and RxNorm_Inde

RxNorm and Orange book

Hi, Does cTAKES 4.0.0 still make use of the Orange Book and RxNorm_Index as indicated in the docs here: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+Dictionaries+and+Models ? I ask because we are building our own dictionary via the dictionary creator GUI and have included RxNorm

Re: Threading and cTAKES (on Spark) [EXTERNAL]

single pipeline on n threads and > running a single document through the pipeline on each thread. > -- It is entirely up to the pipeline to determine the concurrency of > processing documents. > -- The more thread-safe annotators that don't require locking, the more > utilized the

Threading and cTAKES (on Spark)

Hi, I am following up on a discussion previously in the "re: ctakes web service" thread from this month. Apologies if I summarize anyone's comments incorrectly. Sean had commented that it would not be advisable to create a pool of pipelines and dispatch 1 per thread in the same process because the

Re: ctake web service [EXTERNAL]

gh that > certainly wasn't everything. It was easier to write the wrappers. Plus, I > could rubber stamp and quickly wrap any ae that I came across for testing > or use to be ts. > > > Cheers for the curiosity, > > Sean > > > > > _

Re: ctake web service [EXTERNAL]

there. As each instance is instantiated, I > re-read the piper file - creating a new engine which is assigned to a Pool > member. > > Peter > > On Sat, Mar 9, 2019 at 9:20 AM Jeffrey Miller wrote: > > > Thanks for your response Sean- we are still working on this (and have

Re: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL]

nfluence/signup.action > > Cheers, > Sean > > ____ > From: Jeffrey Miller > Sent: Friday, February 22, 2019 10:57 AM > To: dev@ctakes.apache.org > Subject: Re: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL] > > Thank you Sean, that cl

Re: ctake web service [EXTERNAL]

gardless, the rest of the pipeline would crash. > > Jeff, can you share information about your efforts on spark? If we could > get that working and in standard ctakes it would be fantastic. > > I hope that this information is useful. > > Sean > > > >

Re: ctake web service [EXTERNAL]

Is there any known reason that you can't create a pipeline pool, but keep everything in the same process? Is it safe to load multiple pipelines in the same process as long as only one thread can access each one at a time (we plan to use this in a Spark pipeline). One caveat I have noticed- it seems

Re: DefaultFastPipeline.piper and LVG Annotator [EXTERNAL]

tely be updated. Both the diagram and the > page on lvg include information that precedes (does not account for) the > existence of the fast dictionary lookup. > > Sean > > > > From: Jeffrey Miller > Sent: Tuesday, February 19

DefaultFastPipeline.piper and LVG Annotator

Hi, I was wondering if the LVG Annotator is included DefaultFastPipeline.piper . I have tried to trace through all the includes, but I cannot