CTAKES FAST DICTIONARY

Hi Sean I have created a dictionary with 6-7 vocabs with filtered semtypes. that includes *[Disease or Syndrome]* When i search the term "herpes zoster" i am getting multiple cuis e.g Ctakes matches: *"herpes" *to and *"herpes zoster"* My Question is why not it returned the "herpes zoster" m

Re: CTAKES FAST DICTIONARY

To Add more here is the query on dictionary SELECT * FROM "PUBLIC"."CUI_TERMS" WHERE "TEXT" LIKE 'herpes zoster' 42338 1 2 herpes zoster zoster On Wed, Feb 15, 2017 at 3:14 PM, shahid ashraf wrote: > Hi Sean > > I have created a dictionary with 6-7 vocabs with filtered semtypes. that > i

finding synonyms words for given medical words form umls

Hi Sean, How can we find synonyms words for given medical words from umls, Example : pain is a medical word, how can i get pain word related all synonyms words from umls. please give me any solution for this issue. regards, shyam k.

RE: finding synonyms words for given medical words form umls

Hi Shyam, If I understand you correctly, to get synonyms from the umls, go here: https://utslogin.nlm.nih.gov/cas/login?service=https%3A%2F%2Futs.nlm.nih.gov%3A443%2F%2Fj_spring_cas_security_check%3Bjsessionid%3D73C54CF8B4F00AD1538881044F2F52FE 1. Sign in 2. Type your medical words in the "term"

Re: CTAKES FAST DICTIONARY

Sean Anything on this... On Wed, Feb 15, 2017 at 3:21 PM, shahid ashraf wrote: > To Add more here is the query on dictionary > > > SELECT * FROM "PUBLIC"."CUI_TERMS" WHERE "TEXT" LIKE 'herpes zoster' > > 42338 > > 1 > > 2 > > herpes zoster > > zoster > > > On Wed, Feb 15, 2017 at 3:14 PM, s

Re: Ctakes is not thread safe

Please unsubscribe me. Regards, On 2/14/17, 1:46 AM, "shahid ashraf" wrote: Caution: This email came from outside Kaiser Permanente. Do not open attachments or click on links if you do not recognize the sender. __

Re: CTAKES FAST DICTIONARY

Please un-subscribe me. Regards, On 2/15/17, 9:22 AM, "shahid ashraf" wrote: Caution: This email came from outside Kaiser Permanente. Do not open attachments or click on links if you do not recognize the sender. __

RE: Drug NER missing dosage

Anyone have insight on this issue? Thanks, Erin -Original Message- From: Erin Nicole Gustafson Sent: Monday, February 13, 2017 10:22 AM To: dev@ctakes.apache.org Subject: Drug NER missing dosage Hi all- I am running the Drug NER component as a part of the clinical pipeline. My goal is

Phenotype-specific entities

Hi all, I would like to be able to only identify entities that are relevant for some specific phenotype. One step towards achieving this would be to build a custom dictionary with a limited set of semantic types. However, this is not quite specific enough to only identify mentions related to on

RE: Phenotype-specific entities

Hi Erin, Yes, creating your customized dictionary is the way to go. You can prune by semantic types of interest and then remove branches that are not relevant to your specific phenotype. I am not aware of cTAKES implementing such a tool for a very customized dictionary. You can also start with

Re: Phenotype-specific entities

Guergana, thank you. Is there anything in cTAKES now for walking the UMLS ontology (e.g. for finding hypernyms, synonyms, etc.)? Dima > On Feb 15, 2017, at 12:45, Savova, Guergana > wrote: > > Hi Erin, > Yes, creating your customized dictionary is the way to go. You can prune by > semant

RE: Phenotype-specific entities

I don't believe there is a tool for walking the UMLS ontology, Dima. But Sean should confirm that his dictionary building tool does not have that functionality. I think you can use the UMLS tables to get that information. It has been quite a while I have used these tables, but I remember I was

RE: Phenotype-specific entities [SUSPICIOUS]

The dictionary gui doesn't walk the ontology. There are umls tables that list relations, wherein things like "isa" (is a) relations may satisfy a hypernym requirement. If you have the umls rrf files look at mrrel.rrf. The structure is basically concept1|..| concept2|..|relationtype|.. See s

Re: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS]

Lol was just about to send this: https://github.com/tmills/umls-graph-api It points at your umls META directory, reads in the ctakes list of TUIs, and builds a neo4j graph database with all the ISA links, and has a simple API for getting parent/child CUIs. I used it for coreference. Tim ___

RE: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

Hi Tim, Lol rbay, I remembered your talking about this and wondered if you would bite! Cheers! Sean -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Wednesday, February 15, 2017 2:26 PM To: dev@ctakes.apache.org Subject: Re: Phenotype-specific e

RE: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

Thanks, all! -Erin -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, February 15, 2017 1:28 PM To: dev@ctakes.apache.org Subject: RE: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] Hi Tim, Lol rbay, I remembered your tal

Re: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS]

Very nice! Thank you, Tim and Sean. Dima > On Feb 15, 2017, at 13:25, Miller, Timothy > wrote: > > Lol was just about to send this: > https://github.com/tmills/umls-graph-api > > It points at your umls META directory, reads in the ctakes list of TUIs, and > builds a neo4j graph database wi

Re: Drug NER missing dosage

Hello Dev, Please remove me from this mailing list. Thanks. Regards, Piyush Jain On Mon, Feb 13, 2017 at 11:24 AM Erin Nicole Gustafson < erin.gustaf...@northwestern.edu> wrote: > Hi all- > > I am running the Drug NER component as a part of the clinical pipeline. My > goal is to extract the dr