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 reason over. You can set up expressions (rules) that look like this. (Yes, this case is already covered in the dictionary, but it's an example) Matcher A: (lemma=="be"); Matcher B: /partially|partly/; Matcher C: /vaccinated/; Rule vaccinated|CUI1234|SNOMED5678: A? B? C; You get the Annotation you've delegated to this task, with the entity value "vaccinated|1234|5678" and the range which spanned the tokens that caused the annotation rule to fire (See Stanford's Tokens Regex) Peter On Tue, May 18, 2021 at 1:29 PM Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > 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: Finan, Sean <sean.fi...@childrens.harvard.edu> > Sent: Tuesday, May 18, 2021 11:55 AM > To: dev@ctakes.apache.org > Cc: Himanshu Shekhar Sahoo > Subject: Re: rule-based lookup for custom lexicon [EXTERNAL] [SUSPICIOUS] > > * External Email - Caution * > > > Hi Greg, > > From 30,000 ft, I think that you would want to use the RutaEngine. > > > https://urldefense.com/v3/__https://uima.apache.org/d/ruta-current/tools.ruta.book.html*ugr.tools.ruta.ae.basic__;Iw!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickztninUTU$ > > https://urldefense.com/v3/__https://javadoc.io/doc/org.apache.uima/ruta-core/latest/org/apache/uima/ruta/engine/RutaEngine.html__;!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickzI7QF5CI$ > > https://urldefense.com/v3/__http://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-core/src/main/java/org/apache/uima/ruta/engine/RutaEngine.java__;!!NZvER7FxgEiBAiR_!6YH1mXOYKMXiRAvLt8yPYWLMMklVu7YuK7KW1hde-iOew4ufAIPpkFHnsJxSvv8r5GjWickzJJ96zT4$ > > That seems to be the actual analysis engine that loads and uses rules to > create annotations. > While you could use an xml descriptor or use the piper "set" command and > do things like mapping ruta to ctakes type systems, I would take the > alternate approach of "copying" the initialize(..) and process (..) methods > and modify them to use ctakes types directly. > > Disclaimer: I know very little about uima ruta. At some point I did look > into it but it was for a specific (ctakes-derivative) project and I didn't > go further than basic doc perusal. > > If you move forward with this please let us all know what you find. I > think that there will be great interest in the community. > > Sean > ________________________________________ > From: Greg Silverman <g...@umn.edu.INVALID> > Sent: Tuesday, May 18, 2021 11:13 AM > To: dev@ctakes.apache.org > Cc: Himanshu Shekhar Sahoo > Subject: Re: rule-based lookup for custom lexicon [EXTERNAL] > > * External Email - Caution * > > > Hi Sean, > I was wondering if there was a way to use rule-base lookup of a custom > lexicon within cTAKES (say a locally curated list of covd-19 symptoms). > When I Googled around, I stumbled on UIMA Ruta, but couldn't find anything > wrt to cTAKES specifics. > > Thanks! > > > Greg-- > > On Tue, May 18, 2021 at 10:04 AM Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > To which ctakes component(s) are you referring? > > ________________________________________ > > From: Greg Silverman <g...@umn.edu.INVALID> > > Sent: Sunday, May 16, 2021 6:02 PM > > To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo > > Subject: rule-based lookup for custom lexicon [EXTERNAL] > > > > * External Email - Caution * > > > > > > I looked all over and could not find any information on how to add this > > pipeline component to cTAKES. I assume it uses UIMA Ruta? > > > > Thanks in advance! > > > > Greg-- > > -- > > Greg M. Silverman > > Senior Systems Developer > > NLP/IE < > > > https://urldefense.com/v3/__https://healthinformatics.umn.edu/research/nlpie-group__;!!NZvER7FxgEiBAiR_!6hN356eDesvWNYzsrDMaXgF6IkZw313QU2QUQw5M8Jysvh1K1JxjEBeztZicX1DM2jC0o7_0qAA$ > > > > > Department of Surgery > > University of Minnesota > > g...@umn.edu > > > > > -- > Greg M. Silverman > Senior Systems Developer > NLP/IE < > https://urldefense.com/v3/__https://healthinformatics.umn.edu/research/nlpie-group__;!!NZvER7FxgEiBAiR_!8uKf_4SXyKdCmvlMHvRGddxlzofg64D4_zsPdCThqeMAyn2akyMNI8wqM6yNUZA2N93F-aAsR7I$ > > > Department of Surgery > University of Minnesota > g...@umn.edu >
