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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Information Extraction using ontology
Date Fri, 28 Dec 2012 15:37:43 GMT
Hi Deepal,
If I understand correctly, you were planning to have an annotator  that iterates through all
of the UMLS CUI's identified by cTAKES and then map them to the heartfaid ontology class/code.
I am not aware of anything that does specifically this, but there is an open ticket that is
trying to do something similar for Drugs classes (RxNorm to NDF-RT mapping) (https://issues.apache.org/jira/browse/CTAKES-107).
It does seem like something that may be useful for others if you would like to contribute
that to the community though...

--Pei

> -----Original Message-----
> From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]
> Sent: Thursday, December 27, 2012 10:28 PM
> To: ctakes-dev@incubator.apache.org
> Cc: ctakes-user@incubator.apache.org
> Subject: Re: Information Extraction using ontology
> 
> Hello Pei,
> 
> The dictionary is an ontology i.e. a .owl file (Reference:
> http://lis.irb.hr/heartfaid/ontology/) . I am not sure whether it is subset of
> UMLS but its definitely based on UMLS since they have relations such as
> 'UMLS Synonym'
> An example of mapping terms would be:
> 1. UMLS lookup annotator returns 'Hypertension' as medical concept.I want
> to assert that it corresponds to Hypertension class on this ontology whose
> parent is Blood Pressure and relations include TreatedBy, Could Include etc.
> 
> Hence I want to build a annotator that provides mapping between ctakes
> annotator results and owl classes. Does the dictionary lookup component
> allow to plug in dictionaries in .owl or .rdf format?
> 
> Thanks
> Deepal Dhariwal
> 
> On Thu, Dec 27, 2012 at 10:31 AM, Chen, Pei
> <Pei.Chen@childrens.harvard.edu>wrote:
> 
> > Hi Deepal,
> > Within the dictionary lookup component, you can also plugin other
> > custom dictionaries in additional to the UMLS ones.
> > The dictionary itself can be in different formats (MySQL, HSQLDB,
> > Lucene, CSV text file) and could be configured via the xml files.
> > Is this what you were referring to?  Do you have an example of
> > "mapping terms to the corresponding classes?"
> > Just curious, Is the heart ontology a subset of UMLS?
> >
> > Thanks,
> > --Pei
> >
> > > -----Original Message-----
> > > From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]
> > > Sent: Thursday, December 27, 2012 12:17 AM
> > > To: ctakes-user@incubator.apache.org;
> > > ctakes-dev@incubator.apache.org
> > > Subject: Information Extraction using ontology
> > >
> > > Hello all,
> > >
> > > I have a heart ontology and I want to extract terms from a clinical
> > > text
> > that
> > > correspond to classes in the ontology. cTAKES UMLS Lookup Annotator
> > > returns UMLS terms from a given piece of text. Could I modify the
> > annotator
> > > to extract terms from the ontology and is there is some other
> > > component
> > of
> > > cTAKES that would allow me to do so. I am trying to set up a cTakes
> > pipeline
> > > where I first extract medical terms from text using UMLS lookup then
> > filter
> > > cardio vascular terms and identify relations between them using an
> > ontology.
> > >
> > > Thanks
> > > Deepal Dhariwal
> >

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