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From Deepal Dhariwal <deepaldhari...@gmail.com>
Subject Re: Information Extraction using ontology
Date Sun, 30 Dec 2012 11:42:56 GMT
Hello Pei,

I am aiming for an annotator that provides mapping between UMLS CUI's and
ontology classes. If I could write a generic code that provides mapping
between cTakes results and any ontology then it might be useful to the
community.
Let me know your views on this annotator.

Thanks
Deepal Dhariwal

On Fri, Dec 28, 2012 at 10:37 AM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

> 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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