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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Information Extraction using ontology
Date Fri, 18 Jan 2013 17:50:58 GMT
Hi Deepal,
I am assuming the mapping would be through UMLS CUI's.
For example, for each CUI identified by the cTAKES UMLS Dictionary Lookup annotator.

Just putting some ideas out there:
One would need a data structure to represent the Cardio Classes (perhaps a hashmap of some
sort) that maps CUI's to the classes/instances.
And then also a process to load that structure from the RDF (from either flat file, db, etc.)
format?
One might also need a place holder in the CAS (type system) to store the identified classes?

--Pei

> -----Original Message-----
> From: Deepal Dhariwal [mailto:deepaldhariwal@gmail.com]
> Sent: Wednesday, January 16, 2013 11:21 AM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: Information Extraction using ontology
> 
> Hello all,
> 
> So what I am aiming is as follows:
> 1. Extract UMLS medical terms from a given clinical narrative using ctakes
> umls lookup annotator 2. Identify cardio vascular terms from above set.
> These terms are classes / instances of heart failure ontology.  I want to make
> this mapping generic so that if in future I am targeting carcinogenic terms, I'll
> would just need to change underlying ontology.
> 3. Lastly I want to run a reasoner over the rdf triples obtained from above
> step.
> 
> For example: Find the timi score of patient 1. Extract all medical terms from
> clinical narrative 2. Extract cardio vascular terms such as whether the patient
> has congestive heart failure, whether he is an active smoker etc. using heart
> failure ontology 3. Run the sparql query of form :
> timi score = does patient have chf + age > 65 + active smoker?
> 
> Hence I need guidance on an annotator that would map ctakes terms to
> heart failure ontology and allow to run reasoner over it. Any suggestions
> would be of great help.
> 
> 
> Thanks
> Deepal Dhariwal
> 
> On Mon, Dec 31, 2012 at 9:00 AM, Lin, Chen
> <Chen.Lin@childrens.harvard.edu>wrote:
> 
> > This mapping sounds very interesting and has potential usage for other
> > projects. I will be curious to follow its progress. Thank you, Deepal,
> > for digging this!
> >
> > Best,
> > Chen
> >
> > Sent from my iPhone
> >
> > On Dec 30, 2012, at 6:43 AM, "Deepal Dhariwal"
> > <deepaldhariwal@gmail.com>
> > wrote:
> >
> > > 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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