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:[email protected]] > Sent: Thursday, December 27, 2012 10:28 PM > To: [email protected] > Cc: [email protected] > 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 > <[email protected]>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:[email protected]] > > > Sent: Thursday, December 27, 2012 12:17 AM > > > To: [email protected]; > > > [email protected] > > > 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 > >
