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 >
