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" <[email protected]> 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 > <[email protected]>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:[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 >>>> >>
