Hello all, I am executing ctakes CPE from Eclipse i.e. ctakesCPEGUI.java. I want to access and process the (UMLS) Concept Annotations and NumToken Annotations. I went through the src but couldnt find the the exact class which I would need to modify to implement my Ontology Lookup Annotator. I want to check each UMLS concept present in document, then check whether there is a corresponding instance in Heartfaid Ontology and if so assert a fact about the patient. Kindly let me know how to programmatically access Concept Annotation results.
Thanks Deepal Dhariwal On Fri, Jan 18, 2013 at 12:50 PM, Chen, Pei <[email protected]>wrote: > 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:[email protected]] > > Sent: Wednesday, January 16, 2013 11:21 AM > > To: [email protected] > > 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 > > <[email protected]>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" > > > <[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 > > > >>>> > > > >> > > > >
