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Posted to dev@ctakes.apache.org by Deepal Dhariwal <de...@gmail.com> on 2013/01/16 17:19:56 UTC
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
<Ch...@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" <de...@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
> > <Pe...@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
> >>> <Pe...@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
> >>>>
> >>
>
RE: Information Extraction using ontology
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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
> <Ch...@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"
> > <de...@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
> > > <Pe...@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
> > >>> <Pe...@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
> > >>>>
> > >>
> >