Re: [Obo-phenotype] Representing autism phenotypes

[Amar D. <da...@st...>]

Thanks Chris and Bill.

We look forward to working with the OBO community on the use of OWL 
+SWRL in modeling phenotypes, building upon our experiences with  
clinical trial data and autism phenotypes.

Amar

On Jan 25, 2008, at 2:36 PM, Bill Bug wrote:

> I would strongly agree with Chris's suggestion that those  
> interested in learning more about how OWL + SWRL together
>
> A  description logic formalism such as OWL can be used to  
> explicitly capture the nuanced relations amongst biomedical  
> entities (objects & processes). Using these OWL representations,  
> SWRL Rule-based logic can then be used to capture the detailed  
> phenotype classification of clinical instruments/assessments used  
> to link clinical observations to disease staging (e.g., if  
> Phenotype X AND (phenotype Y OR Phenotype Z), then subject has  
> disease A/stage A.II).  Consider each phenotype assertion (e.g.,  
> Phenotype X) as a PhenoXML statement making use of PATO qualities  
> and a variety of OBO ontology-based entity descriptions.  These  
> statements may also include numeric constraints (e.g., blood serum  
> level of compound C between n and m).
>
> As you can see, this also has significant benefit toward our goal  
> of providing explicit and computable representations of phenotype  
> that can be linked to disease state.
>
> I'd also recommend checking out the following manuscript by Dr. Das  
> and his colleagues:
>
> 	Using Semantic Web Technologies for Knowledge-Driven Querying of  
> Biomedical Data	[i.e., The EPOCH Project - http://bmir.stanford.edu/ 
> projects/view.php/epoch]
> 	http://www.springerlink.com/content/x1u3j1h03362783g/
> 	http://bmir.stanford.edu/file_asset/index.php/1165/SMI-2007-1245.pdf
>
>
> For those more interested in the technical nuts-n-bolts of how this  
> is all made to work in the context of a large RDBMS data  
> repository, I'd also recommend the following also published by Dr.  
> Das and his Stanford colleagues:
>
> 	Efficiently Querying Relational Databases Using OWL and SWRL
> 	http://bmir.stanford.edu/file_asset/index.php/1163/SMI-2007-1244.pdf
>
> I expect
>
> Cheers,
> Bill
>
> On Jan 24, 2008, at 8:53 PM, Chris Mungall wrote:
>
>> I saw a very interesting presentation by Amar Das today on his labs
>> work on representing phenotypes associated with autistic spectrum
>> disorders.
>>
>> Amar uses logical rules (encoded in the semantic web rule language
>> SWRL) to represent autism phenotypes associated with standard autism-
>> based "instruments" (assays perfomed by psychiatrists and other
>> domain specialists I believe). Some examples phenotypes would be
>> those related to the age at which certain language skills are
>> acquired by the bearer of the phenotype.
>>
>>   Amar extended PATO (using the OWL translation) adding new
>> phenotypes as subclasses of existing classes. This approach
>> highlighted some of the gaps we have in existing OBO ontologies - for
>> example "language acquisition". I believe we have some high pitched
>> mouse squeaking in GO, but nothing for language acquisition and
>> certainly nothing for more detailed clinical psychiatric phenotypes.
>>
>> As far as behaviour-related phenotypes go, I know there are a few of
>> you interested in better ways of representing complex behavior
>> phenotypes, so there may be some opportunity for synergy here. I
>> believe Dr Das is already working with BIRN (their approach also
>> involved using the BIRNLex ontology)
>>
>> Home page here:
>> http://bmir.stanford.edu/labs/view.php/das_lab
>>
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>
>
>
> William Bug, M.S., M.Phil.                                          
> 		email: wb...@nc...
> Ontological Engineer (Programmer Analyst III)		work: (610) 457-0443
> Biomedical Informatics Research Network (BIRN)
> and
> National Center for Microscopy & Imaging Research (NCMIR)
> Dept. of Neuroscience, School of Medicine
> University of California, San Diego
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>
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>
>