Re: BioRDF [Telcon]

Hi All,

Here is one Use Case to review for today thanks to the efforts of my  
colleagues on the BIRN Ontology Task Force, Maryann Martone and  
Jessica Turner. It is representative of the low-hanging fruit  
approach we are taking - one where minimal ontology-based annotation  
on large data sets using a semantic framework covering specific  
neuroscience domains will help us to progressively add more utility  
to the BIRN infrastructure appropriate to meet the needs of the  
broadest range of neuroscientists.  This is also a neuroimaging Use  
Case, so it should dovetail nicely with the discussion Daniel Rubin  
will be leading.

There are a considerable collection of Use Cases covering a wider  
range of topics from molecular data in mouse models to clinical  
assessments which we (the BIRN OTF) are now proceeding through to  
provide a sufficient amount of detail so as to help us more clearly  
define our semantic infrastructural requirements.  I'll send more of  
these around later as they become available.

Cheers,
Bill


BIRN Use Case #1:  Locating specific types of functional neuroimaging  
data sets through the BIRN infrastructure
A researcher wants to examine all fMRI datasets where the subject is  
given a working memory task.  Through the simple web interface, the  
user enters “fMRI data and working memory task”.   The BIRN mediator  
searches the BIRNLex lexicon+ontology framework to find those  
behavioral paradigms listed under working memory tasks.  The mediator  
then dispatches a distributed query to those data repositories which  
have been registered to it in search of fMRI data where subjects have  
been administered these tasks.  In order to understand the results in  
context, the web interface provides the relevant portion of the  
hierarchy and indexes each result to the relevant term.

The  mediator in this case performs two essential functions:  1)  it  
allows a query to be issued across multiple data resources without  
the need to query each one separately;  2)  it utilizes the knowledge  
contained in BIRNLex to expand the query beyond the specified term to  
find data that is relevant to the query.

This use case requires a level of deeper integration than simple  
keyword indexing of data sources can provide, because the user is  
asking for only those scans from subjects that were given a working  
memory test.   Simple keyword descriptions of a resource do not  
provide adequate information for performing this type of query.  For  
example, the current description of the data content of the fMRI Data  
Center (www.fmridc.org) includes the following:
anatomical / structural, behavioral.sensory performance.olfaction,  
neuroimaging.functional

Keyword searching would be able to indicate the fMRI data center as  
one resource that might have relevant data but would not be able to  
return the specific data sets desired without the user performing an  
additional query and sorting through the results, weeding out all the  
false positives.

The goal of the BIRN Infrastructure in this context is to provide  
enabling technology not only capable off-loading some of the more  
simple semantically-driven tasks normally carried out by an expert  
neuroscience investigator, but to also provide a general knowledge  
supplement to cover those sub-domains a given neuroscientist may not  
know in detail.  This example demonstrates both such forms of  
cognitive augmentation.  In providing a semantic framework to  
describe the general categories of behavioral protocol known to test  
working memory, an investigator knowledgeable in that field is saved  
the often tedious task of sorting through the results of a broad,  
keyword search for working memory, whereas one less familiar with the  
field is able to identify the data sets of interest without prior  
knowledge of the specific behavioral paradigm tests.  It also covers  
the fact many data sets will be annotated with the specific  
behavioral paradigm with no specific mention of working memory. This  
works because the identified data repositories have been annotated  
using BIRNLex and the mediator is capable of using both the preferred  
terms and lexical variants as well as the underlying semantic graph  
to more efficiently identify the desired data sets.


On Jan 5, 2007, at 2:02 PM, Susie Stephens wrote:

>
> Here's a reminder for Monday's BioRDF call.
>
> Date of Call: Monday January 8, 2007
> Time of Call: 11:00am Eastern Time
> Dial-In #: +1.617.761.6200 (Cambridge, MA)
> Participant Access Code: 246733 ("BIORDF")
> IRC Channel: irc.w3.org port 6665 channel #BioRDF
> Duration: ~1 hour
>
> Agenda
> - Review action items.
> - Kei Cheung will provide a status update regarding the BMC  
> Bioinformatics paper.
> - Daniel Rubin will highlight the use of images within scientific  
> queries.
> - Bill Bug will describe some of the most appropriate use cases  
> from BIRN.
> - Finalize decisions regarding the best venue for the demo.
> - AOB.
>
>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu