Re: BioRDF [Telcon]

Me, too.

I'm on IRC, but no one else appears to have arrived, yet.

Cheers,
Bill

On Jan 8, 2007, at 11:08 AM, Kei Cheung wrote:

> Hi All,
>
> I tried to call the BioRDF conference, but I kept getting the  
> message saying my access code "246733" was incorrect.
>
> Thanks,
>
> -Kei
>
> William Bug wrote:
>
>> 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 <http://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  
>> <mailto:William.Bug@DrexelMed.edu>
>>
>>
>>
>>
>
>
>

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