Re: BioRDF [Telcon]

Hi Susie, Kei, et al.

I'm sorry I can't joint today. I have to leave for a lunch meeting  
now. Will catch up with you later.

Sorry about that.

Joanne

On Jan 8, 2007, at 11:09 AM, William Bug wrote:

> 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
>
>
>
>

Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: jluciano@predmed.com