Re: BioRDF [Telcon]

Hi Bill,

I was transferred by the operator to the biordf call (press *0).

Thanks,

-Kei

William Bug wrote:

> The Telcon is today at 11 AM, EST, correct?
>
> 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 
> <mailto:William.Bug@DrexelMed.edu>
>
>
>
>

Received on Monday, 8 January 2007 16:14:45 UTC