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 - [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
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 - [EMAIL PROTECTED]
