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 - [EMAIL PROTECTED]