Hi Ivan,
Here's the revision of the abstract that was drawn directly from the
Banff presentation PDFs:
posted by Bill Bug on 5/12 as a summary both of Don & Matthias
copy and
the Banff presentations -William Bug 5/12/07 10:22 PM
Accelerating integrative neuroscience research through Semantic Web
technology
The enormous scientific and clinical progress hastened via large-
scale
efforts to systematically express public bio-molecular sequence and
structure databases according to community-shared syntax has been
considerably enhanced in the last decade via systematic, explicit
association of semantic expressions defining relevant, meaningful
properties and relations (e.g., the molecular function, cellular
component, and biological function described by The Gene Ontology).
This is part of a larger effort to apply consistent semantic
annotations
to biomedical information from a variety of sources (public data
repositories, scientific literature corpi, clinical trials and
medical
reports, etc.). The goal is to facilitate semantically-driven data
integration and queries, thus avoiding duplication of research
effort,
uncovering deep, meaningful correlations across a broad spectrum of
experiments, and making more effective use of basic and clinical
research. In the treatment of complex human diseases,
accelerating such
broad-scoped biomedical knowledge discovery is most urgently needed,
especially to alleviate the enormous damage and suffering caused
both to
individuals and society by the myriad of neurodegerative diseases
such
as Alzhiemer's, Parkinson's, and MS. Here the W3C Semantic Web
Health
Care/Life Science Interest Group provides a focused demonstration
of how
to specifically effect such gains by using W3C-sponsored Semantic Web
technology (SemWebTech) - RDF, OWL, and the cornucopia of robust
tools
built on these core formalisms. We demonstrate how SemWebTech
specifically excels at: fusing data across scientific disciplines;
enhancing specificity of evidentiary provenance; re-combining
original
data in novel ways via inference and querying at varying granularity
levels; extensively characterizing data inconsistencies; greatly
extending automation of these tasks. A SemWebTech application
typically
begins with careful modeling of the underlying biological reality
represented as simple subject-predicate-object statements (RDF
triples)
via unambiguous, network-accessible identifiers (URIs). These triple
stores (or RDF triple representations of original data
repositories) are
then enhanced via reasoner inferencing, which can also extend the
complexity and expressivity of queries. SemWebTech queries are
resolved
via SPARQL, and RDF-driven visualization tools both simplify result
presentation and promote uncovering complex relations. In this
specific
demo we focus on exploring the molecular pathology of amyloid-driven
damage in Alzheimer's disease. We show how SemWebTech can
specifically
aid in exploring dendritic cell biology seeking candidate genes,
proteins, molecular functions, and cellular components effected by
maturation of amyloid placques in dendrite-rich neuropil. We also
demonstrate identification of potential drug targets to treat
AD-associated cortical Pyramidal cell pathophysiology using a
relevant
domain-restricted ontology and an RDF triple representation of
related
literature and bio-molecular data repositories. We demonstrate a
mashup
combing queries results againsts an RDF triple representation of
descriptive information from the Allan Brain Atlas with the Google
Maps
interface can provide a very flexible, alternative query and
visualization framework to the ABA's 20,000 gene-specific
histologically
imaged C57Bl/6J mouse brains. Finally, we use the Lisp Semantic Web
(LSW) tool for real-time interactive queries exploring a 200
Megatriple
repository of MeSH annotated literature. Future work will extend
this
demonstration by adding OWL-based ontologies describing several
well-known neuroinformatics repositories (e.g., SenseLab, the Brain
Architecture Management System (BAMS), the Cell-Centered Database
(CCDB), PDSP Ki database), linking to RDF triple views of their
underlying data repositories, and adding de novo constructed
neuroscience RDF repositories such as the SWAN-based Alzheimer
Research
Forum hypotheses collection. We will use these to extensively
explore
APP effects on fast-inactivating K+channels (I.K.A) in CNS neurons
- an
emerging research focus - to uncover fundamental etiopathological
mechanisms in AD. We will also demonstrate use of the ABA/Google
Maps
mashup in other neuroinformatic tools - i.e., the Mouse BIRN Atlasing
Tool (MBAT).
It's pretty dense. Folks felt it was too jargon filled for a
neuroscience community - and too narrowly focussed on the demo
presentations themselves. Perhaps both of those characteristics
would
make this version (or a minor edit of it to better suit it to a blog
post and eliminate some of the non-standard shorthand - e.g.,
SemWebTech) would fit the purpose you describe below?
Again - I would defer to Alan and Susie as the Banff presenters to
determine to whether they believe this truly encapsulates what they
presented - and the future directions those presentations pointed
toward.
Cheers,
Bill
On May 16, 2007, at 5:07 AM, Ivan Herman wrote:
I have seen the mail of Bill Bug on the abstract, and I was
wondering
whether somebody of your group could write a one-two paragraph
abstract
on the demo, with pointers, that could be added to the Semantic Web
Activity News:
http://www.w3.org/2001/sw/anews
this is, in fact, a blog whose rss feeds are picked up quite
widely. If
you agree in a small text, Eric or Tonya should blog it on the
page (it
looks better if it is published under their name and not mine)
Ivan
Alan Ruttenberg wrote:
I have updated the page http://esw.w3.org/topic/HCLS/
Banff2007Demo with
slides, pointers to the triple store etc.
-Alan
--
Ivan Herman, W3C Semantic Web Activity Lead
URL: http://www.w3.org/People/Ivan/
PGP Key: http://www.cwi.nl/%7Eivan/AboutMe/pgpkey.html
FOAF: http://www.ivan-herman.net/foaf.rdf
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]
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