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Re: Banff demo

From: Ivan Herman <ivan@w3.org>
Date: Wed, 16 May 2007 12:04:53 +0200
Message-ID: <464AD745.5050705@w3.org>
To: William Bug <William.Bug@DrexelMed.edu>
Cc: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>

that is certainly way too long and complicated for the audience of the
SW activity log. The text should be of 1-2 shorter paragraphs and aimed
at SW techies...


William Bug wrote:
> 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 - William.Bug@DrexelMed.edu
> <mailto:William.Bug@DrexelMed.edu>


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

Received on Wednesday, 16 May 2007 10:04:51 UTC

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