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Re: Banff demo

From: William Bug <William.Bug@DrexelMed.edu>
Date: Wed, 16 May 2007 07:00:42 -0400
Message-Id: <CFCA6D81-3CD3-478B-8FFE-9FB725D3AC6F@DrexelMed.edu>
Cc: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
To: Ivan Herman <ivan@w3.org>
To break it down a bit more -

If the intent is to solely summarize the demo Alan gave as opposed to  
the demo supplemented by Susie's introduction, here's the portion of  
what is given below that was intended to summarize the PDF of Alan's  
presentation - devoid of any context-setting or pedagogical  
background that the SW techies may either not need or not care about:

"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 how a mashup combining query  
results from an RDF triple representation describing the content of  
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 200,000,000 triple repository of  
MeSH annotated literature."

This is still probably still too dense and overlong but certainly  
does distill what was in Alan's slides, so it might offer a  
foundation via which the desired copy can be derived.

The other aspects that MAY be relevant are the admittedly rather  
dense statements of what the demo was intended to illustrate (from  
Susie's presentation) - and where this effort is already intended to  
go in the future (some not future - but already present in some form):

intention:
"We demonstrate how SemWebTech excels at: fusing data across  
scientific disciplines; more specifically representing experimental  
evidence; 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."

Future:
"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 more extensively explore Amyloid Precursor Protein  
(APP) and plaque effects on various aspects of CNS nerve cell biology  
- a major research focus seeking to uncover novel 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)."

As Chico Marx once said ('Duck Soup', 1933), "I am a shut up now."

Cheers,
Bill

On May 16, 2007, at 6:04 AM, Ivan Herman wrote:

> Bill,
>
> 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...
>
> Ivan
>
> 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

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





Received on Wednesday, 16 May 2007 10:58:22 UTC

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