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Re: Evidence of Significance of Semantic Web for Life Sciences - a couple of more examples

From: Amit Sheth <amit.sheth@wright.edu>
Date: Sun, 22 Jan 2012 14:23:27 -0500
To: "Luciano, Joanne Sylvia" <jluciano@cs.rpi.edu>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
Cc: Oliver Ruebenacker <curoli@gmail.com>
Message-id: <6A067FEE-3FCD-414F-A6BA-C28ACABCB2DC@wright.edu>

As already discussed,  I would not like to claim that any work will conclusively show what 
SW can do for LS that cannot be done otherwise-- 
it is like asking (for many problems) during the first decade when
computers start to become available: can computers do things that cannot be done without?
and you can replace computers by some other technology, and get similar answers.
And yet computers, and many technologies are indispensable now.

Among the growing list of papers that Joanne and others shared--
here are a couple more recent ones that involve evaluations in the context of biomedical research
and demonstrate to varying  degree benefits of using SW approach/technologies:

Priti P. Parikh, Todd A. Minning, Vinh Nguyen, Sarasi Lalithsena, Amir H. Asiaee, Satya S. Sahoo, Prashant Doshi, Rick Tarleton, and Amit P. Sheth. 'A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi.' Public Library of Science (PLOS) Neglected Tropical Diseases,  6(1): e1458. doi:10.1371/journal.pntd.0001458, Jan 2012.

Satya S. Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P. Sheth. 'A Unified Framework for Managing Provenance Information in Translational Research.' BMC Bioinformatics 2011, 12:461 doi:10.1186/1471-2105-12-461

Already shared:

David J. Wild, Ying Ding, Amit P. Sheth, Lee Harland, Eric M. Gifford, Michael S. Lajiness, Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research, Drug Discovery Today, Available online 29 December 2011, ISSN 1359-6446, 10.1016/j.drudis.2011.12.019.

I had summarized some of the applied SW projects in HCLS in this ONI/HHS invitational workshop talk
(Ora covered broader aspects of SW, I covered specific examples in HCLS):

Semantic Web for 360-degree Health: State-of-the-Art & Vision for Better Interoperability


Amit Sheth Twitter Blog LinkedIn Home Page
@ Kno.e.sis - Ohio Center of Excellence in Knowledge-enabled Computing
LexisNexis Ohio Eminent Scholar, Wright State University

On Dec 22, 2011, at 12:32 PM, Luciano, Joanne Sylvia wrote:

> Oliver,
> I'm wondering if these references would help -- (these are just a few - and I stuck to the biomedical domain) 
> We (below) have a paper in press in the journal Pharmacogenomics, that makes the case for semantic technologies in personalized medicine (title, abstract, and co-authors below).
> Matthias Samwald -  Medical University of Vienna, University of Technology Vienna, Austria
> Adrien Coulet LORIA – INRIA Nancy–Grand-Est, Cedex, France
> Iker Huerga -Elsevier, PA, USA
> Robert L Powers - Predictive Medicine, Inc., MA , USA
> Joanne S Luciano - Tetherless World Constellation, Rensselaer Polytechnic Institute, Troy, NY USA
> Robert R Freimuth - Mayo Clinic, MN USA
> Frederick Whipple - Genomics Education Initiative, CA USA
> Elgar Pichler, Northeastern University,MA USA
> Eric Prud’hommeaux World Wide Web Consortium/MIT, MA USA
> Michel Dumontier Carleton University, Ottawa, Canada
> M Scott Marshall Leiden University Medical Center, University of Amsterdam, The Netherlands
> Semantically enabling pharmacogenomic data for the realization of personalized medicine
> Understanding how each individual’s genetics and physiology influences pharmaceutical response is crucial to the realization of personalized medicine and the discovery and validation of pharmacogenomic biomarkers is key to its success. However, integration of genotype and phenotype knowledge in medical information systems remains a critical challenge. The inability to easily and accurately integrate the results of biomolecular studies with patients’ medical records and clinical reports prevents us from realizing the full potential of pharmacogenomic knowledge for both drug development and clinical practice. Herein, we describe approaches using semantic web technologies, in which pharmacogenomic knowledge relevant to drug development and medical decision support is represented in such a way that it can be efficiently accessed both by software and human experts. We suggest that this approach increases the utility of data, and that such computational technologies will become an essential part of personalized medicine, alongside diagnostics and pharmaceutical products.
> Also, last year I co-taught Semantic e-Science and Advanced Semantic Technologies with Deborah McGuinness (mentioned in Alexander Garcia's email).  We require semester projects from our students in which they are required to articulate what the semantic technologies they use were and how they added value).  Not many of these (yet) are in the biomedical domain yet (that's why I'm now at RPI), but we have made a few cases in papers coming out of the HCLSIG work:
> http://www.biomedcentral.com/1471-2105/8/S3/S2  (Highly Accessed)
> Advancing translational research with the Semantic Web
> Alan Ruttenberg1, Tim Clark2, William Bug3, Matthias Samwald4, Olivier Bodenreider5,Helen Chen6, Donald Doherty7, Kerstin Forsberg8, Yong Gao9, Vipul Kashyap10, June Kinoshita11, Joanne Luciano12, M Scott Marshall13, Chimezie Ogbuji14, Jonathan Rees15,Susie Stephens16, Gwendolyn T Wong11, Elizabeth Wu11, Davide Zaccagnini17, Tonya Hongsermeier10, Eric Neumann18, Ivan Herman19 and Kei-Hoi Cheung20*
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102889/
> The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
> Joanne S Luciano,<corrauth.gif>1,2 Bosse Andersson,3 Colin Batchelor,4 Olivier Bodenreider,5 Tim Clark,6,7 Christine K Denney,8 Christopher Domarew,9Thomas Gambet,10 Lee Harland,11 Anja Jentzsch,12 Vipul Kashyap,13Peter Kos,6 Julia Kozlovsky,14 Timothy Lebo,1 Scott M Marshall,15,16James P McCusker,1 Deborah L McGuinness,1 Chimezie Ogbuji,17 Elgar Pichler,18 Robert L Powers,2 Eric Prud’hommeaux,10 Matthias Samwald,19,20,21 Lynn Schriml,22 Peter J Tonellato,6 Patricia L Whetzel,23Jun Zhao,24 Susie Stephens,25 and Michel Dumontier<corrauth.gif>26
> We also had a special issue of the Journal of Biomedical Informatics:  
> Semantic mashup of biomedical data
> Kei-Hoi Cheung <REcor.gif>, <REemail.gif>, Vipul Kashyap, Joanne S. Luciano, Huajun Chen, Yimin Wang,Susie Stephens
> Hope this helps. 
> and 
> Happy Holidays
> Joanne
> On Dec 21, 2011, at 11:39 AM, Oliver Ruebenacker wrote:
>>     Hello,
>>  I am looking for evidence I can quote to convince non-experts of the
>> significance of applying Semantic Web to biomedical research,
>> especially computational cell biology.
>>  I need a recorded public statement from a source recognizable as
>> authoritative to a non-expert: e.g. could be from a relevant
>> government agency, a well-known research institution (including major
>> grad schools and companies), a well-known (i.e. well-known outside the
>> field) expert, some one where a brief look at the biography
>> immediately suggests he or she is an authority, some one quoted in
>> major media, etc.
>>  Significance could mean abstract things like advancing science and
>> health care, but even better would be tangible things like: saves
>> lives, saves money, cures cancer/malaria/AIDS, creates jobs, etc.
>>  Thanks a lot!
>>     Take care
>>     Oliver
>> -- 
>> Oliver Ruebenacker, Computational Cell Biologist
>> Virtual Cell (http://vcell.org)
>> SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
>> http://www.oliver.curiousworld.org
Received on Sunday, 22 January 2012 19:24:08 UTC

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