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Re: Evidence of Significance of Semantic Web for Life Sciences

From: Luciano, Joanne Sylvia <jluciano@cs.rpi.edu>
Date: Thu, 22 Dec 2011 17:32:05 +0000
To: Oliver Ruebenacker <curoli@gmail.com>
CC: public-semweb-lifesci <public-semweb-lifesci@w3.org>
Message-ID: <F66AD269-79A1-46FE-A5AA-CB5EA0F668E3@rpi.edu>
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<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins1>, Tim Clark2<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins2>, William Bug3<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins3>, Matthias Samwald4<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins4>, Olivier Bodenreider5<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins5>,Helen Chen6<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins6>, Donald Doherty7<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins7>, Kerstin Forsberg8<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins8>, Yong Gao9<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins9>, Vipul Kashyap10<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins10>, June Kinoshita11<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins11>, Joanne Luciano12<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins12>, M Scott Marshall13<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins13>, Chimezie Ogbuji14<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins14>, Jonathan Rees15<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins15>,Susie Stephens16<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins16>, Gwendolyn T Wong11<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins11>, Elizabeth Wu11<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins11>, Davide Zaccagnini17<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins17>, Tonya Hongsermeier10<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins10>, Eric Neumann18<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins18>, Ivan Herman19<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins19> and Kei-Hoi Cheung20<http://www.biomedcentral.com/1471-2105/8/S3/S2/#ins20>*


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,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 Dumontier26

We also had a special issue of the Journal of Biomedical Informatics:
Semantic mashup of biomedical data

Kei-Hoi Cheung <http://www.sciencedirect.com/science/article/pii/S1532046408001020#cor1> [Corresponding Author Contact Information] <http://www.sciencedirect.com/science/article/pii/S1532046408001020#cor1> , [E-mail The Corresponding Author] <mailto:kei.cheung@yale.edu> , 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





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Received on Thursday, 22 December 2011 17:32:37 UTC

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