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

From: Robert Stanley <rstanley@io-informatics.com>
Date: Thu, 26 Jan 2012 18:54:00 -0800
Message-ID: <08AE3015BD5DF149951910A5E851F010B7B9AF@MAIL-02.io-informatics.com>
To: "Amit Sheth" <amit.sheth@wright.edu>, "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Cc: "Luciano, Joanne Sylvia" <jluciano@cs.rpi.edu>
 

Nice comment Amit.  

 

Many HCLS / systems biology and precision medicine use cases move from
theoretically possible but not practically achievable (note historically
failed or "re-aligned" HCLS information sharing and disease surveillance
standards), to efficiently achievable using semantic technologies. 

 

In case you hadn't seen it already (I hope I didn't already send this!):

R. Stanley, B. McManus, R. Ng, E. Gombocz, J. Eshleman, C. Rockey:"Case
Study: Applied Semantic Knowledgebase for Detection of Patients at Risk
of Organ Failure through Immune Rejection" Joint Case Study of IO
Informatics and University British Columbia (UBC), NCE CECR PROOF Centre
of Excellence, James Hogg iCAPTURE Centre, Vancouver, BC, Canada, March
29, 2011 
W3C Semantic Web Use Cases and Case Studies
<http://www.w3.org/2001/sw/sweo/public/UseCases/IOInformatics/>  <
http://www.w3.org/2001/sw/sweo/public/UseCases/IOInformatics/ >

Here is another example that significantly benefitted by application of
semantic tools and methods

 

T.N. Plasterer, R. Stanley, E. Gombocz: "Correlation Network Analysis
and Knowledge Integration" In: "Applied Statistics for Network Biology:
Methods in Systems Biology", M. Dehmer, F. Emmert-Streib, A. Graber, A.
Salvador (Eds.) Wiley-VCH, Weinheim, ISBN: 978-3-527-32750-8
<http://www.wiley.com/WileyCDA/WileyTitle/productCd-3527327509.html>
(2011)

 

You may find other useful references here:

 

http://www.io-informatics.com/news/articles.html

 

 

All the best,

 

Bob Stanley

IO Informatics

 

 

From: Amit Sheth [mailto:amit.sheth@wright.edu] 
Sent: Sunday, January 22, 2012 11:23 AM
To: Luciano, Joanne Sylvia; public-semweb-lifesci
Cc: Oliver Ruebenacker
Subject: Re: Evidence of Significance of Semantic Web for Life Sciences
- a couple of more examples

 

 

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
<http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001458>
.' 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
<http://www.biomedcentral.com/1471-2105/12/461/abstract> .' 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
<http://www.sciencedirect.com/science/article/pii/S1359644611004764> ,
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
<http://www.slideshare.net/apsheth/semantic-web-for-360degree-health-sta
teoftheart-vision-for-better-interoperability> 

 

 

Cheers,

Amit

 

Amit Sheth Twitter <http://twitter.com/amit_p>  Blog
<http://amitsheth.blogspot.com>  LinkedIn
<http://www.linkedin.com/in/amitsheth>  Home Page
<http://knoesis.org/amit> 

@ Kno.e.sis <http://knoesis.org>  - 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 <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,<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>
<http://www.sciencedirect.com/science/article/pii/S1532046408001020#cor1
> , <REemail.gif> <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 <http://vcell.org/> )
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org
<http://www.sbpax.org/> )
http://www.oliver.curiousworld.org <http://www.oliver.curiousworld.org/>


 

 
Received on Friday, 27 January 2012 02:54:34 GMT

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