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

From: robert Stevens <robert.stevens@manchester.ac.uk>
Date: Fri, 6 Apr 2012 15:18:37 +0100
Message-ID: <08161C1AC3BF4A888A0D1ECCA1AA761B@manchestcc7bbd>
To: "Robert Stanley" <rstanley@io-informatics.com>, "Amit Sheth" <amit.sheth@wright.edu>, "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Cc: "Luciano, Joanne Sylvia" <jluciano@cs.rpi.edu>
Perhaps a rather tardy response, but I was waiting for a paper to come out.... (the first one here)


we've recently had this paper:
The KUPKB: a novel Web application to access multiomics data on kidney
disease. <http://www.ncbi.nlm.nih.gov.gate2.inist.fr/pubmed/22345404>
Klein J, Jupp S, Moulos P, Fernandez M, Buffin-Meyer B, Casemayou A,
Chaaya R, Charonis A, Bascands JL, Stevens R, Schanstra JP.
FASEB J. 2012 Feb 17. [Epub ahead of print]
that has used the Kidney and Urinary Pathway KB (http://www.kupkb.org) to find hypotheses that have been validated in the wet lab. (there's also a copy at http://www.cs.man.ac.uk/~stevensr/papers/faseb-2012.pdf)

I'd also add
K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, and R. Stevens. Protein classification using ontology classification. Bioinformatics, 22(14):e530-538, 2006. (DOI)
where Katy Wolstencroft used reasoning over an ontology of protein phosphatases to not only catalogue the enzymes in a genome, but find ones that had been forgotten and find one putative new style of phosphatase.

and finally, I'll add
P.W.Lord, R.D. Stevens, A. Brass, and C.A.Goble. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation.. Bioinformatics, 19(10):1275-83, 2003.
which introduced the use of a well known  measure of semantic similarity  into bioinformatics via GO  and it's annotations - a technique now widely used in various settings.


  ----- Original Message ----- 
  From: Robert Stanley 
  To: Amit Sheth ; public-semweb-lifesci 
  Cc: Luciano, Joanne Sylvia 
  Sent: Friday, January 27, 2012 3:54 AM
  Subject: RE: Evidence of Significance of Semantic Web for Life Sciences - a couple of more examples


   

  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/ >

  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 (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.' 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

   

   

  Cheers,

  Amit

   

  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 Friday, 6 April 2012 14:18:37 GMT

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