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2013 dec 26_bgu_israel_seminar_l_luciano
1. Semantic eHealth:
Getting more out of biomedical data using
Semantic Technology
"
Joanne S. Luciano,
The Shraga Segal Department of Microbiology, Immunology and Genetics
Seminar date Thursday, 26.12.13 at 14:15
Deichman Building (M8), 101
Ben-Gurion University
PhD!
Be’er Sheva, Israel
Dozor Visiting Scholar, Ben-Gurion University of the Negev 2013!
Rensselaer Polytechnic Institute, University of California, Irvine, USA"
"
Host: Dr. Eitan Rubin, Tel. 052-8897143 erubin@bgu.ac.il"
The Shraga Segal Dept. of Microbiology, Immunology & Genetics"
AND NIBN"
Ben-Gurion University"
Building 39, room -113"
POB 653, Beer Sheva 84105, Israel"
1
2. Instructor
Education
Research
Interests
Joanne S. Luciano
Deputy Director
Web Science Research Center
Email: jluciano@uci.edu
BS Boston University
MS Boston University
PhD Boston University
Harvard Medical School (Post Doc)
Use and Develop Technology.
Infrastructure and Analytics to Advance
Science and Increase its Utility to
Improve Health Outcomes
Life Science & Healthcare
Pathways, Influenza, Trans Med
Semantic Technologies
Web Ontology Languaege (OWL)
Application
Ontology Evaluation
Areas
Medicine - Major Depressive Disorder
Environmental Monitoring
Supply Chain
Financial
2
3. Timeline"
(earlier work: 10 years in Software Research & Development and Product Development)"
World Congress on
Neural Networks,
July 11-15, 1993,
Portland, Oregon SIG
Mental Function and
Dysfunction
Sam Levin
Patents Offered at
Ocean Tomo
Auction Chicago, IL
PhD
US Patents
No. 6,063,028
Awarded
BioPAX
Thesis Proposal
Approved
1995
1993
1994
2000
Linked Data
W3C HCLS
Poster Presented
BioDASH
ISMB 1997
EPOS
PSB 1998
US Patent No.
Workshop Neural Modeling of
6,317,73
Cognitive and Brain Disorders
Awarded
Jackie Samson,
Mc Lean Hospital
Depression
Research
Patents Sold
to Advanced
Biological
Laboratories
Belgium
Center for!
Multidisciplinary
Research
and!
Depression!
Treatment!
Selection!
!
!
Yuezhang
Xiao
Master’s
Thesis
(RPI)
2001 2006
1997
1996
EMPWR
U Pitt
Greg Siegle
Collaboration
2008 2009 2010 2011
2013
?
2014
I-Choose
Rensselaer
(RPI)
Health
Web Science Book
Brendan Ashby
Master’sThesis (RPI)
3
10. Research Goals"
Properly diagnose and properly
match patient with the best individualized
treatment option available, including
non-drug treatments
Illuminate recovery
course
(personalized)
10
10
36. Data, Not Programs
Data Dictionaries:
Without a data
dictionary, a
database
management
system [or any
program] cannot
access data from
the database.”1
Better,
But….
36
1. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html.
36
37. Data, Not Programs
Data Dictionaries:
Enable Reuse:
Keep information
the data
the data
Without a data
dictionary, a
database
management
system [or any
program] cannot
access data from
the database.”1
No!
37
1. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html.
37
39. Metadata (Webified)
Instead of textual labels
<bp:smallMolecule rdf:ID= #pyruvate >
<bp:Xref>
<bp:unificationXref rdf:ID= #unificationXref119">
<bp:DB>LIGAND</bp:DB>
<bp:ID>c00022</bp:ID>
</bp:unificationXref>
</bp:Xref>
</bp:smallMolecule>
Use actual URIs
39
39
40. Metadata (Webified)
SADI Web Services
Query results
return
links to the original
data!
See: sadiframework.org
Semantic
Automated
Discovery
and
Integration
(SADI)
Adapted from Mark Wilkinson webscience20-120829124752-phpapp01
40
46. BioPAX Ontology
"
a set of
interactions
parts
how the parts are known to
interact
Level 1 v1.0 (July 7th, 2004)
46
46
47. BioPAX - Simplify
>200 DBs and tools
Application
Database
User
Before BioPAX
With BioPAX
Common “computable semantic” enables scientific
discovery
47
49. Thank You!
Special thanks to
Dozor Scholarship Award
Ben-Gurion University of the
Negev
Ronit Temes
Lecturer,
Department of Microbiology and
Immunology
Faculty of Health Sciences
Eitan Rubin
Email: erubin@bgu.ac.il
49