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Data Driven Medicine:Data, Not Programs
Sharing, Not HoardingIndividuals, Not Populations
CAS Interdisciplinary Innovation Forums
BIG DATA FORUM
June 5, 2012
Joanne S. Luciano, PhDResearch Associate ProfessorTetherless World ConstellationRensselaer Polytechnic Institute
2
Times have changed
Keep the information about the data with the data, then it can be (re)used• The end of the blockbuster era • The right treatment to the right
patient at the right time• Lowering cost of pharmaceutical
development• Improved patient response to
treatment• Aging population• Technology (Web and Mobile)• Shifts in thinking
Photo: http://www.flickr.com/photos/sepblog/4014143391/
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Data Driven Medicine:
Data, Not Programs
Sharing, Not Hoarding
Individuals, Not Populations
Data, Not Programs
41. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html.
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Data, Not Programs
51. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html.
12Feet?Years?December?Noon?Dozen?
Data, Not Programs
Data Dictionaries:
Without a data dictionary, a database management system [or any program program]cannot access data from the database.”1
61. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html.
Duh!
Fox CI and X-informatics - CSIG 2008, Aug 11
7
Shifting the Burden from the Userto the Provider
Data-Information-Knowledge Ecosystem
8
Data Information Knowledge
Producers Consumers
Context
PresentationOrganization
IntegrationConversation
CreationGathering
Experience
9
Data Driven Medicine:
Data, Not Programs
Sharing, Not Hoarding
Individuals, Not Populations
10
Sharing, Not Hoarding
Now get it out there, where it can do some good.
Photo: http://www.flickr.com/photos/sepblog/4014143391/
http:// WEB PAGE URL
http:// DATUM
Yes, you can share dataand you can know you arereferring to the same thing ifit has the same URI.
The Semantic Web is the New Global Web of Data
It is about standards for publishing, sharing and querying knowledge drawn from diverse sources
It makes possible the answeringsophisticated questions using
background knowledge
Predictive Medicine, Inc. © 2010 12 27 October 2008
• BioPathways Consortium
• BioPAX
• W3C Semantic Web for Health Care and Life Sciences (HCLSIG)
Establishing Communities of Interest/Practice
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MetabolicPathways
MolecularInteractionNetworks
SignalingPathways
GeneRegulation
BioPAXLevel 1
Biological Pathways of the Cell
BioPAXLevel 2
BioPAXLevel 3
BioPAXLevel 4
BioPAX What’s a pathway?Depends on who you ask!
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BioPAX
Biological PAthway eXchange
An abstract data model for biological pathway integration
Initiative arose from the community
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phosphoglucoseisomerase 5.3.1.9
OWL(schema)
Instances (Individuals)
(data)
BioPAX Biochemical Reaction
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BioPAX Ontology
Level 1 v1.0 (July 7th, 2004)
parts
how the parts are known to interact
a set ofinteractions
Before BioPAX With BioPAX
Common “computable semantic” enables scientific discovery
>150 DBs and tools
Database
Application
User
BioPAX - Simplify
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Data Driven Medicine:
Data, Not Programs
Sharing, Not Hoarding
Individuals, Not Populations
Predictive Medicine, Inc. © 2010
Order and Time
Symptoms Improve
is Different for CBT and
DMI
Differential Equation Modeling
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Individuals, Not Populations
Social WebBlogsPatients Like Me
Cure Together
Photo: http://www.flickr.com/photos/sepblog/4014143391/
http://curetogether.com/depression/ig/treatment-effectiveness-vs-popularity
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Individuals, Not Populations
Photo: http://www.flickr.com/photos/sepblog/4014143391/
http://safety-code.org/
Quickly retrieve pharmacogenomic markers of patients when needed
No central storage of data is necessary, giving patients full control over their personal health information.
Personalized MedicineComponents
• Understand disease heterogeneity• Comprehend disease progression• Determine genetic and environmental contributors• Create treatments against relevant targets
– drugs against relevant targets (molecular structures)– Yoga against stress– Exercise against obesity– Elimination against food intolerance or allergy
• Develop markers to predict response• Identify concrete endpoints to measure response
Predictive Medicine, Inc. © 2010 23
Timeline
20091993
World Congress on
Neural Networks, July 11-15,
1993, Portland, Oregon
SIGMental
Function andDysfunctionSam Levin
Jackie Samson,Mc Lean Hospital
Depression
Research
1996
1995
20081994
Patents Soldto
Advanced Biological
Laboratories
Belgium
Patents Offered at
Ocean Tomo
Auction Chicago, IL
US Patent No.
6,317,73Awarded
US PatentsNo.
6,063,028Awarded
2001
2000
PhDThesis
Proposal Approved
Workshop Neural
Modeling of
Cognitive and Brain Disorders
BioPAX
?Linked Data
W3C HCLSBioDASH
EPOS
2006
EMPWR
Poster Presented ISMB 1997PSB 1998
1997
Predictive Medicine, Inc. © 2010 24
Neural Modeling of Depression
1996 Luciano, J., Cohen, M. Samson, J. “Neural Network Modeling of Unipolar Depression,” Neural Modeling of Cognitive and Brain Disorders, World Scientific Publishing Company, eds. J. Reggia and E. Ruppin and R. Berndt. Book cover; chapter pp 469-483.
Luciano Model highlighted on book cover
Workshop 1995 Book 1996
Predictive Medicine, Inc. © 201025
Take Home Message(AMIA 2010)
We need to shorten the time
tighten the loop between research and practice;
15 years + is too long,
way too long
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Perspective
“While it took 2,300 years after the first report of angina for the condition to be commonly taught in medical curricula, modern discoveries are being disseminated at an increasingly rapid pace. Focusing on the last 150 years, the trend still appears to be linear, approaching the axis around 2025.”
The Healthcare Singularity and the Age of Semantic Medicine, Michael Gillam, et al, The Fourth Paradigm: Data-Intensive Scientific Discovery Tony Hey (Editor), 2009
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Take Home Message
Now You Try It!
Challenge: What can you do (combine) with your data? What will you find?http://data-gov.tw.rpi.edu/wiki/Tutorials