Semantic eHealth:



Getting more out of biomedical data using

Semantic Technology
"
Joanne S. Luciano,

The Shraga Segal...
Instructor
Education

Research
Interests

Joanne S. Luciano
Deputy Director
Web Science Research Center

Email: jluciano@u...
Timeline"
(earlier work: 10 years in Software Research & Development and Product Development)"

World Congress on
Neural N...
Overview"
Introduction "
Depression Research"
"How did a nice girl like me,"
"
"wind up in a field like this?"

Changing Ti...
Translational Medicine"
•  Rapid transformation of laboratory findings into
clinically focused applications "
•  ‘From benc...
HUGE PROBLEM"
Characterized by persistent and pathological sadness,
dejection, and melancholy"
Prevalence (US)"
"6% year (...
Widespread"

Predictive Medicine, Inc. © 2010

7
Treatment Choice Vague

No easy answer"

Predictive Medicine, Inc. © 2010

8
Overview"
•  Why we did this work - to improve quality of life for millions
of people suffering from depression"

•  How w...
Research Goals"
Properly diagnose and properly
match patient with the best individualized
treatment option available, incl...
Treatment Response Study"
Today’s	
  talk	
  focuses	
  on:	
  
Response	
  to	
  treatment
	
  

Predictive Medicine, Inc...
Depression Background"
• 
• 
• 
• 
• 

Clinical Depression"
Treatment"
Symptom Measurement"
No specific diagnosis"
No speci...
Clinical Data"
Symptoms"
" -HDRS (0-4 scale)"
"

Treatment"
-Desipramine (DMI)"
-Cognitive Behavioral Therapy (CBT)"
"

Ou...
Hamilton 

Psychiatric Scale for Depression"
Clinical Instrument standard measure in clinical trials. "
Example of first th...
Why Model?"
Recasting	
  the	
  problem	
  into	
  mathematical	
  terms	
  
makes	
  it:	
  
"

Easier to understand"
Eas...
Workshop 1995
Book 1996

Neural	
  Modeling	
  of	
  
Depression	
  

Luciano Model

1996 Luciano, J., Cohen, M. Samson, J...
Understanding Recovery

Predictive Medicine, Inc. © 2010

17

17
Understanding Recovery"

Predictive Medicine, Inc. © 2010

18

18
Depression Data"
7 Symptom Factors

!

"Physical:"
"
"
"
"
"Performance:
"Psychological:
"
"
"
"
2 Treatments
"

!!

"E Sl...
Overview 

Recovery Model and Parameters"

W

A

C
M

Predictive Medicine, Inc. © 2010

E
ES
MS

20

20
Recovery Equation

(Luciano Model) 

"

= +
+
+
Predictive Medicine, Inc. © 2010

21

21
Example Patient (CBT)"
Individual Patient Recovery Pattern and Error"

Fit of Model on for individual patient captures tre...
Patient Group (CBT)"
Recovery Pattern and Error"

Model on data for patient treatment group captures
23
entire pattern. Go...
Latency"

Predictive Medicine, Inc. © 2010

24

24
Treatment Effects 

and Interaction Effects"
CBT
Sequential

DMI:
•  Interactions > 2x
•  Loops

Predictive Medicine, Inc....
Different Response Patterns "
for Different Treatment"
Order and Time a
symptom improves
are both different 

"
This is im...
Conclusion (Depression)"
•  Why we did this work - to improve quality of life for millions
of people suffering from depres...
Overview"
Introduction "
Depression Research"
"How did a nice girl like me,"
"
"wind up in a field like this?"

Changing Ti...
Overview"
Introduction "
Depression Research"
"How did a nice girl like me,"
"
"wind up in a field like this?"

Changing Ti...
Part 2, Changing Times"

1.  Intro to Data Science"
Shifts (programs to data, populations to individuals, hoarding to shar...
Data Driven Medicine:
"
Data, Not Programs
(Technology)
Sharing, Not Hoarding
(Policy)
Individuals, Not Populations
(Scien...
Data Science?
"
How do work with data?"
How do you treat your data?"
"
How easy is it for you to use data?"
Yours? Someone...
Data, Not Programs

12
33
1. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.ht...
Data, Not Programs

12

Feet?
Feet?
Years?
Years?
December?
December?
Noon?
Noon?
Dozen?
Dozen?

34
1. Webopedia. “Data Di...
NHANES (Sample)
"
National Health and Nutrition Examination Survey

35
Data, Not Programs
Data Dictionaries:
Without a data
dictionary, a
database
management
system [or any
program] cannot
acce...
Data, Not Programs
Data Dictionaries:

Enable Reuse:
Keep information
the data
the data

Without a data
dictionary, a
data...
Metadata (simplified)
Biochemical Reaction

<reaction
id=“pyruvate_dehydrogenase_rxn”/>
<listOfReactants>
<speciesRef spec...
Metadata (Webified)
Instead of textual labels
<bp:smallMolecule rdf:ID= #pyruvate >
<bp:Xref>
<bp:unificationXref rdf:ID= ...
Metadata (Webified)
SADI Web Services
Query results
return
links to the original
data!
See: sadiframework.org
Semantic
Aut...
Data Sharing (Shafu)
"

Predictive Medicine, Inc. © 2010

41
Establishing	
  	
  
Communities	
  of	
  Interest/Practice	
  
BioPathways	
  Consortium	
  
	
  
	
  
	
  
BioPAX	
  	
 ...
BioPAX	
  -­‐	
  Enabling	
  	
  
Cellular	
  Network	
  Process	
  Modeling	
  
Glycolysis

Metabolic
Pathways

Protein-P...
BioPAX 



Biological PAthway eXchange
"
An abstract data model for biological
pathway integration"
"
Initiative arose fro...
BioPAX Biochemical Reaction
"

OWL
(schema)

Instances
(Individuals)
(data)

phosphoglucose
isomerase

5.3.1.9
45

45
BioPAX Ontology
"
a set of
interactions

parts

how the parts are known to
interact
Level 1 v1.0 (July 7th, 2004)

46

46
BioPAX - Simplify
>200 DBs and tools

Application

Database
User
Before BioPAX

With BioPAX

Common “computable semantic” ...
Welcome	
  and	
  Thanks	
  for	
  
listening.	
  
You’re	
  part	
  of	
  the	
  World	
  Wide	
  
Web	
  Community.	
  Y...
Thank You!
Special thanks to
Dozor Scholarship Award
Ben-Gurion University of the
Negev
Ronit Temes
Lecturer,
Department o...
Contact Info"
Joanne S. Luciano, BS, MS, PhD"
Academic:!
"j.luciano@uci.edu"
"Rensselaer Polytechnic Institute, Troy, NY"
...
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2013 dec 26_bgu_israel_seminar_l_luciano

  1. 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. 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. 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
  4. 4. Overview" Introduction " Depression Research" "How did a nice girl like me," " "wind up in a field like this?" Changing Times & What they mean for" "Science, Technology, and Policy" Tools, Standards, Web Scale" Predictive Medicine, Inc. © 2010 4 4
  5. 5. Translational Medicine" •  Rapid transformation of laboratory findings into clinically focused applications " •  ‘From bench to bedside and back’" •  “and back” includes patients!" Predictive Medicine, Inc. © 2010 5 5
  6. 6. HUGE PROBLEM" Characterized by persistent and pathological sadness, dejection, and melancholy" Prevalence (US)" "6% year (18 million)" "16% experience it in their lifetime" Cost " "44 Billion (1990)" Impact" "1% Improvement means (180, 000 people helped)" "1% Improvement means (440 million in savings)" Predictive Medicine, Inc. © 2010 6 6
  7. 7. Widespread" Predictive Medicine, Inc. © 2010 7
  8. 8. Treatment Choice Vague
 No easy answer" Predictive Medicine, Inc. © 2010 8
  9. 9. Overview" •  Why we did this work - to improve quality of life for millions of people suffering from depression" •  How we did it - used differential equations (“neural network”) to model and compare response to different antidepressant treatments" •  What we found - different response patterns for the two treatments - the order and timing of improvement of symptoms were different" •  What we think it means - improvement in selection of treatment thereby reducing unnecessary costs and suffering. Potentially saving lives" Predictive Medicine, Inc. © 2010 9 9
  10. 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
  11. 11. Treatment Response Study" Today’s  talk  focuses  on:   Response  to  treatment   Predictive Medicine, Inc. © 2010 11 11
  12. 12. Depression Background" •  •  •  •  •  Clinical Depression" Treatment" Symptom Measurement" No specific diagnosis" No specific treatment" Predictive Medicine, Inc. © 2010 12 12
  13. 13. Clinical Data" Symptoms" " -HDRS (0-4 scale)" " Treatment" -Desipramine (DMI)" -Cognitive Behavioral Therapy (CBT)" " Outcome" " - Responders" Predictive Medicine, Inc. © 2010 13 13
  14. 14. Hamilton 
 Psychiatric Scale for Depression" Clinical Instrument standard measure in clinical trials. " Example of first three items of 21 items that measure individual" Symptom intensity. Predictive Medicine, Inc. © 2010 14 14
  15. 15. Why Model?" Recasting  the  problem  into  mathematical  terms   makes  it:   " Easier to understand" Easier to manipulate" Easier to analyze" Predictive Medicine, Inc. © 2010 15 15
  16. 16. Workshop 1995 Book 1996 Neural  Modeling  of   Depression   Luciano Model 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. Predictive Medicine, Inc. © 2010 16
  17. 17. Understanding Recovery Predictive Medicine, Inc. © 2010 17 17
  18. 18. Understanding Recovery" Predictive Medicine, Inc. © 2010 18 18
  19. 19. Depression Data" 7 Symptom Factors ! "Physical:" " " " " "Performance: "Psychological: " " " " 2 Treatments " !! "E Sleep "M, L Sleep "Energy " "Work & Interests "Mood " "Cognitions "Anxiety " " " " " " " " " " " " " ! " "Cognitive Behavioural Therapy (CBT)" "Desipramine (DMI)" " " " "Responders = improvement >= 50% on HDRS total " "N = 6 patient each study" "6 weeks " = 252 data points (converted to daily) " " " each study (CBT and DMI)" " " " " " " " " " " " "" " ! Clinical Data " " " Predictive " Medicine, Inc. © 2010 19 19
  20. 20. Overview 
 Recovery Model and Parameters" W A C M Predictive Medicine, Inc. © 2010 E ES MS 20 20
  21. 21. Recovery Equation
 (Luciano Model) 
 " = + + + Predictive Medicine, Inc. © 2010 21 21
  22. 22. Example Patient (CBT)" Individual Patient Recovery Pattern and Error" Fit of Model on for individual patient captures trends but 22 not entire pattern. Not good enough." Predictive Medicine, Inc. © 2010 22
  23. 23. Patient Group (CBT)" Recovery Pattern and Error" Model on data for patient treatment group captures 23 entire pattern. Good Predictive Medicine, Inc. © 2010fit of Model to data." 23
  24. 24. Latency" Predictive Medicine, Inc. © 2010 24 24
  25. 25. Treatment Effects 
 and Interaction Effects" CBT Sequential DMI: •  Interactions > 2x •  Loops Predictive Medicine, Inc. © 2010 DMI (delayed) CONCURRENT 25 25
  26. 26. Different Response Patterns " for Different Treatment" Order and Time a symptom improves are both different 
 " This is important because it shows how an antidepressant medication could lead to a suicide.
 
 By giving a suicidal patient DMI, you could increase the patients energy before the suicidal thoughts improve. This could give them the energy to act on those suicidal thoughts." DMI CBT Predictive Medicine, Inc. © 2010 CBT (talk: no drugs) 
 DMI (drug: tricyclic antidepressant)" 26
  27. 27. Conclusion (Depression)" •  Why we did this work - to improve quality of life for millions of people suffering from depression" •  How we did it - used differential equations (“neural network”) to model and compare response to different antidepressant treatments" •  What we found - different response patterns for the two treatments - the order and timing of improvement of symptoms were different" •  What we think it means - improvement in selection of treatment thereby reducing unnecessary costs and suffering. Potentially saving lives." Predictive Medicine, Inc. © 2010 27 27
  28. 28. Overview" Introduction " Depression Research" "How did a nice girl like me," " "wind up in a field like this?" Changing Times & What they mean for" "Science, Technology, and Policy" Tools, Standards, Web Scale" Predictive Medicine, Inc. © 2010 28 28
  29. 29. Overview" Introduction " Depression Research" "How did a nice girl like me," " "wind up in a field like this?" Changing Times & What they mean for" "Science, Technology, and Policy" Tools, Standards, Web Scale" Predictive Medicine, Inc. © 2010 29 29
  30. 30. Part 2, Changing Times" 1.  Intro to Data Science" Shifts (programs to data, populations to individuals, hoarding to sharing)" What makes data useful?" Can we exploit the web to access data?" 2.  Tools to Integrate Biomedical Data" By Hand " Using Tools " Automated Integration and Using the Web to Compute (SADI Services)" 3.  Knowledge Standards and Best Practices that enable web scale Integration" Connecting data" 5 Stars" 5 Stars not enough" Predictive Medicine, Inc. © 2010 30 30
  31. 31. Data Driven Medicine: " Data, Not Programs (Technology) Sharing, Not Hoarding (Policy) Individuals, Not Populations (Science) " 31 31
  32. 32. Data Science? " How do work with data?" How do you treat your data?" " How easy is it for you to use data?" Yours? Someone else’s?" " What makes data easy or hard to reuse?" What if anything can be done about it?" Predictive Medicine, Inc. © 2010 32
  33. 33. Data, Not Programs 12 33 1. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html. 33
  34. 34. Data, Not Programs 12 Feet? Feet? Years? Years? December? December? Noon? Noon? Dozen? Dozen? 34 1. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html.34 34 1. Webopedia. “Data Dictionary.” Available online at www.webopedia.com/TERM/d/data_dictionary.html.
  35. 35. NHANES (Sample) " National Health and Nutrition Examination Survey 35
  36. 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. 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
  38. 38. Metadata (simplified) Biochemical Reaction <reaction id=“pyruvate_dehydrogenase_rxn”/> <listOfReactants> <speciesRef species=“NADP+”/> <speciesRef species=“CoA”/> <speciesRef species=“pyruvate”/> </listOfReactants> <listOfProducts> <speciesRef species=“NADPH”/> <speciesRef species=“acetyl-CoA”/> <speciesRef species=“CO2”/> </listOfProducts> <listOfModifers> <modifierSpeciesRef species=“pyruvate_dehydrogenase_E1”/ > </listOfModifiers> </reaction> Synonyms <species id=“pyruvate” metaid=“pyruvate”> <annotation xmlns:bp=“http://biopax.org/release1/bio <bp:smallMolecule rdf:ID=“#pyruvate” > <bp:SYNONYMS>pyroracemic acid</bp:SYNONYMS <bp:SYNONYMS>2-oxo-propionic acid</bp:SYNONY <bp:SYNONYMS>alpha-ketopropionic acid</bp:SYN <bp:SYNONYMS>2-oxopropanoate</bp:SYNONYMS <bp:SYNONYMS>2-oxopropanoic acid</bp:SYNONY <bp:SYNONYMS>BTS</bp:SYNONYMS> <bp:SYNONYMS>pyruvic acid</bp:SYNONYMS> </bp:smallMolecule> </annotation> </species> 38 38
  39. 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. 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
  41. 41. Data Sharing (Shafu) " Predictive Medicine, Inc. © 2010 41
  42. 42. Establishing     Communities  of  Interest/Practice   BioPathways  Consortium         BioPAX               W3C  Semantic  Web  for  Health  Care  and  Life  Sciences  (HCLSIG)   Predictive Medicine, Inc. © 2010 42 42
  43. 43. BioPAX  -­‐  Enabling     Cellular  Network  Process  Modeling   Glycolysis Metabolic Pathways Protein-Protein Molecular Interaction Networks Apoptosis Signaling Pathways TFs in E. coli Gene Regulatory Networks Integrate these different conceptual models different implementations Do it in stages… BioPAX Level 1, Level 2, Level 3, Level 4 43
  44. 44. BioPAX 
 
 Biological PAthway eXchange " An abstract data model for biological pathway integration" " Initiative arose from the community ! 44 44
  45. 45. BioPAX Biochemical Reaction " OWL (schema) Instances (Individuals) (data) phosphoglucose isomerase 5.3.1.9 45 45
  46. 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. 47. BioPAX - Simplify >200 DBs and tools Application Database User Before BioPAX With BioPAX Common “computable semantic” enables scientific discovery 47
  48. 48. Welcome  and  Thanks  for   listening.   You’re  part  of  the  World  Wide   Web  Community.  You’re  level  of   involvement  is  whatever  suits   you!   Predictive Medicine, Inc. © 2010 48 48
  49. 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
  50. 50. Contact Info" Joanne S. Luciano, BS, MS, PhD" Academic:! "j.luciano@uci.edu" "Rensselaer Polytechnic Institute, Troy, NY" University of California – Irvine, CA" Consulting:! jluciano@predmed.com" Predictive Medicine, Inc., Belmont, MA" Predictive Medicine, Inc. © 2010 50
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