Difference between revisions of "Tutorial: Introduction to Biomedical Ontology for Clinical and Translational Research"

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'''10:30am Foundations of Biomedical Ontology (Barry Smith)'''
 
'''10:30am Foundations of Biomedical Ontology (Barry Smith)'''
  
 +
[http://ontology.buffalo.edu/smith/ppt/CTS-Ontology_2012/Tutorial/Introduction_to_Ontology.ppt Slides]
 
::What is an ontology and what is it useful for?
 
::What is an ontology and what is it useful for?
 
::The problem of data silos
 
::The problem of data silos
 +
::Linked Open Data, Semantic Web, OBO vs. OWL, Protégé, and other basics
 
::NIH mandates for sharing and reuse of research data
 
::NIH mandates for sharing and reuse of research data
  
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'''12:00 pm Lunch Break'''
 
'''12:00 pm Lunch Break'''
  
−
'''1:00pm The Ontology Landscape  (Barry Smith and Nigam Shah)'''
+
'''1:00 pm Examples of Research Done with NCBO Technology (Nigam Shah and Rob Wynden)'''
  
−
::[http://www.bioontology.org/ The National Center for Biomedical Ontology] (NCBO)
+
[http://goo.gl/Oz3N0 Slides]
−
::The Semantic Web and [http://linkeddata.org/ Linked Open Data]
+
::Examples of ontology-driven analyses for drug-safety
−
:::[http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL endpoint]
+
::: We will discuss the applications of an ontology-based annotation workflow to 9.5 million clinical documents--from the electronic health records of approximately one million adult patients from the STRIDE Clinical Data Warehouse, part of Stanford's CTSA Informatics platform--to identify statistically significant patterns of drug use and to conduct drug safety surveillance. We will discuss how drug–disease co-occurrences and the temporal ordering of drugs and disease mentions in clinical notes can be examined for statistical enrichment and used to detect potential adverse events.
−
::Open Biomedical Ontologies (OBO) and the OBO Foundry
 
−
::The CTSA Ontology Landscape
 
  
−
'''2:30pm Refrreshment Break'''
+
::Examples of data integration using NCBO BioPortal
 +
:::Discussion and demo of the  [https://community.i2b2.org/wiki/display/HOM/HOM+Home Health Ontology Mapper]
  
−
'''3:00pm Introduction to NCBO Technology (Nigam Shah)'''  
+
'''2:30pm Refreshment Break'''
  
−
::(1) [http://www.bioontology.org/wiki/index.php/NCBO_REST_services Web Services] and [http://bioportal.bioontology.org/ BioPortal]
+
'''3:00pm Overview of Uses of NCBO Technology for Building Ontology Communities (Nigam Shah)'''
−
:::[http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services Search service]
 
−
:::[http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Term_services Term services]
 
−
:::[http://www.bioontology.org/wiki/index.php/Annotator_Web_service Annotator Web Service]
 
−
::(2) [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your project]
 
−
::(3) Examples of use of NCBO services for data retrieval, integration and reasoning
 
−
::: [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index]
 
−
::: [http://www.mooneygroup.org/stop/input Enrichment Analysis] and http://www.ncbi.nlm.nih.gov/pubmed/21550421
 
−
::(5) Examples of CTSA use cases enabled by NCBO technology
 
−
::: [https://community.i2b2.org/wiki/display/HOM/HOM+Home Health Ontology Mapper]
 
−
::: [https://community.i2b2.org/wiki/display/NCBO/NCBO+Ontology+Tools Importing Ontologies into i2b2 Hive]
 
  
−
'''5:30pm Close'''
+
[http://goo.gl/j3qyd Slides]
 +
::(1) Potential CTSA use cases
 +
::(2) Examples of use of NCBO services for data retrieval, integration and reasoning
 +
::(3) [http://www.bioontology.org/wiki/index.php/NCBO_REST_services Web Services] and [http://bioportal.bioontology.org/ BioPortal]
 +
::(4) [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your project]
  
−
Faculty: Barry Smith (Buffalo / NCBO) and Nigam Shah (Stanford / NCBO)
+
 
 +
 
 +
'''4:00 pm Creating the CTSA Ontology Landscape (Barry Smith, Alex Diehl, Melissa Haendel)
 +
::This session is designed to identify elements of a CTSA ontology coordination strategy to be discussed on April 26, drawing on existing ontology efforts within the CTSA Consortium, including ontology coordination efforts such as:
 +
:::[http://obofoundry.org Open Biomedical Ontologies (OBO) Foundry]
 +
:::[http://code.google.com/p/ogms/ Ontology for General Medical Science]
 +
::::[http://ontology.buffalo.edu/smith/ppt/CTS-Ontology_2012/Tutorial/Modularity.pptx Slides]
 +
:::[https://confluence.crbs.ucsd.edu/display/NIF/Download+NIF+Ontologies NIF Standard Ontologies]
 +
::::[http://ontology.buffalo.edu/smith/ppt/CTS-Ontology_2012/Tutorial/Diehl.pptx Slides]
 +
:::[http://obofoundry.org/wiki/index.php/UBERON:Main_Page Uberon]
 +
::::[http://ontology.buffalo.edu/smith/ppt/CTS-Ontology_2012/Tutorial/Haendel.uberon.pptx Slides]
 +
:::[http://ctsaconnect.org/ CTSAConnect]
 +
::::[http://ontology.buffalo.edu/smith/ppt/CTS-Ontology_2012/Tutorial/Haendel_CTSAconnect.pptx Slides]
 +
 
 +
== '''Goals''' ==
  
 
This tutorial will provide participants with an understanding of how ontologies and terminologies are used in a variety of contexts in clinical and translational research.  
 
This tutorial will provide participants with an understanding of how ontologies and terminologies are used in a variety of contexts in clinical and translational research.  
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*Understand the biomedical ontology landscape
 
*Understand the biomedical ontology landscape
 
*Understand the national infrastructure available for data annotation and knowledge management
 
*Understand the national infrastructure available for data annotation and knowledge management
−
*Learn about NCBO supported Web service workflows for clinical and translational research.
+
*Learn about NCBO supported Web service workflows for clinical and translational research
 +
*Understand the basics of biomedical ontology coordination
  
−
The National Center for Biomedical Ontology ([http://bioontologies.org NCBO]) offers a range of Web services that allow users to access biomedical terminologies and ontologies, to use ontology terms to create pick lists and lexicons, to identify terms from controlled terminologies and ontologies that can describe and index the contents of online data sets (data annotation), and to recommend particular terminologies and ontologies that would be appropriate for data-annotation tasks. The tutorial will demonstrate the use of NCBO resources to facilitate tasks such as semantic data integration, information retrieval, structured data entry, and knowledge management. We will review example use cases for analyses using disease ontologies and for applying NCBO tools to compute the risk of having a myocardial infarction on taking Vioxx (rofecoxib) for Rheumatoid arthritis.
+
The National Center for Biomedical Ontology ([http://bioontology.org NCBO]) offers a range of Web services that allow users to access biomedical terminologies and ontologies, to use ontology terms to create pick lists and lexicons, to identify terms from controlled terminologies and ontologies that can describe and index the contents of online data sets (data annotation), and to recommend particular terminologies and ontologies that would be appropriate for data-annotation tasks. The tutorial will demonstrate the use of NCBO resources to facilitate tasks such as semantic data integration, information retrieval, structured data entry, and knowledge management. We will review example use cases for analyses using disease ontologies and for applying NCBO tools to compute the risk of having a myocardial infarction on taking Vioxx (rofecoxib) for Rheumatoid arthritis.
  
 
=='''Tutorial Participants'''==
 
=='''Tutorial Participants'''==
 +
 +
Pankaj Agarwal (Bioinformatics Shared Resource, Duke Cancer Institute)
  
 
Joel Amoussou (Focused eHealth Innovations, Columbia, MD)
 
Joel Amoussou (Focused eHealth Innovations, Columbia, MD)
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Aziz Boxwala (University of California at San Diego)
 
Aziz Boxwala (University of California at San Diego)
−
 
−
Olga Brazhnik (National Center for Advancing Translational Sciences, NIH)
 
  
 
Ling Chin (NIAID/DIADS, NIH)
 
Ling Chin (NIAID/DIADS, NIH)
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Alexander Diehl (University at Buffalo)
 
Alexander Diehl (University at Buffalo)
 +
 +
Kristi R. Eckerson (Emory University / Atlanta CTSA Institute)
  
 
Sharon Elcombe (Mayo Clinic CTSA)
 
Sharon Elcombe (Mayo Clinic CTSA)
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Adela Grando (University of California at San Diego)
 
Adela Grando (University of California at San Diego)
 +
 +
Melissa Haendel (Oregon Health & Science University / CTSA Connect)
  
 
Karen Hanson (New York University Langone Medical Center)
 
Karen Hanson (New York University Langone Medical Center)
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Kathleen Hayden (University of Michigan Health System – Medical Center Information Technology)
 
Kathleen Hayden (University of Michigan Health System – Medical Center Information Technology)
  
−
Lisa Jackson (University of Arkansas for Medical Sciences)
+
Aileen Hsueh (Mitre)
 +
 
 +
Lisa Jackson (Translational Research Institute, University of Arkansas for Medical Sciences)
  
 
Pankaj Jaiswal (Center for Genome Research and Biocomputing, Oregon State University)  
 
Pankaj Jaiswal (Center for Genome Research and Biocomputing, Oregon State University)  
  
 
Mark Jensen (University at Buffalo)
 
Mark Jensen (University at Buffalo)
 +
 +
Alla Karnovsky (University of Michigan)
  
 
Warren Kibbe (Northwestern University Clinical and Translational Sciences Institute)
 
Warren Kibbe (Northwestern University Clinical and Translational Sciences Institute)
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Tom Mish (University of Wisconsin, Madison CTSA)
 
Tom Mish (University of Wisconsin, Madison CTSA)
 +
 +
Ketty Mobed (University of California at San Francisco)
  
 
Jihad Obeid (Medical University of South Carolina)
 
Jihad Obeid (Medical University of South Carolina)
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Amitava Shee (University of Michigan / Michigan Institute for Clincal & Health Research)
 
Amitava Shee (University of Michigan / Michigan Institute for Clincal & Health Research)
 +
 +
Carl Shipp (University of Arkansas for Medical Sciences)
  
 
Barry Smith (University at Buffalo / NCBO)
 
Barry Smith (University at Buffalo / NCBO)
  
 
Dagobert Soergel (University at Buffalo)
 
Dagobert Soergel (University at Buffalo)
−
 
−
Nicholas H. Steneck (Research Ethics Program, University of Michigan / Michigan Institute for Clinical and Health Research)
 
  
 
Alisa Surkis (New York University School of Medicine)                   
 
Alisa Surkis (New York University School of Medicine)                   
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Alan VanBiervliet (CTSA Steering Committee Member, NLM Respresentative)
 
Alan VanBiervliet (CTSA Steering Committee Member, NLM Respresentative)
  
−
Patricia Whetzel (Stanford University / NCBO)
+
Trish Whetzel (Stanford University / NCBO)
 +
 
 +
Rob Wynden (University of California at San Francisco)
  
 
Debbie Yoshihara (University of Wisconsin, Madison CTSA)
 
Debbie Yoshihara (University of Wisconsin, Madison CTSA)
  
 
Xin Zheng (Yeshiva University / Einstein CTSA)
 
Xin Zheng (Yeshiva University / Einstein CTSA)

Latest revision as of 07:08, 25 April 2012

Schedule: Tuesday, April 24, 9:30am-5:30pm

9:30am Registration and Coffee

10:30am Foundations of Biomedical Ontology (Barry Smith)

Slides

What is an ontology and what is it useful for?
The problem of data silos
Linked Open Data, Semantic Web, OBO vs. OWL, Protégé, and other basics
NIH mandates for sharing and reuse of research data
Examples of Biomedical Ontologies
  • Gene Ontology (GO)
  • Ontology for General Medical Science (OGMS)
  • Infectious Disease Ontology (IDO)
  • Mental and Neurological Disease Ontologies

12:00 pm Lunch Break

1:00 pm Examples of Research Done with NCBO Technology (Nigam Shah and Rob Wynden)

Slides

Examples of ontology-driven analyses for drug-safety
We will discuss the applications of an ontology-based annotation workflow to 9.5 million clinical documents--from the electronic health records of approximately one million adult patients from the STRIDE Clinical Data Warehouse, part of Stanford's CTSA Informatics platform--to identify statistically significant patterns of drug use and to conduct drug safety surveillance. We will discuss how drug–disease co-occurrences and the temporal ordering of drugs and disease mentions in clinical notes can be examined for statistical enrichment and used to detect potential adverse events.
Examples of data integration using NCBO BioPortal
Discussion and demo of the Health Ontology Mapper

2:30pm Refreshment Break

3:00pm Overview of Uses of NCBO Technology for Building Ontology Communities (Nigam Shah)

Slides

(1) Potential CTSA use cases
(2) Examples of use of NCBO services for data retrieval, integration and reasoning
(3) Web Services and BioPortal
(4) Using NCBO Technology in your project


4:00 pm Creating the CTSA Ontology Landscape (Barry Smith, Alex Diehl, Melissa Haendel)

This session is designed to identify elements of a CTSA ontology coordination strategy to be discussed on April 26, drawing on existing ontology efforts within the CTSA Consortium, including ontology coordination efforts such as:
Open Biomedical Ontologies (OBO) Foundry
Ontology for General Medical Science
Slides
NIF Standard Ontologies
Slides
Uberon
Slides
CTSAConnect
Slides

Goals

This tutorial will provide participants with an understanding of how ontologies and terminologies are used in a variety of contexts in clinical and translational research.

By the end of the tutorial, participants will be able to:

  • Understand the biomedical ontology landscape
  • Understand the national infrastructure available for data annotation and knowledge management
  • Learn about NCBO supported Web service workflows for clinical and translational research
  • Understand the basics of biomedical ontology coordination

The National Center for Biomedical Ontology (NCBO) offers a range of Web services that allow users to access biomedical terminologies and ontologies, to use ontology terms to create pick lists and lexicons, to identify terms from controlled terminologies and ontologies that can describe and index the contents of online data sets (data annotation), and to recommend particular terminologies and ontologies that would be appropriate for data-annotation tasks. The tutorial will demonstrate the use of NCBO resources to facilitate tasks such as semantic data integration, information retrieval, structured data entry, and knowledge management. We will review example use cases for analyses using disease ontologies and for applying NCBO tools to compute the risk of having a myocardial infarction on taking Vioxx (rofecoxib) for Rheumatoid arthritis.

Tutorial Participants

Pankaj Agarwal (Bioinformatics Shared Resource, Duke Cancer Institute)

Joel Amoussou (Focused eHealth Innovations, Columbia, MD)

Douglas Anderson (Smart Content Team, Elsevier)

Sivaram Arabandi (Smart Content Strategy, Elsevier)

Theodora Bakker (New York University Langone Medical Center)

Rimma Belenkaya (Albert Einstein College of Medicine / CTSA Research Informatics Core)

Aziz Boxwala (University of California at San Diego)

Ling Chin (NIAID/DIADS, NIH)

Elaine Collier (National Center for Advancing Translational Sciences, NIH)

Lindsay Cowell (North and Central Texas Clinical and Translational Science Initiative / University of Texas Southwestern Medical Center at Dallas)

Alexander Cox (University at Buffalo)

Alexander Diehl (University at Buffalo)

Kristi R. Eckerson (Emory University / Atlanta CTSA Institute)

Sharon Elcombe (Mayo Clinic CTSA)

Michael Ferrante (University of Wisconsin Medical Foundation)

Davera Gabriel (Clinical & Translational Science Center, University of California, Davis)

Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)

Bob Gehrke (Mayo Clinic CTSA)

Adela Grando (University of California at San Diego)

Melissa Haendel (Oregon Health & Science University / CTSA Connect)

Karen Hanson (New York University Langone Medical Center)

Daniel Harris (University of Kentucky Center for Clinical and Translational Science)

Kathleen Hayden (University of Michigan Health System – Medical Center Information Technology)

Aileen Hsueh (Mitre)

Lisa Jackson (Translational Research Institute, University of Arkansas for Medical Sciences)

Pankaj Jaiswal (Center for Genome Research and Biocomputing, Oregon State University)

Mark Jensen (University at Buffalo)

Alla Karnovsky (University of Michigan)

Warren Kibbe (Northwestern University Clinical and Translational Sciences Institute)

Justin Lancaster (BiomedServer, Lebanon NH)

Michael Lin (Mayo Clinic CTSA)

Aenoch Lynn (Duke Biobank, Duke Translational Medicine Institute)

Donald A. McClain (University of Utah Center for Clinical & Translational Science)

Eneida A Mendonça (University of Wisconsin - Madison Institute for Clinical and Translational Research)

Tom Mish (University of Wisconsin, Madison CTSA)

Ketty Mobed (University of California at San Francisco)

Jihad Obeid (Medical University of South Carolina)

John Mark Ockerbloom (University of Pennsylvania Libraries)

Jessica Peterson (Smart Content Team, Elsevier)

Taylor Pressler (The Ohio State University Center for Clinical and Translational Science)

Blake Roessler (Research Innovation, University of Michigan / Michigan Institute for Clinical and Health Research)

Jody Sachs (National Center for Advancing Translational Sciences, NIH)

Michael Sayre (National Institute on Minority Health and Health Disparities, NIH)

Richard Scheuermann (North and Central Texas Clinical and Translational Science Initiative / University of Texas Southwestern Medical Center at Dallas)

Titus Karl Ludwig Schleyer (University of Pittsburgh Center for Dental Informatics)

Anne Seymour (Biomedical Library, University of Pennsylvania)

Nigam Shah (Stanford Center for Biomedical Informatics Research / NCBO)

Amitava Shee (University of Michigan / Michigan Institute for Clincal & Health Research)

Carl Shipp (University of Arkansas for Medical Sciences)

Barry Smith (University at Buffalo / NCBO)

Dagobert Soergel (University at Buffalo)

Alisa Surkis (New York University School of Medicine)

Jessica Tenenbaum (Duke Translational Medicine Institute)

Carlo Torniai (Oregon Health & Science University / CTSA Connect)

Alan VanBiervliet (CTSA Steering Committee Member, NLM Respresentative)

Trish Whetzel (Stanford University / NCBO)

Rob Wynden (University of California at San Francisco)

Debbie Yoshihara (University of Wisconsin, Madison CTSA)

Xin Zheng (Yeshiva University / Einstein CTSA)

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