Difference between revisions of "Clinical and Translational Science Ontology Workshop"

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Davera Gabriel (Clinical & Translational Science Center, University of California, Davis)
Davera Gabriel (Clinical & Translational Science Center, University of California, Davis)
Solomon T. Garner, Jr. (Jackson State University / RCMI Translational Research Network Data Technology Coordinating Center)
Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)
Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)

Revision as of 12:37, 12 January 2012

The National Center for Biomedical Ontology will hold a Clinical and Translational Science Ontology Tutorial and Workshop in its series of training and dissemination events.

Venue: Hilton Garden Inn Baltimore Airport


Tutorial: April 24, 2012
Workshop: April 25-26, 2012

Organization: Barry Smith (NCBO / Buffalo), Jessica Tenenbaum (Duke), Rob Wynden (UCSF)

Registration: Please write to Barry Smith

The Tutorial will provide an introduction to ontology methods and technology for students and researchers. Topics highlighted in the tutorial will be of particular interest to individuals at institutions conducting clinical and translational research, including institutions which have or are interested in obtaining CTSA (Clinical and Translational Science Award) grants.

The Workshop will provide an opportunity for those involved in ontology-related projects in the field of clinical and translational science to present on-going work and to review what has been achieved thus far. It will conclude with consideration of plans and strategies for enhanced coordination of ontology development initiatives in the field of clinical and translational science in the future.


Tutorial (Tuesday, April 24, 10.30am-6pm)

10:00am Registration

10:30am Foundations of Biomedical Ontology

What is an ontology and what is it useful for?
The problem of data silos
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

1:00pm The Ontology Landscape

The National Center for Biomedical Ontology (NCBO)
The Semantic Web and Linked Open Data
BioPortal SPARQL endpoint
Open Biomedical Ontologies (OBO) and the OBO Foundry

2:30pm Break

3:00pm Introduction to NCBO Technology

(1) Web Services and BioPortal
Search service
Term services
Annotator Web Service
(2) Using NCBO Technology in your project
(3) Examples of use of NCBO services for data retrieval, integration and reasoning
Resource Index
Enrichment Analysis and http://www.ncbi.nlm.nih.gov/pubmed/21550421
(5) Examples of CTSA use cases enabled by NCBO technology
Health Ontology Mapper
Importing Ontologies into i2b2 Hive

5:30pm Close

For further information see here

Workshop Day 1: Wednesday, April 25, 9am-5pm (Draft Schedule)

Major Ontology Initiatives relevant to Clinical and Translational Research
Chris Chute (Mayo): Data Governance and Normalization within the Mayo Clinic Enterprise
The principles and practice of data governance, as undertaken across the Mayo Clinic enterprise, will be reviewed and discussed, with particular emphasis on vocabulary harmonization and practice using NCBO tools for research. Extension to larger-scale consortia including the ONC HIT Standards Committee,SHARPn, ISO, and CIMI will be considered.
Joseph M. Gunnels and Jihad S. Obeid (Medical University of South Carolina): An Ontology for Informed Consents and Other Research Permissions
During the development of a comprehensive system for managing informed consents and permissions for research involving human participants, considerable effort is dedicated to laying down the foundation for a semantic web infrastructure and an underlying ontology to help standardize the development of electronic informed consents and the capture of underlying data. The objective is to allow future connections with other semantic web applications and pooling of data from multiple research projects.
Melissa Haendel (Oregon) and Jon Corson-Rikert (Cornell): VIVO and eagle-i Ontology Initiatives
VIVO is a platform for managing researcher profiles at or across institutions in support of research expertise location. eagle-i is a system for researchers to share and search for research resources. Both VIVO and eagle-i are ontology-driven, and thereby enable publication of Linked Open Data and complex queries regarding expertise and funding outcomes in the translational science domain. We describe how VIVO and eagle-i ontologies reuse domain standard ontologies for maximum interoperability, and show how they are being used by software applications in the context of the CTSAs.
Jessica Tenenbaum (Duke): Ontologies for Omic-Scale Datasets
The use of "omic"-scale biomarkers to enable personalized medicine is becoming an increasingly important facet of translational biomedical research. Ontologies such as the Gene Ontology (GO) and the Ontology for Biomedical Investigations (OBI) can be used to facilitate data sharing, re-use, integration, and querying. This presentation will cover some of the more commonly used ontologies and how they may be applied to these ends.
Harold Lehmann (Baltimore): The Human Studies Database (HSDB) and the Ontology of Clinical Research (OCRe)
Shawn Murphy (Partners): i2b2-Specific Ontologies
Richard Scheuermann and Lindsay Cowell (Dallas): NLP-Based Mapping of Textbook Pathology to Ontology for General Medical Science (OGMS)
Information about disease pathogenesis and disease course is available almost exclusively as free text and is therefore not easily accessible for query and analysis. We are addressing this problem by developing an ontology-driven NLP system for the mapping of basic pathology knowledge from free text to terms from OBO Foundry ontologies. In particular, we are using the Ontology of General Medical Science, with its tripartite structure of disease-disorder-disease_course, as the basic framework for the system. We will discuss preliminary results and describe planned use cases.
Nigam Shah (Stanford): Making Sense of Unstructured Data in Medicine using Ontologies: An Overview of NCBO Technology
Changes in biomedical science, public policy, information technology, and electronic heath record (EHR) adoption have converged recently to enable a transformation in the delivery, efficiency, and effectiveness of health care. The true richness and complexity of health records lies within the clinical notes, which are free-text reports written by doctors and nurses in their daily practice. We have developed a scalable annotation and analysis workflow that uses public biomedical ontologies and is based on the term recognition tools developed by the National Center for Biomedical Ontology (NCBO). For further details see here

Workshop Day 2: Thursday, April 26, 9am-4pm (Draft Schedule)

9:00am EHR, Ontology and Interoperability
Rob Wynden (UCSF): The CTSA Health Ontology Mapper (HOM).
The CTSA Health Ontology Mapper is an open source project to translate locally encoded patient encounter data, claims data and notes into standard biomedical terminologies by leveraging a real-time integration with the NCBO BioPortal REST services for access to biomedical ontologies and maps.
William Hogan (Arkansas): Referent Tracking and Demographic Data Ontology
Numerous problems in the field of ontology are the consequence of (1) failure to pay attention to the instances about which we are collecting data, and (2) the lack of formal mechanisms to track instances and instance data, to relate instance data properly to representational units in ontologies, and to represent all these things unambiguously in the context of EHR data. This presentation will demonstrate Referent Tracking as a solution to these deficiencies with application to various particular use cases such as demographics data.
12:00pm Lunch
1:00pm Next Steps
How can we measure the value brought by ontology-based approaches?
How can we ensure high-quality and high-value approaches?
How can we promote a consistent approach across the CTSA consortium?


Theodora Bakker (New York University Langone Medical Center)

Olga Brazhnik (National Center for Advancing Translational Sciences, NIH)

Mathias Brochhausen (Translational Research Institute, University of Arkansas for Medical Sciences)

Chris Chute (Mayo / NCBO)

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

Alexander Diehl (University at Buffalo)

Michael Ferrante (University of Wisconsin Medical Foundation)

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

Solomon T. Garner, Jr. (Jackson State University / RCMI Translational Research Network Data Technology Coordinating Center)

Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)

Peter Good (National Human Genome Research Institute, NIH)

Joseph M. Gunnels (Medical University of South Carolina)

Melissa Haendel (Oregon Health & Science University)

Karen Hanson (New York University Langone Medical Center)

William Hogan (Translational Research Institute, University of Arkansas for Medical Sciences)

Pankaj Jaiswal (Oregon State University)

Pathak Jyotishman (Mayo Clinic / NCBO)

Warren Kibbe (Northwestern University Clinical and Translational Sciences Institute)

Harold Lehmann (Johns Hopkins / Institute for Clinical and Translational Research

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

Shawn Murphy (Partners Healthcare Research Computing / Harvard Medical School)

Mark Musen (Stanford Center for Biomedical Informatics Research / NCBO)

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)

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

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

Barry Smith (University at Buffalo / NCBO)

Dagobert Soergel (University at Buffalo)

David Stack (University of Wisconsin-Milwaukee / CTSI of Southeast Wisconsin)

Shumei S. Sun (Virginia Commonwealth University / CTSA Biomedical Informatics Core)

Alisa Surkis (New York University School of Medicine)

Umberto Tachinardi (University of Wisconsin Medical Foundation)

Jessica Tenenbaum (Duke Translational Medicine Institute)

David Towers (University of Wisconsin Medical Foundation)

Rob Wynden (University of California at San Francisco)

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