Clinical and Translational Science Ontology Workshop

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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), Jessica Tenenbaum (Duke), Rob Wynden (UCSF)

The Tutorial will provide a beginners' 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)

An Introduction to Biomedical Ontology for Clinical and Translational Research

  • Part I: Foundations of Biomedical Ontology
  • Part II: Ontology Technology: From the Semantic Web to the NCBO Bioportal

See schedule 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.
Melissa Haendel (Oregon) and Jon Corson-Rikert (Cornell): eagle-i and VIVO Ontology Initiatives
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)
William Hogan (Arkansas) and Werner Ceusters (Buffalo): Referent Tracking and Demographic Data Ontology
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.
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?


Participants will include:

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

Alexander Diehl (University at Buffalo)

Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)

Melissa Haendel (Oregon Health Sciences University)

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

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

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

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

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

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

Barry Smith (University at Buffalo / NCBO)

Dagobert Soergel (University at Buffalo)

Jessica Tenenbaum (Duke Translational Medicine Institute)

Rob Wynden (University of California at San Francisco)