Ontology structured dental records and their analysis using Semantic Web technologies

May 28, 2015
Free for Members and Non-Members - No Fee
Alan Ruttenberg-Director of Clinical and Translational Data Exchange, University at Buffalo School of Dental Medicine

Structured data for health records is notoriously difficult to manage and share because of the wide variety of representations chosen and the lack of transparency of proprietary systems. Here I demonstrate a principled approach to representation based on the ontological realism and practices developed in the Open Biological/Biomedical Ontology community (OBO). As an example we take twelve years of private dental practice data and translate it into OWL(Ontology Web Language) using OBO Foundry  principles. The results are stored in a GraphDB, a triple store that can calculate a subset of OWL inference. We then use the R statistics environment to query data using SPARQL and analyze it, in this case using survival analysis to assess longevity of resin restorations.

While this project has used existing data for development, the proposal is that new systems adopt a similar strategy, taking advantage of open systems and community practices to build the EMR of the future. In this vision, representations that underly an EMR would be useful for typical operational needs but at the same time substantially more accessible for researchers and others than the developers of such systems. Development of the representation could enjoy the same benefits as are seen in the model organism community using OBO ontologies – scalability, distributed responsibility for term development and maintenance and focus on quality. Using semantic web technologies means that systems can be built with and based on open standards that will be the foundation of a semantic web.

You should register for this webinar if you are interested in ontology or information architecture or are have done or plan to do health care research, or if you are a developer of such systems and are looking for new ideas.

Learning Objectives

After viewing this webinar, the learner should be better able to:

  • Understand ontologies and ontological realism
  • Discuss semantic web standards such as OWL and SPARQL
  • Be aware of organization and practices of the OBO Foundry
  • Learn practical advice about how to apply these technologies to health care data

Speaker Information

Alan Ruttenberg is a leader in the field of biomedical ontology.  He has organized national and international workshops and driven ontology development efforts in a variety of biomedical disciplines. Following a decade of working in the pharmaceutical industry, he moved to the Creative Commons. There he engaged in W3C standardizations efforts around OWL and development of working prototypes that demonstrate how OBO Foundry ontologies, semantic web technologies, and public databases work together.

Ruttenberg is a Coordinating Editor of the OBO Foundry initiative, where he participates in review of developing ontologies and recognizes and promotes opportunities for tighter integration across ontologies. He has held leading positions in development and logical encoding in a number of ontologies, among them the Ontology for Biomedical Investigations, the Protein Ontology, the Basic Formal Ontology, the Infectious Disease Ontology, the Information Ontology and the Ontology for Oral Health and Disease.  Areas of expertise include data integration, ontology for science and medicine, bioinformatics, computational biology, open science, semantic web technologies, user interface, parallel computing, and facilitation.

This webinar series is being made freely available to AMIA members and non-members alike through a generous grant by Dr. Daniel Pihlstrom in honor of the memory of his wife, Dr. Heather Hill and the Dr. Heather K. Hill Foundation, and her many contributions to the field of dental informatics.

Biography of Dr. Heather K. Hill: Dr. Heather Kraemer Hill, born on September 10, 1973, in St. Paul, Minn., was the daughter of Gayle and Brian Hill.  She earned a Bachelor of Science in 1996 and a Doctor of Dental Surgery in 2000 from the University of Minnesota and a master's degree in biomedical informatics in 2010 from Oregon Health and Sciences University.  In 1997 she married Dr. Daniel Pihlstrom, in Minneapolis, Minn.  In addition to her husband, Daniel, she is also survived by her daughters, Kira and Raquel Pihlstrom of Lake Oswego.  She died on April 30, 2011 in Portland.