Message from the Director
At the Stanford Center for Biomedical Research (BMIR) we develop cutting-edge ways to acquire, represent, and process information about human health. Our work enables the Institute of Medicine’s vision for a Learning Health System by translating biomedical data into actionable insights for decision making. Our research advances the state of the art in semantic technology, biostatistics, and the modeling of biomedical systems to benefit clinical and translational research as well as patient care.
BMIR Colloquia and Research in Progress typically occur on Thursdays from 12:15 pm - 1:15 pm during the academic year, in Room X275 of the Medical School Office Building, 1265 Welch Road, Stanford, CA.
"Semantic Methods for Biomedical Knowledge Discovery"
Michel Dumontier, PhD
BMIR, Stanford University
The Protégé project represents an effort within BMIR that has run continuously for more than 25 years. Protégé provides a development environment for authoring ontologies and electronic knowledge bases, either via a comprehensive desktop client or via a Web interface that makes the infrastructure needed for creating an ontology as simple as that needed for creating a Google doc. With more than 225,000 registered users, Protégé is the most widely adopted ontology-engineering system in the world. In BMIR, we use Protégé for many of our internal projects in the area of ontology and terminology engineering, decision support, and knowledge-based pattern detection. Ongoing research in the Center explores methods to enhance collaboration among groups of distributed developers who may use Protégé, and to mine usage data collected during ontology editing to simplify future editing operations for Protégé users.
BMIR has been designated a Collaborating Center of the World Health Organization (WHO). In this role, we are adapting and disseminating technology developed within BMIR to drive the authoring, deployment, and evaluation of terminological classifications and ontologies developed by the WHO for use in the member states of the United Nations. These ontologies include the eleventh revision of the International Classification of Diseases (ICD-11), the International Classification of Traditional Medicine (ICTM), and several others. BMIR's Protégé ontology-engineering environment provides the basis of a special tool that our group has developed for the WHO to support the construction of ICD-11, a process that involves scores of expert developers located across the globe. BMIR also provides guidance to the WHO regarding the modeling of medical concepts and the mapping of WHO terminologies to other classification systems.
The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computingsupported by the National Institutes of Health. NCBO brings together scientists from BMIR and from several other international institutions to address the challenge of applying semantic technologies to problems such as creating metadata to annotate large data sets, integrating data from heterogeneous sources, driving natural language processing, and facilitating the creation of electronic knowledge bases to drive decision support. The NBCO maintains the largest repository of biomedical ontologies in the world in its BioPortal resource, which also allows users to visualize these ontologies and to explore how their terms relate to one another. The NCBO Resource Index uses the terms in the BioPortal ontology collection to index a large assortment of biomedical data sets. NCBO supports vigorous dissemination and outreach activities. The Center collaborates actively with a wide range of biomedical scientists, and eagerly solicits new collaborations.
Protégé team receives "Ten Year Award" from Semantic Web Science Association for most influential paper published in ISWC 2004
At this year's International Semantic Web Conference in Riva del Garda Italy (ISWC 2014), the Semantic Web Science Association presented the Protégé team with an award for the paper published in the Proceedings of ISWC 2004 judged to have the greatest impact on the field.
Mark Musen receives NIH Big Data to Knowledge (BD2K) Center of Excellence grant
The Center for Expanded Data Annotation and Retrieval (CEDAR) is a newly funded Center of Excellence supported by the NIH Big Data to Knowledge (BD2K) initiative. CEDAR is based organizationally at Stanford University, with key collaborators at the University of Oxford, Yale University, and Northrup Grumman Corporation.