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.
Check back soon for Spring quarter colloquia schedule!
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.
BMIR is recruting a new faculty member
The Stanford Center for Biomedical Informatics Research (BMIR) within the Department of Medicine and the Stanford Cancer Institute seek to recruit a new faculty member to join the Department as an Assistant Professor or Associate Professor in the Medical Center Line or Non-Tenure Research Line.
Nigam Shah receives AMIA New Investigator Award
We are delighted to announce that the American Medical Informatics Association has named Nigam Shah this year's recipient of its New Investigator Award. As AMIA notes, "This award recognizes an individual for early informatics contributions and significant scholarly contributions on the basis of scientific merit and research excellence. The criteria for nomination include significant scientific productivity in informatics, multiple significant scientific publications and demonstrated commitment to AMIA." Congratulations!…