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Photo of James Brinkley.
James Brinkley

Photo by Gavin Sisk


James Brinkley: Structural informatics provides a way to deal with information glut; The Science in Medicine Lecture

“Medicine is full of complex information management problems that are worth solving,” says Dr. James Brinkley, director of the UW’s Structural Informatics Group.

“My own bias is to want to make useful things, and I choose specific problems, and then let the work be driven by solving the problems. I guess you could say I’m more of an engineer than a theoretician — I really like to build things.”

And with colleagues in several departments at the UW and elsewhere, Brinkley is building systems that will allow physicians and scientists to integrate and visualize the glut of information about the human body that is emerging as the 21st century begins.

Among his current projects is a Human Brian Project grant from the National Institutes of Health to develop a structural information framework for brain mapping. In simplistic terms, the brain mapping effort is coming up with a 3-D, computer-based template that can then be used to support overlays of various kinds of information about brain function.

This effort involves many other UW colleagues, Brinkley notes, from Dr. George Ojemann, professor of neurological surgery, who has been physically mapping brain function for many years to avoid critical regions in surgery for epilepsy, to Dr. David Corina, associate professor of psychology, who works with Ojemann to understand language processing in the brain. Other colleagues come from electrical engineering, radiology and computer science, as well as biological structure and biomedical informatics.

“In part because of the dramatic advances in imaging, including functional MRIs and PET scans, there is a tremendous amount of information available on brain structure and function, but we don’t have very good tools to integrate all of this and make it useful,” Brinkley notes.

The brain mapping project follows the common theme of all the work that the Structural Informatics Group takes on: that the physical structure of the body — from large-scale organ systems to cellular and molecular levels — can be used to organize information.

In fact, it was Brinkley who coined the term “structural informatics” in 1991. He defines it as “a branch of biomedical informatics dealing with methods for generating, storing, retrieving, analyzing and displaying information about the physical structure of the body.”

Of the many problems the group is addressing, including complex database and image processing needs, one of the most difficult is teaching the computer how to distinguish between the brain and the rest of a head when it interprets an image, Brinkley says. “Getting the computer to find the brain and extract that part of the image is really tricky. Working with Professor Linda Shapiro, a computer science expert in image understanding, we want to eventually develop a visualization of the brain similar to what a surgeon can see, and then be able to overlay various functions onto that visualization.”

Along with the Human Brain Project, Brinkley and his group work on the Digital Anatomist, a longstanding UW project that uses 3-D images and online atlases for anatomy education; the Foundational Model of Anatomy, a fundamental resource for describing anatomy developed by Dr. Cornelius Rosse; and the Virtual Soldier, a project funded by the Defense Advanced Research Projects Agency (DARPA) with the goal of reducing battlefield casualties.
Beginning in January 2003, Brinkley is also the principal investigator for a three-year planning grant from the National Library of Medicine to develop an interdisciplinary center for structural informatics at the UW, a center that would provide additional support for the many interdisciplinary links already in place. The planning grant, which includes Dr. Peter Tarczy-Hornoch as co-principal investigator, is jointly sponsored by the Biological Structure and Biomedical and Health Informatics units

Brinkley himself is based in the School of Medicine’s Department of Biological Structure as a research professor; he also has a joint appointment in the Department of Medical Education and Biomedical Informatics and an adjunct appointment in the Department of Computer Science and Engineering, part of the College of Engineering.

When he entered the UW School of Medicine after graduating from Amherst College, Brinkley thought he wanted to become a family doctor. He earned his M.D. degree in 1974, but by then was thinking of another road. He went to the National Institutes of Health for a student fellowship on “computers in clinical medicine” at a time when that seemed to be an idea for the distant future.

Now there are programs for medical students who also want to earn Ph.D.s in informatics, but not then. He worked for a while in the ultrasound unit of the UW’s Center for Bioengineering, and then in 1977 went to Palo Alto to become an interdisciplinary Ph.D. student at Stanford. After he got the Ph.D. in medical computer engineering, in 1984, he spent the next four years at the Knowledge Systems Lab in Stanford’s Department of Computer Science. That lab has worked on many leading-edge projects, but is perhaps best known for its artificial intelligence (AI) work.

In 1988, Brinkley came back to Seattle to join the Department of Biological Structure and work with Rosse and others in the department on developing what would later become structural informatics.

For a look at some of the projects Brinkley is working on, see the projects page of the Structural Informatics Group: http://sig.biostr.washington.edu/projects


by Claire Deitz, University Week


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