|
 Brinkley, James, M.D., Ph.D.
Professor
brinkley@u.washington.edu
Anx-148
543-3954
Personal Web Page: http://sig.biostr.washington.edu/~brinkley/
I am director of the UW Structural Informatics Group (SIG, http://sig.biostr.washington.edu), an interdisciplinary team of computer scientists, engineers and biologists, whose goals
are 1) to develop methods for representing both spatial and symbolic information about the physical
organization of the body, at levels ranging from macroscopic anatomy to molecules, and 2) to develop
Web-accessible computer applications that utilize these representations to solve practical problems in
clinical medicine, research and education. Other faculty include Cornelius Rosse, emeritus professor of
Biological Structure, and Linda Shapiro, professor of Computer Science and Engineering. SIG is housed in
the Department of Biological Structure, with close affiliations with Medical Education and Biomedical
Informatics, and Computer Science and Engineering. Current collaborators are from the departments of
Biological Structure, Neurosurgery, Radiology, Psychology, Pediatrics, Physiology, Bioengineering and Electrical Engineering, among others.
The rationale for a group in structural informatics is that structure is the foundation for understanding in
biology. Therefore, if we can develop methods for representing and organizing information about structure,
we will be in a position to not only manage the vast amount of structural information (e.g., images,
sequences, 3-D models), but also to develop a structural information framework that can form the basis for
organizing much of the data and knowledge in biomedicine.
Projects within SIG are chosen both for their immediate practical need and for their role in developing a
structural information framework. Current projects include:
The Foundational Model of Anatomy, a symbolic description ("ontology") of the structure of the body,
starting at the macroscopic level, and increasingly extending to the molecular level.
The Digital Anatomist Information System, a web-accessible information system that uses the evolving
foundational model to integrate anatomical information such as images, 3-D models, and textual
descriptions into an intelligent system that can customize the presentation of anatomical information
depending on the background and needs of the users. Current emphasis is on query generation for the
foundational model, image databases, and dynamic 3-D scene generation over the web.
The Virtual Soldier, a DARPA-funded effort which is one step towards the "Digital Human", a simulated
model of the human body. The SIG contribution is to use the foundational model as a means for integrating
diverse sets of data and simulation models in an overall conceptual architecture based on anatomy.
The UW Human Brain Project, a structure-based information system for organizing, managing and
visualizing human brain mapping data, with emphasis on understanding language organization in the brain.
Current emphasis is on a neuroanatomical ontology that is a subset of the foundational model, the
automatic generation of local lab-based experiment management systems , the integration of multi
-modality language data obtained from locally-maintained experiment management systems, and the
visualization of the integrated results on 3-D web-accessible models of the brain.
An NIH Biomedical Information Science Technology Initiative (BISTI) planning grant to create an Interdisciplinary Center for
Structural Informatics. Work during this planning phase has led to the submission of a joint proposal, with Medical
Education and Biomedical Informatics, and Computer Science and Engineering, for a full Center. Current projects funded
under the planning grant include an information system for experimental data related to cataract formation (with the John
Clark lab), the development of methods for aligning different ontologies with the foundational model, and the development of
methods for sharing distributed experimental data.
References
See http://sigpubs.biostr.washington.edu/ for additional publications
Brinkley, J.F. Structural informatics and its applications in medicine and biology. Academic Medicine 1991;66(10):589-59
http://sig.biostr.washington.edu/overview/si.html
Rosse C, Mejino JL, Modayur BR, Jakobovits RM, Hinshaw KP, Brinkley JF. Motivation and organizational principles for
anatomical knowledge representation: the Digital Anatomist symbolic knowledge base. Journal of the American Medical
Informatics Association 1998;5(1):17-40
http://sig.biostr.washington.edu/publications/online/KBpaper.pdf
Brinkley JF, Wong BA, Hinshaw KP, Rosse C. Design of an anatomy information system. Computer Graphics and
Applications 1999;19(3):38-48 http://sigpubs.biostr.washington.edu/archive/00000024/
Hinshaw KP, Poliakov AV, Martin RF, Moore EB, Shapiro LG, Brinkley JF. Shape-based cortical surface segmentation for
visualization brain mapping. Neuroimage 2002;16(2):295-316 http://sig.biostr.washington
.edu/publications/online/neuroimage2002
Jakobovits RM, Rosse C, Brinkley JF. An open source toolkit for building biomedical web applications. J Am Med Ass.
2002;9(6):557-590 http://sigpubs.biostr.washington.edu/archive/00000134/
Fong C, Rosse C, Clark JI, Shapiro L, Brinkley JF. An ontology-based image repository for a biomedical research lab. In:
MEDINFO 2004. In Press; 2004. http://sigpubs.biostr.washington.edu/archive/00000144/
http://sigpubs.biostr.washington.edu/archive/00000144/.
|
