To:                  Class MEDED 534, Fall 2000

From:              Jim Brinkley, MD, PhD,

                        Research Professor

                        Cornelius Rosse, MD, DSc,


Date:               9/15/00

Subject:           Anatomy component of the course

Enclosure:       What is anatomy, tutorial. Pre-class exercises to be completed prior to the start of the first class on Sept 25. See http://sig.biostr.washington/edu/education/modules/whatisanatomy/tutorial.html


We welcome you to the anatomy component of Biology for Informaticists. Anatomy is the first knowledge domain you will meet in this course, as it is in almost all educational pathways in the health sciences. There is a good reason for that: anatomy provides the foundation for essentially all biomedical disciplines; its concept domain and terminology are indispensable for biomedical discourse and for reasoning about biomedical processes. In other words, manifestations of health or disease may be regarded as attributes of anatomical structures ranging in size and complexity from macromolecules to organs, organ systems and the whole body itself.

In a like manner, the informatics of anatomy, which is a major component of the field wehave defined as Structural Informatics, provides a foundation for biomedical informatics. Whatever field of biomedical informatics you will pursue as your professional career, you will encounter anatomical concepts and a large number of terms that are associated with them. It is our belief that you will be significantly assisted in your work if you have an understanding of how anatomical information is organized. Therefore, our goal is to provide you with hands-on experience in Structural Informatics, so that you can build on this experience when you begin to address real-world problems in informatics.

Structural Informatics is a new, exciting and evolving field. We, ourselves, are actively contributing to this evolution and it is our intention to motivate you to become involved in this process yourself. The time-honored and traditional textbooks and atlases can no longer satisfy the ways in which informaticists and practicing health care providers need anatomical information. There is a need for rethinking and reorganizing the science of anatomy in order to exploit the opportunities offered by both graphical and symbolic approaches to knowledge representation, which are made possible by information science and technology. This is a requirement for applying anatomical knowledge to solve problems in clinical medicine and in the management of biomedical information.


Our purpose in this course segment is to make you aware of some of the challenges that present themselves in structural informatics. We regard the anatomy segment of this course as the startof a laboratory in structural informatics that will eventually include modules ranging from the level major body parts and systems to the molecular level. We want to involve you in the process of defining and prioritizing the problems that need to be solved in order to create these modules. We hope that a number of you will remain actively engaged in solving these and related problems during your training, well after you have completed this course. 


Because we seek your active involvement, we have designed this course segment in a rather unconventional way. There are three components to each class:

1.     Pre-class preparation

2.     In-class interactions

3.     Recapitulation/synthesis


We support an educational philosophy that de-emphasizes didactic presentations (lectures), and instead, places the initiative in the hands of the learner. Therefore, in-class activities are built entirely on the pre-class preparation that each student must complete before a particular class begins. This is a requirement even for the first introductory class.

We have attempted to point you to resources with which you can accomplish your pre-class preparation. We invite you, however, to be adventurous and also strike out on your own. Share your experiences during class and let us all learn from you.


The style of in-class activities will be discussion and demonstration, including those presented by members of the class. We will be responsible for assuring that this format results in the completion of learning objectives specified for each class. As mentioned before, the key to attaining these objectives is pre-class preparation. So, please get into this habit by completing the exercises for the first class before you come to the first class.

We recognize that the usual expectations of an anatomy course are to memorize hundreds, even thousands of terms; that is, a “bottom-up” approach. We will take a different, “top-down” approach that has many parallels with object-oriented programming: 


The first classes will deal with the transformation of anatomy as an old-fashioned science into a major component of Structural Informatics, a newly emerging field of biomedical informatics. This will include consideration of concept domains, the kinds of information anatomy deals with, traditional and modern sources of this information, and the methods available for its representation. Next, we have selected “organ” as a class of anatomical structure, and will consider, in general terms, the kinds of information associated with organs. The organ subclass “lung” will then be used as a specific example for instantiating a “knowledge organization template” (KOT) that captures organ-related information. The KOT is analogous to the instance variables of a class in object-oriented programming. The final sessions will extend this template to the cellular level, then will put all the information together to gain an understanding of the process of respiration.


This will be an entirely new course for us to teach. We regard it as an experiment. We anticipate learning more from you than you will probably learn from us. We are certain that your contributions to the anatomy component of the course will have a significant influence on how we will teach this course to future cohorts of informaticists. We hope that you will be in for as exciting a time as we know we will.