Midterm

1. Biology of the heart (20 points)

During class we have used the lung and respiratory system as an example of the kind of information that is associated with classical biology. Part of the goal was to provide you with a framework for organizing information about other anatomical structures. Such a framework in anatomy class has been called a Knowledge Organization Template (KOT). Like a frame or object in programming, the attributes of such a KOT depend on the type of the anatomical structure. Part of the KOT for the class “organ” is as follows:

Name
Synonyms
Definition
External appearance (surfaces, shape, features)
Internal anatomy (parts)
Input/Output (blood, nerves, lymph, additional depending on the organ)
Relationships (location, adjacent organs, continuities)
Histological structure (kinds of tissues and cells)
Function

Your job is to fill in these attributes for the heart, in 1-2 pages, but no more. These pages can include up to two illustrations. You may use any source, including books from the library and online resources, but you should cite these sources at the end of the entire exam. The illustrations can be from any source, but the source of the illustrations must also be cited.

The values of the attributes should just be text, augmented by up to two illustrations. Note that the same structure can appear in more then one attribute value. In the case of function you should briefly describe the cardiac cycle, that is, the sequence of events that cause blood to flow into and out of the heart.

2. Querying the FMA (20 points, max 1 page)

In the remaining questions we will explore how to represent and use in computer applications the type of information described in question #1. As discussed in class one type of anatomical information is symbolic information about concepts and relationships, of which part-of relationships are particularly difficult because there are so many ways to divide something up.

If you have not already done so use the FME to look at the Heart. Note that there are a fairly large number of structures listed under the “Part” heading on the right hand frame.

Suppose you want to query the FMA to return just one kind of part from the general “Part” heading for use in some external application. In particular you want to return just the Right atrium, Left atrium, Right ventricle and Left ventricle. Your job is to write such a query in StruQL, run the query in OQAFMA, and show both the query and result. Hint: look at the information in the FME, and look at the examples in the OQAFMA paper.

The correct answer to this question involves no text, just screenshots of the query and its output. If you can't get the right answer then an explanation of what you tried could get you partial credit.

3. Image Retrieval (20 points)

Look at the Digital Anatomist Image Manager application, click on “Public Images” and try searching for images that show any of the four parts of the heart noted in question #2 (Right atrium, etc). Describe the design of a more “intelligent” search feature for the Image Manager that would allow a single query to find images that depict any of Right atrium OR Left atrium OR Right ventricle OR Left ventricle. Such a feature can assume it has access to the OQAFMA server. Generalize the notion of an intelligent image search feature by sketching ideas on how the Emily interface (which generates OQAFMA queries) could be linked to the Image Manager as an intelligent image query formulator for image retrieval. A system architecture diagram would make your design easier to follow.

4. Simulation (20 points)

The problem here is how to represent in computable form the function portion of the KOT you developed in question 1. Based on the readings and class discussion describe some approaches to simulating heart function, and the tradeoffs among these different approaches.

5. Socio-technical issues (20 points)

Imagine that you are the informatics expert in a biology department. The chair of your department comes to you and says that all the anatomy professors are retiring or dying, and the new faculty only want to do (and are only trained to do) research and teaching at the molecular level since that is where all the new research is. Your chairman and others are trying to resolve this crisis, and are hoping that computer technology can help alleviate the shortage. Can computer technology eventually completely do away with the need for dissection and traditional classroom instruction? Justify your answer.