TUTORIAL
PURPOSE
Provide an understanding of
· the kinds of entities that constitute the body
· the kinds of information that relates to these entities
PRE-CLASS OBJECTIVES
· Classify the physical entities that constitute the human body in terms of size and physical characteristics.
· Using the resources provided, generate a structured list of the kinds of information associated with different kinds of anatomical entities.
· Based on your general experience and the resources provided, propose a classification of the different kinds of anatomical information.
PREPARATION FOR CLASS
1. Update your knowledge
Revisit the “Recapitulation” sections of the tutorial for the previous class and update/enhance the documents you generated based on what you have learned in class.
2.
Classify
the physical entities that constitute the human body.
Exercise: What kind of things make up your body?
Generate a list of about two dozen examples of material objects (e.g., spine, eye, big toe, elbow, red blood cell, fat) which the human body is composed of.
Adopt some kind of system (e.g., from top to toe) to generate this list and state what that system is.
Rearrange your list according to size ranging from molecules to the whole body itself.
Add to the list as you do this resorting, and name the categories according to which you are structuring the list.
What is an anatomical structure? Formulate a definition in writing.
Do all items in your list qualify as anatomical structures?
Write “structure” after each item that meets the criteria of your definition.
Would you consider blood and urine to be anatomical structures?
Think of other constituents of the body that you consider similar in nature to blood and urine and add them to the list.
What would you call such things?
Write that term after each of the appropriate items.
Would you consider the cavity inside the skull or the stomach to be an anatomical structure?
Think of other constituents of the body that you consider similar in nature to these cavities.
Propose a name for this class of entities and write that name after corresponding items.
Having considered such entities as cavities and blood and urine, revisit your definition of anatomical structure, and rewrite it, if you can improve on your first version (but save all evolving versions).
Share your definitions (and also other documents that you generate) with members of the class and your instructors.
Having completed this exercise, consult your resources.
Resources:
The resources contain answers to several of the questions in the above exercise, but we urge you to complete the exercise before consulting the resources. The purpose is for you to formulate your own ideas and then modify and enhance them as you progress through the pre-class tutorial and the in-class interactions. This approach establishes a cognitive model of your own making and you can actively modify and enhance this model as you acquire new information.
(This statement applies to all exercises, but it will not be repeated for future exercises and tutorials.)
Rosse et al. 1998: Motivation and organizational principles for anatomical knowledge representation: the Digital Anatomist symbolic knowledge base. JAMIA 5:17-40.
Foundational Model Builder (FMB):
First, read the preamble to the FMB. This preamble presents more information than you need for this tutorial. Use your judgement.
Then, access the FMB itself. This is a Java applet. The applet will take a few minutes to load, after which you will be asked to login.
Type the user name and password that were supplied to you during class. After you have logged in, it will several minutes for the data to load (don’t give up!) Once the data are loaded you can follow the following instructions:
Navigate the default ‘is-a’ hierarchy of the FM, which is the ‘Anatomy Ontology’; henceforth we will refer to it as such, or as ‘Ao’.
Double click on ‘Anatomical entity’.
Take your time as you double click and open up the nodes of this ontology.
Read the definitions of the classes as you open them up (‘definition’ command is at bottom of page). You can also access all the definitions at once.
Focus on high level nodes and their definitions.
The information is vast, you can only sample it.
The purpose is that by navigating the ontology you should gain an impression of the range and complexity of the ‘material physical anatomical entities’ that constitute the body.
Recapitulation:
Using the ‘find term’ function of FMB, locate in the ontology (-is a- hierarchy) several of the terms in each category of the list you generated.
What is the hierarchy of classes to which the Ao assigns these terms?
Don’t just look at the immediate parent of the term in the hierarchy.
Check out the definitions of these classes.
Make a new list of the objects you generated but this time group them according to the classes of anatomical entities defined in the Foundational Model (FM).
Revise your definition of anatomical structure.
You need not agree with FM definitions or even with the structure of Ao classes. We welcome your feed back and suggestions.
Make a list of questions and topics you want to discuss in class.
3.
Using
the resources provided, generate a structured list of the kinds of information
associated with different kinds of anatomical entities.
Exercise: What
are we talking about?
In other words, what do anatomy textbooks or other sources say about anatomical structures, anatomical spaces, etc.?
In order to gain an impression of the kinds of information that falls in the domain of anatomy(science), scan the following sections of two RGR chapters:
Chapter 19: The Thorax in General; pp. 422-427.
Chapter 20: The Lungs; p. 442. and pp. 452-454.
Your objective is not to learn this anatomy, but to focus on the verbs, rather than on the names of different anatomical entities (e.g., sternum, bronchopulmonary segment).
Ask yourself, what kinds of relationships do these verbs describe for the different anatomical structures (e.g., it has parts, surfaces, is adjacent to.., attaches, surrounds, develops from, etc.).
With the same objective in mind, explore two or three anatomy programs on the web (see Anatomy Websites resource).
You might have in the back of your mind the question “How do web-based programs compare with the hard-copy text as a source of different kinds of anatomical information?”
Return to the Foundational Model and find out the kinds of relationships that the model incorporates.
Use your own initiative for gaining this information.
Give some thought to the relative ease or difficulty of obtaining information about relationships from the FM, in comparison with the textbook and the websites.
Recapitulation:
Make a list of the descriptive verbs that are used to capture the
relationships between different anatomical entities.
Base this list on RGR chapter sections and the web sites you explored
and the FM.
Propose a classification of these “anatomical relationships” and regroup
your verb list accordingly.
The class interaction will deal with metaclasses or templates, which
formalize the kinds of anatomical information and relationships associated with
different classes of anatomical entities.
4. Based on your general experience and
the resources provided, generate a list of the methods that are currently in
use for representing anatomical information.
Exercise: How is anatomical information represented
and communicated?
You have now looked at chapters from anatomy books with images embedded
in text, other web-based programs, and the FM.
Your own term lists also represent anatomical information.
These sources use various methods for communicating anatomical
information.
What are these methods?
Based on your experience and common sense, generate a list and
categorize these methods.
Consider other methods that may not be included in the sources you
surveyed.
5. Based on your general experience and
the resources provided, propose a classification of the different kinds of
anatomical information.
Completion of the exercises in the previous objectives should give you
a good idea of the classes of physical entities that constitute the body, the
relationships that exist between these entities, and also the methods that are available
for representing the information that relates to these entities.
A remaining question is how can we classify anatomical information.
This question relates to informatics research that is primarily
concerned with anatomical information.
Formulate a classification of your own and revise it after you have
read:
Resource
Brinkley 1991: Structural informatics and its applications in
medicine and biology. AcadMed; 66: 589-591.
Recapitulation:
Review the work you have done in this tutorial.
Based on the introduction to structural informatics provided by this
tutorial, consider the challenges and problems that need to be addressed in
structural informatics.
What problem would you select to work on if you were offered a
well-paid position in a structural informatics lab?
You may want to give some thought to this question, and develop it
after the class.
We will reiterate this request once we have dealt with some specific
anatomy. It should be interesting to see how your ideas and priorities evolve
during the class.
Please share your proposal with the course instructors and members of
the class.