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Definition and Purpose
The Foundational Model Explorer (FME) is an Internet based software application developed for viewing the content and organization of the Foundational Model of Anatomy (FMA). It is being developed by the Structural Informatics Group at the University of Washington. The initial purpose of the FME is to provide a simple and intuitive interface to the FMA for domain experts, in the field of anatomy, participating in the evaluation of the FMA. Once the evaluation is completed, we will adapt the FME for use by students and other potential users requiring anatomical information.

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Basic Features
The FME display consists of two panes: a hierarchical tree may be opened up in the pane on the left side; if a class is selected in the hierarchical tree, the pane on the right side displays the information that has been entered in the FMA for that class. The information associated with a given class is organized in so-called slots. Each slot has a name (e.g., Definition, Parts) and some content, which is that particular slot’s value (e.g., the English definition and the names of parts of the selected class, respectively). For an explanation of the interactive features of the FME, see the Knowledge Navigation Section. For a guided tutorial check out the Conducted Tour.

In the left pane, the default tree is a subclass hierarchy, based on the -is a- or -kind of- relationship; it is the instantiation of the Anatomy taxonomy (At) component in the high level scheme of the Foundational Model of Anatomy. Apart from the slots Preferred Name and Synonyms, other slots relate to the Anatomical Structural Abstraction (ASA) component in the FMA’s high level scheme.

Hierarchies based on various part-whole relationships can also be opened up in the left pane. Once a class has been highlighted in the subclass hierarchy, you can choose a relationship from a drop down list labeled Select navigation tree type. Some other transitive relationships (e.g., -branch of- and -tributary of-) are also available.

The Search facility matches a search term to the preferred name, as well as to the Latin name, or synonym of an FMA class (if such exist). The tree is expanded to reveal the matching class and the information about this class is displayed. The wildcard ‘*’ is allowed in the search term and will match to any sequence of characters. For example the search term ‘h*d’ matches the class names ‘Head’ and ‘Hepatic cord’ (amongst others). The search function is not case sensitive. If more than one class name matches with the search term, a list of matching terms is presented for the user to choose between.

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Knowledge Navigation
The subclass hierarchy (Anatomy taxonomy or At) represents the basic semantic structure or backbone of the Foundational Model of Anatomy. Gaining familiarity with the At, along with the definitions of its classes is critical for understanding the underlying organizational scheme of the FMA. The button Options allows you to select the preferred behavior of nodes in the subclass or part-of hierarchies. The Help menu contains explanations of the FME’s interface features as well as a brief description of how to navigate within this environment.

If you click on a plus icon in front of a node (i.e., term) in the hierarchy, the children of the corresponding class will be displayed in the tree. The relationship between parent classes and their children is indicated in the navigation tree type window. If you click on the term itself in the tree, the class name (term) will appear highlighted (selected) and the pane on the right will display the information, contained in the FMA, about that class. Clicking on a minus icon will hide the children of a node.

For some of the slot values in the right pane, there are links to other classes. These values appear in blue and are boldfaced. Clicking on such a term within a slot causes the term to appear in the hierarchy, and the right pane will now display the information about the newly selected class. For example, if you are viewing the class ‘Heart’ and then click on ‘Wall of heart’ in the ‘Parts’ slot, the hierarchy on the left will be expanded to reveal ‘Wall of heart’ (as long as the class ‘Wall of heart’ occurs somewhere in the current relational hierarchy). ‘Wall of heart’ appears highlighted in the left pane, and the right pane should show the information about the wall of the heart.

This example illustrates the interrelation of various classes in the FMA. These interrelations are more comprehensively explored in the Conducted Tour.

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Conducted Tour
The objectives of the conducted tour are to illustrate the

Terms and Classes
The official source for anatomical terms is Terminologia Anatomica (TA for short). TA is a term list compiled with the intent to standardize anatomical terms. By contrast, the Foundational Model of Anatomy represents anatomical classes and anatomical relationships. A class is a unit of thought, whereas a term is a unit of speech. The difference between these two units is explained in the publication Terminologia (p. 11-12), and is illustrated by the first exercise.

Exercise 1.
Objective: illustration of the relationship between class and term.

Enter in the search field of the FME the term ‘oviduct’.
The term that appears in the left pane highlighted in blue is ‘Uterine tube’.
Inspect the terms that appear in slots Preferred name and Synonyms.
For those familiar with anatomy, all the terms in these two slots conjure up the thought of one of a pair of tubular structures that extends laterally from the uterus. An unlabeled image of this structure would provoke the same unit of thought, or class.

The FMA represents such classes and associates with them a unique identification number, omitted from the FME, (e.g., for Uterine tube: FMAID 18235), and also all the terms that we can find in anatomical discourse and the literature referring to this class. Thus the FMA is a class-centered, rather than a term-centered, source of anatomical information.

Of all the available terms we select one as the Preferred name of the class, and include all the others as Latin names or English Synonyms, as appropriate.

Click on the small icon ‘i’ next to the Preferred name and Synonyms labels to obtain an explanation of the rationale for making these assignments.
Unless there are reasons to do otherwise, we select the English TA term that is most descriptive of the classes as a preferred name. However, the FMA includes thousands of classes missing from TA, some of which have never been named and others that exist in the literature. We assign a UWDID and a preferred name to each of these classes as well. The rules for such naming procedures will be described elsewhere.

The FMA contains substantial documentation of the origin and authorities for the terms that are entered in the knowledge source. Such information can be viewed only through Protégé-2000, the authoring program for the FMA.

The preferred name serves as the most useful identifier of a class, because (unlike a numerical ID) it is meaningful to humans and is also processable by machines (computers) without ambiguity. The latter property requires that both preferred names and synonyms uniquely refer only to one class. In other words, the FMA does not allow homonyms, terms that have more than one meaning (e.g., the homonym ‘muscle’ may refer to an organ, such as the biceps, or to a tissue, such as smooth muscle). Homonyms are present in TA (Terminologia; p. 12-13), and when we encounter them, we modify them in order to make them unique for each of the classes to which they refer [e.g., ‘muscle(organ)’ and ‘muscle(tissue)’].

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Principles of Classification
Anatomy textbooks, lectures and other instructional resources include a substantial amount of information that is not strictly anatomical (e.g., function, pathological lesions, diseases, clinical cases). The Foundational Model of Anatomy is constrained by design to a structural context. This means that all classes entered in the FMA must be defined in structural terms and must be grouped into classes on the basis of the structural properties (i.e., attributes) that they share. Only in such structural context is it possible to establish an inheritance hierarchy (taxonomy), in which there is only one root and the relationship between subclasses and super-classes is strictly the –is a- relationship.

Although the most intuitive way of thinking about anatomy is along the -part of- relationship, it is necessary to establish the classes of anatomical entities on the basis of the -is a- relationship, so that the properties of anatomical classes (displayed as the slots of the FME) can be associated with the classes and then inherited by their descendants. Once such an inheritance hierarchy (taxonomy) is established, the classes can be rearranged according to the various part-of relationships illustrated in the navigation type tree field of the FME.

Exercise 2.
Objective: illustration of the rearrangement of classes in different hierarchies
and the permanence of the association between classes and their attributes.

Make sure that ‘Uterine tube’ is selected in the left pane (At).
Inspect the slots in the right pane that are associated with this class.
Make sure that the navigation type tree field shows subclass; i.e., that you are
viewing the At.
Inspect the super-classes or parents of ‘Uterine tube’.
Note that the ‘Uterine tube’ is a kind of ‘Organ with organ cavity’. Note also that the immediate neighbors (siblings)
of ‘Uterine tube’ are similar kinds of organs. Do you see the structural
similarity between all these organs?
If you are in doubt, read the definition of ‘Uterine tube’ and that of several of
its siblings. (You need to click on the term to get the definition and other slots
to appear in the right pane.)
Is the definition of ‘Organ with
organ cavity’ true for all of its descendants (children)?
What distinguishes theses descendants from one another?

Next note that ‘Organ with
organ cavity’ is one of the members of the class ‘Cavitated organ’.
What are the subclasses of ‘Cavitated organ’? What distinguishes these subclasses from one another?
You may find it instructive to move up the hierarchy until you reach the root of At: Anatomical entity.

You may find it informative to refer to publication Definitions

Most of the classes you have encountered are lacking from TA and other traditional anatomy sources. Since discourse in anatomy proceeds usually at the level of classes such as the uterine tube, the high-level classes of the FMA may be ignored, since all the information in common practical usage is associated with anatomical entities such as the uterine tube. You may wish to return to this exercise and explore how the simple structural attributes, in terms of which these classes are defined, are inherited along the subclass hierarchy. You will find ‘spatial dimension’, ‘mass’ and ‘inherent 3D shape’ at the bottom of the right pane.

Return to ‘Uterine tube’ in the At and select it.
In navigation type tree field select systemic part.
Note that the hierarchy has changed: the root is now body, the nodes of the hierarchy are the organ systems, and the link between the nodes is the systemic part-of/has-part relationship.
Also note, that as long as ‘Uterine tube’ is selected in the hierarchy, the same information remains associated with it in the right pane.

You may like to repeat the same exercise by selecting a regional part hierarchy.

If you are interested in the overall organization of the FMA, you may find it informative to refer to publications Principles and Knowledge Base.

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Heterogeneity of Part Relationships
Mejino, J. L. V. and Agoncillo, A. V. and Rickard, K. L. and Rosse, C. (2003) Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy. In Proceedings, American Medical Informatics Association Fall Symposium, pages 450-454.

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Detwiler, L. T. and Mejino, J. L. V. and Rosse, C. and Brinkley, J. F. (2003) Efficient Web-Based Navigation of the Foundational Model of Anatomy. In Proceedings, American Medical Informatics Association Fall Symposium, pages 829.

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