Visible Human, Know Thyself:
The Digital Anatomist Structural Abstraction
Cornelius Rosse, M.D., D.Sc., José L. V. Mejino, M.D., Linda G. Shapiro, Ph.D.,
James F. Brinkley, M.D., Ph.D.
Structural Informatics Group, Departments of Biological Structure and Computer Science,
University of Washington, Seattle, WA
rosse@u.washington.edu
The Visible Human data sets have stimulated a great
deal of activity in the graphical representation of
anatomy. A major challenge is to enhance this
resource of image-based information with
knowledge of its own structure. There is a need for a
symbolic model of the structural organization of the
human body, which could invest with meaning the
graphical information extractable from the clusters
of voxels and their geometric coordinates that make
up the Visible Human data sets. The objective of
this communication is to examine the elements of
structural information such a symbolic model should
encompass, and to assess the extent to which the
Anatomical Structural Abstraction (ASA) of the
Digital Anatomist Foundational Model of Anatomy
(Fm)1 meets this objective.
Elements of Structural Information. In a
biological or anatomical context, the term structure
is associated with two distinct concepts (meanings):
1. a material object generated as a result of
coordinated gene expression, which necessarily
consists of parts (e.g., hemoglobin molecule, cell,
heart, human body); and 2. the manner of
organization or interrelation of the parts that
constitute a structure specified by the first definition
(i.e., the structure of a structure). Both definitions
emphasize the critical need for declaring the
principles according to which units of organization
can be defined in order to be able to state what is
‘whole’ and what is ‘part’. Specifying the manner in
which parts interrelate must satisfy two
requirements: 1. to determine the kinds of parts of
which various structures may be constituted; and 2.
to state the manner of spatial organization of parts
by describing their boundaries, continuities and
attachments, as well as their location, orientation
and spatial adjacencies in terms of qualitative
coordinates (in addition to the quantitative
geometric coordinates, which are embedded in the
Visible Human data sets).
The Anatomical Structural Abstraction. The
ASA is one of the four components of the
Digital Anatomist Foundational Model of
Anatomy (Fm):
Fm = (Ao, ASA, ATA, Mk)
(1)
The Fm is an abstraction that, in accord with
declared principles, describes the physical
organization of the material objects and 3D
spaces that constitute an idealized human body1.
The current model is limited to the static state
and excludes anatomical structures smaller than
the cell. Its backbone is the Anatomy ontology
(Ao), which assigns anatomical entities to
classes according to defining attributes they
share with one another and by which they may
be distinguished from one another2. ASA, the
subject of this communication, is described
after other Fm components. ATA, the
Anatomical
Transformation
Abstraction
describes
time-dependent
morphological
transformations of anatomical structures during
the human life cycle. Mk, Metaknowledge,
comprises the principles, definitions and rules
according to which relationships are
represented in the other three components of
Fm.
The ASA captures the information that is
sufficient and necessary for describing the
structure of any physical object or space that
constitutes the body, as well as that of the entire
human body itself. The ASA of the entire body
may be conceived as a composite of all ASAs of
anatomical structures and anatomical spaces that
are represented in Ao. The Anatomical Structural
Abstraction is distinct from other approaches that
have been proposed for the symbolic description
of anatomical spatial relationships, in that it is
not limited to object recognition in medical
images, it generalizes to all parts of the body and
it accommodates all relationships that are necessary
for describing the 3D structure of the body. The ASA
consists of several components:
ASA = (So, Pn, Bn, SAn)
(2)
where: So = Spatial object ontology
Pn = Part-of network
Bn = Boundary network
SAn = Spatial association network
The So provides an additional axis for classifying
the thousands of anatomical concepts in Ao
according to their spatial dimensions and shape, and
thereby systematizes the description of their spatial
relationships. For instance, through the rules entered
in Mk, part-whole relationships in Pn are restricted
to spatial objects of the same dimension. For
example, the relationship ‘Right atrium’ -has parts‘Cavity of right atrium’, ‘Wall of right atrium’ is
sanctioned because in So all these concepts are
classified as Volume (3D object). On the other hand,
‘Surface of right atrium’ cannot be modeled as part
of ‘Right atrium’, because it is a 2D object. The
correct relationship is specified by Bn: ‘Right
atrium’ -bounded by- ‘Surface of right atrium’,
because the latter is classified as a spatial object of
one lower dimension than the atrium. Pn also
incorporates
an
ontology
of
part-whole
relationships, which are sanctioned according to the
assignment of a concept to classes of Ao and So. For
instance the relationship -has lobe- is sanctioned if
the ‘whole’ is classified as a “Parenchymatous
organ’ in Ao and a ‘Cone’ ‘Semicone’ or
‘Polyhedron’ in So.
The Spatial Association Network (SAn) itself encompasses subnetworks of various relationships:
SAn = (Ctn, Atn, Ln, On, Ajn)
where: Ctn
Atn
Ln
On
Ajn
(3)
= Continuity network
= Attachment network
= Location network
= Orientation network
= Adjacency network
The latter three subnets of the SAn make use of
traditional anatomical descriptors of orientation and
location (anterior, posterior, etc.) as qualitative
coordinates in terms of the shape of the spatial object
that is being described.
We began to represent the Fm as an extension and
enhancement of the UMLS semantic network. A
semantic net, however, is not sufficiently
expressive for modeling the multiple
relationships that constitute the ASA. Therefore,
we are in the process of migrating the model to
Protégé, a frame-based system designed for
accommodating multiple relationships, supporting inheritance and correlating several
ontologies3. The Ao, So and Pn components of
Fm, along with relevant elements of Mk have
been implemented for macroscopic anatomy.
Work is in progress on the structural networks
of the ASA. The Visible Human geometric data
sets serve for verifying spatial relationships we
model and also for validating the ASA schemes
that we develop. This work would be greatly
facilitated by the availability of 3D graphical
models for all anatomical structures that can be
segmented from the volumetric data.
It is our contention that the Digital Anatomist
Foundational Model as a whole, and its
Anatomical Structural Abstraction in particular,
will furnish the formal representation of
knowledge that will provide for the intelligent
navigation of the Visible Human data sets.
Through appropriately designed interfaces, the
Fm will be instrumental in revealing the
structure of the human body not only to experts
but also to any user who has a need for
interacting with the Visible Human.
Supported by National Library of Medicine
contract, LM 83510 and grants LM 06822 and
LM 06316.
References
1.Rosse C, Shapiro LG, and Brinkley JF. The Digital
Anatomist Foundational Model: principles for
defining and structuring its concept domain. J Am
Med Inform Assoc Proc AMIA’98 Annual
Symposium 1998;820-824.
2.Rosse C, Mejino JL, Modayur BR, Jakobovits R,
Hinshaw KP, Brinkley JF. Motivation and
organizational principles for anatomical knowledge
representation: the Digital Anatomist Symbolic
Knowledge Base. J Am Med Inform Assoc
1998;5:17-40.
3.Musen MA, Gennari JH, Eriksson H, Tu SW, Puerta
AR. PROTÉGÉ II:computer support for
development of intelligent systems from libraries of
components. MEDINFO95, The eighth World
Congress of Medical Informatics, Vancouver, B.C.
Canada, 1995;766-770.