Representation of Structural Relationships in the
Foundational Model of Anatomy
José L.V. Mejino, Jr. M.D.,1 Natalya F. Noy Ph.D., 2 Mark Musen M.D., Ph.D., 2 and Cornelius
Rosse, M.D., D.Sc. 1
Structural Informatics Group, Department of Biological Structure,
University of Washington, Seattle, WA1 and
Section on Medical Informatics, Stanford University School of Medicine,
Stanford, CA 2
ABSTRACT
Previous attempts at the symbolic representation of
anatomical relationships have been largely limited
to partonomy. We propose an ontology of
anatomical relationships and illustrate the
inheritance of structural attributes in the Digital
Anatomist Foundational Model. Our purpose is to
generate a sharable resource that can support
inference about the structural organization of the
body.
INTRODUCTION
The main objective of the terminologies correlated
by UMLS is to serve as repositories of terms that
can be reused with consistency by a variety of
applications.1 In general, current biomedical and
educational applications are designed to present
hard-coded, didactic information, or they support
low-level, look-up functions with no, or at best
limited, capabilities for inference. The semantic
structure
of
today's
controlled
medical
terminologies (CMTs) seems adequate for the
needs of such contemporary applications. Nextgeneration applications, however, will have to
incorporate increasing levels of intelligence in
order to meet the demands of the evolving
environment in education and the practice of the
various health professions. Such knowledge-based
applications call for the representation of much
deeper and richer knowledge than that retrievable
from today's CMTs. Since these CMTs primarily
target clinical medicine, they are deficient in basic
science concepts necessary to support reasoning.
Moreover, since relationships between concepts
constitute an important dimension of knowledge,
next-generation knowledge sources must model
comprehensively not only the concepts but also the
relationships that characterize a particular field of
basic science. Therefore, there is a need to
generate enabling knowledge sources at least in
those domains that generalize to diverse fields of
education and clinical practice. Anatomy is such a
fundamental domain.
We are developing the Foundational Model of
anatomy (FM)2,3 as an evolving resource for
knowledge-based applications4. Our intent is that
the FM should furnish, at the highest level of
granularity, not only anatomical concepts but also
the relationships that comprehensively describe
the structural organization of the body. Figure 1
illustrates that three of the four components of the
FM (described elsewhere in these proceedings5,6)
are, in fact, based on different classes of
relationships:
Fm = (AO, ASA, ATA, Mk)
(1)
AO, the Anatomy Ontology, is a type hierarchy
based on the IS-A relationship; ASA, the
anatomical structural abstraction, based on
'structural relationship', is the subject of this
report; ATA, the anatomical transformation
abstraction, is based on relationships that describe
the morphological transformation of anatomical
entities during pre- and postnatal development.
Figure 1. Classes of 'Anatomical relationship' in the
context of its superclasses in the AO of the FM.
Our reports in these proceedings,5,6 as well as
elsewhere,2,3,7-10 are primarily concerned with the
classification of physical anatomical entities
(material objects, spaces, surfaces, lines and
points). In this communication our objective is to
illustrate
the
importance
of
anatomical
relationships for the symbolic modeling of
structural knowledge, a dimension unique to
anatomy among the biomedical sciences.
ANATOMICAL STRUCTURAL
ABSTRACTION
The FM is being developed as an anatomical
enhancement of UMLS. Its classes and
relationships extend the specificity of UMLS
semantic types and relationships. We have
proposed a scheme for representing anatomical
structural relationships in terms of interacting
networks:3,10
ASA = (DO, Pn, Bn, SAn)
(2)
Where: DO = Dimensional ontology
Pn = Part-of network
Bn = Boundary network
SAn = Spatial Association network
DO is a type hierarchy of geometric objects and
shapes, in terms of which the three networks of
ASA may be described at an abstract level. Of the
ASA networks, SAn itself consists of a number of
subnets corresponding to the descendants of the
'Spatial association relationship' class shown in
Figure 2. Since other reports tend to deal with partwhole relationships11,12, in this communication we
illustrate spatial associations, which have received
less attention. The descendants of this relationship
class correspond to a number of axes or viewpoints
in terms of which anatomical spatial associations,
such as location, may be conceptualized. We
illustrate the symbolic modeling of 'Anatomical
adjacency', which poses a particular challenge,
since adjacency is not simply a relationship
between two objects; rather it has attributes, such
as directional vector and right or left laterality.
An anatomical structure, such as the esophagus, or
a part of it, inherits its shape from the DO class
'conventional hollow cylinder'. This shape specifies
the set of adjacency relationships that is allowed
for this shape class. Figure 3 shows these
relationships graphically in terms of a qualitative
radial coordinate system. In Figure 4 the qualitative
coordinate system for cylinder are superimposed
and centered on the esophagus in a section of the
Figure 2. The ontology of structural
relationships. Only some of the subclasses are
opened up.
male Visible Human at the level of the eighth
thoracic vertebra. In Figure 5 the adjacencies of
'T8 part of the esophagus' are expressed
symbolically in terms of these qualitative
coordinates. Although some of these adjacency
relationships remain constant, others change from
one vertebral level to the next. The AO of the FM
represents each vertebral level of the esophagus as
a discrete subzone, which permits the symbolic
modeling of the changing adjacency relationships
of the esophagus as it "passes" from the neck to
the abdomen.
The spatial knowledge captured by the adjacency
relationships shown in Figure 5 is of importance
to a student dissecting the esophagus for the first
time and also to a surgeon planning to remove a
lymph node adjacent to the esophagus through a
mediastinoscope. The FM can provide knowledge
of adjacency relationships appropriate for
applications developed for each of these types of
users. Moreover, since we can represent inverse
values for these relationships, and make
inferences based on their transitivity, the FM
could support inference required for answering
user-generated spatial queries at different levels
of complexity.
Figure 3. Qualitative radial coordinate system
for the DO shape class ‘conventional cylinder’.
Figures 4 and 5 invite comment about the relative
usefulness of geometric and qualitative coordinates
for representing such structural attributes as
location and adjacency. The relationships
expressed in terms of qualitative coordinates could
be derived from the quantitative geometric matrix
of the Visible Human data set. These geometric
coordinates, however, would have to be expressed
as qualitative coordinates in order to make them
intelligible in anatomical discourse. Geometric
coordinates are valid only for one instance,
whereas anatomical qualitative coordinates
describe relationships that hold true in all members
of a species. Only those structures can be
referenced by geometric coordinates that are
visible with a particular imaging modality.
Qualitative coordinates, on the other hand, can
describe the relationship of invisible structures to
visible ones, as illustrated in Figure 5 by the
esophageal plexus, fibrous pericardium and
mediastinal pleura; none of these structures can be
identified in the image of the anatomical section.
Moreover, inference required for reasoning about
structural relationships within the body must make
use of qualitative coordinates. Therefore, the
symbolic representation of structural relationships
in terms of qualitative coordinates is an important
component of the FM.
IMPLEMENTATION
UWDA and FM. We began the development of
the University of Washington Digital Anatomist
(UWDA) vocabulary (the initial iteration of the
FM) as an anatomical enhancement of UMLS13.
Initially we were less concerned with the variety of
anatomical
relationships
than
with
the
classification
and
comprehensiveness
of
anatomical concepts. The authoring tool we
developed was designed to generate parallel
Figure 4. Coordinate system of conventional
cylinder superimposed on T8 part of esophagus.
hierarchies (directed acyclic graphs) which were
based on IS-A, PART-OF, BRANCH-OF and
TRIBUTARY-OF relationships. As we populated
classes of 'Organ part' in the IS-A hierarchy, for
example, we also aligned the concepts along the
transitive PART-OF relationship in another
hierarchy. However, such a link-centric view and
representation of anatomy proved to be
inadequate once we began to appreciate the
complexity of relationships that were necessary
for comprehensively describing the anatomy of
the body. The need for such a comprehensive,
reusable resource led to the Foundational Model,
a conceptualization of the physical organization
(structure) of the human body.
Approximately 50,000 concepts in the AO of the
FM are accessible through the UWDA vocabulary
of UMLS, providing a comprehensive controlled
terminology for macroscopic anatomy. Our
current work entails the instantiation of the ASA
networks of these concepts. The association of
such multi-dimensional relationships with
anatomical concepts calls for a node-centric view
of anatomy, which is beyond the capacity of the
link-centric representation we implemented. The
frame-based knowledge acquisition system
Protégé-200014 has the requisite expressivity and
scalability for comprehensively modeling
anatomical relationships encompassed by the
ASA.
The same will be true for ATA
relationships, once we begin the implementation
of developmental transformations.
Figure 5. Frame-based representation of 'T8 part of esophagus' in AO in the left pane and its attributes in
the right pane.
Modeling the ASA in Protégé-2000. Protégé2000 has been adapted to meet current and
evolving needs of the FM. It is being enhanced by
customized active user-interface components as we
encounter new challenges in modeling.
Protégé-2000 correlates four ontologies within the
FM: the large 'Anatomical entity' ontology (the
AO) and the smaller 'Dimensional object', 'Physical
state' and 'Anatomical entity metaclass' ontologies.
The first three ontologies provide the values for
anatomical relationships, whereas the metaclass
ontology assures the inheritance of the attributes of
concepts represented in the AO. The 'Anatomical
entity metaclass' ontology contains high level
templates for the classes in the AO, which
instantiate the template. Each template is a frame
composed of a set of slots; each slot corresponds to
a defining or other attribute manifested by a
particular AO class. We define a hierarchy of
templates and the attributes are inherited through
the hierarchy. For instance, each concept has a
UWDA-ID number and a preferred name, and it
may have one or more synonyms. Therefore the
template for 'Anatomical entity', which is the root
of the AO, includes slots for each of these
attributes. The templates of all descendants of the
root inherit these slots. When a new concept is
entered in the AO, values must be assigned to each
of these slots (Figure 5).
Figure 5 presents the frame for 'T8 part of
esophagus', which is highlighted in the AO (left
pane). The right pane shows some of the values for
the slots of the 'Zone of esophagus template'
pertinent to the ‘T8 part of esophagus’. Although
they would have different values, the same kinds
of slots specify the anatomical relationships of
cervical or thoracic parts of the esophagus as
those of the parts that correspond to vertebral
levels. The slots for the first two rows of values
are inherited from the template of the root. The
slot 'has intrinsic 3D shape' is first introduced in
the 'Anatomical structure' template as a defining
attribute. This attribute distinguishes 'Anatomical
structure' from 'Body substance' (see Fig. 1.), as
explained in a companion report in these
proceedings.5 The intrinsic shape slot is inherited
by all templates corresponding to descendants of
'Anatomical structure' in the AO, and its values
are provided by the DO.
The 'has orientation' template slot, however, has
to be introduced in the template of 'Physical
anatomical entity', since not only anatomical
structures but also surfaces and lines (classified as
non-material physical anatomical entities) have
orientation (for class hierarchy, see Fig.1). For the
same reason, the location attribute is also
introduced in the 'Physical anatomical entity
template'. On the other hand, slots for the different
classes of location relationships (see Fig. 2) must
be introduced in the templates of selected
descendant classes of 'Physical anatomical entity'.
For instance, the 'contains' slot is introduced in the
template of 'Anatomical space', whereas its
inverse 'contained in' is inserted in the 'Material
physical anatomical entity template', since both
anatomical structures and body substances can be
contained in anatomical spaces. Therefore, in the
frame of 'T8 part of esophagus', 'posterior
mediastinum' can be a value for the relationship
'contained in', since 'posterior mediastinum' is
classified as a 'Compartment', which is a subclass
of 'Anatomical space'.
Adjacencies also refer to location (see Fig.2).
However, they are attributed relationships and
therefore 'has adjacency' itself is modeled as a
frame with its own slots. For a conventional
cylinder, these slots correspond to the radial
coordinates shown in Figure 3. 'Zone of esophagus
template' inherits these slots from the
'Conventional cylinder template'. The adjacency
relationships of 'T8 part of esophagus' are
displayed in Figure 5 as the values of these radial
coordinates. These values are the immediate
adjacencies of this zone of the esophagus. The
concepts that correspond to each of these values
(e.g., fibrous pericardium, azygos vein, thoracic
aorta) also contain adjacency relationships in their
own frames. 'T8 part of esophagus' is a value for
one of the adjacency coordinate slots along a
vector reciprocal to that which relates 'T8 part of
esophagus' to the concept. For example in the
frame of Azygos vein the value for 'left anterior'
coordinate of adjacency would be 'T8 part of
esophagus'. Since adjacency relationships are
transitive along a coordinate vector, it may be
inferred from immediate adjacencies that T8
vertebra (labeled ‘T8’ in Fig 4) is located 'right
posterior' in relation to ‘T8 part of esophagus'. It is
these interacting adjacency relationships that
constitute the adjacency subnet of the SAn
component of the Anatomical Structural
Abstraction.
DISCUSSION
We selected 'T8 part of esophagus' to illustrate the
symbolic representation of detailed structural
relationships within the Foundational Model of
anatomy. We are validating the templates we have
developed so far by assessing the extent to which
they generalize to different classes of anatomical
entities. Our contention is that a logical and
comprehensive symbolic model of anatomical
structure will be indispensable to programs and
applications that call for reasoning about the
human body. By making the FM available as the
UWDA vocabulary of UMLS, we hope to obviate
the need for ad hoc, repetitive and inconsistent
modeling of anatomy by developers of educational
or clinical applications who require detailed
knowledge of specific parts of the body. Our
objective is to enrich this resource by a
comprehensive representation of structural
relationships, which are an integral component of
reasoning about the human body by both humans
and machines.
Acknowledgments
This work was supported in part by contract LM03528
and grant LM06822, National Library of Medicine.
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