Ontology and Bodily Systems
Igor Papakin1, Barry Smith, PhD1,2, Katherine Munn1, Werner Ceusters3, MD
1
Institute for Formal Ontology and Medical Information Science
Faculty of Medicine, University of Leipzig, Leipzig, Germany
2
Department of Philosophy, University at Buffalo, Buffalo, NY
3
Language & Computing nv, Zonnegem, Belgium
ABSTRACT
Contemporary medical science represents the human
body as a system made of systems. Why is this so? And
what does the term ‘bodily system’ mean? On what
principle do we divide the body into systems as we do?
Such questions must be answered if we are to translate
our informal knowledge of the medical domain into a
form that is useable by computers. We provide a
framework for a definition of the term ‘bodily system’
that is able to do justice to the ways in which standard
rosters of bodily systems differ amongst themselves.
The framework can be extended to provide an ontology
of the anatomical domain within which also the
functions of anatomical features can play a role.
INTRODUCTION AND BACKGROUND
Ontology plays an increasingly significant role in
work on terminology and knowledge management
systems in the biomedical domain and we hold that
ontology will play an essential part in the medical
informatics of the future. The term ‘ontology’ must,
however, be understood in the right sort of way.1 The
dominant paradigm might be referred to as ‘applications ontology.’ This holds that the ontologist should
focus primarily on the construction of ontologies as
working applications; the expressive power of an
ontology is thereby limited effectively to that of one
or other version of Description Logic.2 This means
that an ontology, when applied to complex domains
such as those of biomedicine, is forced to deal with
simplified models. There is, however, a second
‘reference ontology’ school of thought, which
focuses primarily on the development of ontological
theories of the entities in given domains. Such
theories are marked by a high degree of representational adequacy and are designed to be used as
controls on the results achieved by working applications rather than as substitutes for these working
applications themselves.3
Three levels of reference ontology can be distinguished in the biomedical domain:
1. formal ontology: a top-level domain-independent
theory involving the use of concepts such as:
object, process, identity, part, location;
2. domain ontology: a top-level theory applying the
structure of a formal ontology to the medical
domain, involving concepts such as: body, disease,
therapy, organ, tissue, cell, and so forth;
3. terminology-based ontology: a very large lowerlevel system, based on medical terminologies such
as UMLS, and involving specific concepts such as:
inflammatory change in the gastric mucosa.
The present paper is a contribution to medical ontology under heading 2, focusing on the question: what
is a bodily system? It thus supplements the work of
Rosse,4 who evaluates the Terminologia Anatomica,5
as a starting-point for generating machine-understandable representations of biomedical concepts. It
also fills a gap in the work of the Digital Anatomist
Project, whose definitions6 use the notion of ‘system’
but leave this notion unanalyzed.
BODILY SYSTEMS IN MEDICINE
Contemporary medical science represents the living
human body (the human organism) as a system made
of systems. The body’s systems serve as major
provinces in our maps of human anatomy and thus
they play a central role also in a variety of domains,
from medical pedagogy and dynamic modeling to
computer visualization. An understanding of the concept system is moreover a necessary part of any
understanding of cognate concepts such as organ and
function, and it is a prerequisite for the understanding
of systemic diseases, both those which are localized
in single systems and also those, such as diabetes,
which affect a plurality of systems simultaneously.
In constructing a domain ontology of medicine we
need to start with the results of medical science as set
forth in standard textbooks. Unfortunately the medical literature provides at best informal definitions of
terms such as ‘bodily system’, ‘organ’, and so forth,
and this helps to explain why there is a less than
perfect agreement on the rosters of bodily systems,
organs, etc. provided by different sources. Medical
textbooks rest on tacit knowledge concerning such
highly general concepts. That is, while their authors
understand perfectly well how the living human body
is organized and what the functions of bodily systems
are – they deal with such systems and their workings
every day of their lives – they do not formulate this
knowledge in an explicit way. We do not wish to
impose spurious precision in an area that is marked
intrinsically by a certain vagueness and informality.
But where for human beings such informality is
acceptable, it becomes problematic where the reasoning of human beings must be simulated inside a
computer. The analyses presented below are intended
as a first step towards making up this gap.
***
The following overview of the adult human body’s
repertoire of systems has been distilled from the
Terminologia anatomica, the National Library of
Medicine classification7 and Wolf-Heidegger’s Atlas
of human anatomy.8
Supportive Systems: These provide the multi-chambered framework (body, container) within which the
other systems are located:
The skin system separates and isolates the organism
from its surroundings and participates actively in
maintaining the organism’s internal environment. Its
functions include thermoregulation, tactile sensitivity,
participation in the maintenance of water balance,
and defence against bacteria and viruses.
The musculoskeletal system is an ordered assembly of
bones, muscles and ligaments that is responsible for
maintaining the body’s shape and for allowing
movement in counteraction with external forces such
as gravity. It also creates an internal framework of
support for the organs of the body.
Systems for Substance-Exchange: These support
the normal (‘legal’) ways in which the organism
exchanges substances both within itself and with the
surrounding world:
The digestive system includes inter alia the oral
cavity, the esophagus, stomach, duodenum, small and
large intestines and salivary glands. It ensures that
solid and liquid substances are absorbed into the body
in such a way that they can serve as energy source
and as building blocks for other body systems.
The respiratory system includes the nasal cavity, larynx, lungs, trachea and bronchus and serves the
body’s gas exchange (absorption of oxygen, excretion of carbon dioxide).
The circulatory system includes the heart and blood
vessels and microcirculatory vessels, as well as blood
itself. It serves as a universal transporter of substances to the cells of the body via two circuits: the
pulmonary and the systemic. The former exchanges
gases with the external medium in the lungs. The
latter supplies all the organs of the body with oxygenated blood and provides for gas exchange between the blood and the cells of other organs.
4. The urogenital system includes the kidneys, the
ureters, the urinary bladder, and the urethra. It is
responsible for excretion from the body of surplus
water and of the waste products that appear in the
cells of the body as a result of physiological
processes, and for regulating the body’s ion balance.
Systems for Regulation: These act as supervisors
and coordinators in the work of the other body
systems:
The immune system includes the thymus, bone
marrow, spleen, lymphatic nodules and lymphatic
vessels as well as the lymphatic tissue in the pharynx,
the intestine, and a population of the immunocompetent cells working through the body. Its first
task is to recognize and break down or eliminate
substances that are dangerous to the body’s integrity.
The nervous system includes the brain and spinal cord
(the central nervous system), together with the
peripheral nerves, ganglia, plexi and sensory organs.
It regulates all the body’s systems and provides the
sensitive (sensory) functions of the body.
The endocrine system consists of the endocrine
glands and of the active endocrine tissue in other
glands. Together these serve as a battery of
transmitters that broadcast instructions to all the cells
of the body.
Note that the above is provided not as a definitive
partition, but rather merely as a benchmark for the
discussions which follow.
TOWARDS AN ONTOLOGY
The task of ontology is not to replace medical science. Rather, its job is to provide a framework within
which medical knowledge can be formalized in a way
which supports causally predictive theories and at the
same time counteracts the effects of terminological
and other inconsistency and imprecision. Such a
framework must start out from the ways medical
knowledge is formulated in the medical literature,
and one criterion of a good definition of ‘system’ is
that it yields a roster of systems that is very like the
standard rosters. As we have seen, however, it needs
to go beyond textbook formulations if it is to achieve
the sort of formal clarity we need for the purposes of
reference ontology.
How, then, are we to define the notion of a bodily
system? The discipline of systems theory is of little
help to us here, since its definition of a system as a
complex of interacting parts9 is far too general for our
purposes and is made more specific only by the use
of mathematical tools which leave unanswered precisely those questions pertaining to the nature of
bodily systems which we are called upon to answer.
We can make some progress, on the other hand, if
we examine how the word ‘system’ is most
commonly used in both technical and non-technical
contexts by speakers of English. The Oxford English
Dictionary defines ‘system’ under the principal heading of ‘an organized or connected group of objects,’
or more precisely: ‘A set or assemblage of things
connected, associated, or interdependent, so as to
form a complex unity; a whole composed of parts in
orderly arrangement according to some scheme or
plan.’ Under the heading ‘Biology’ it gives:
A set of organs or parts in an animal body of the
same or similar structure, or subserving the same
function, as the nervous, muscular, osseous, etc.
systems, the digestive, respiratory, reproductive,
etc. systems …
One might be critical of such definitions on the
grounds that a system is not a mere set or aggregate
but rather something dynamic (think of the solar
system). We can do justice to such criticisms,
however, by distinguishing systems themselves from
the processes in which they are involved, or in other
words from the functioning of systems.10 Systems, on
this view, are no more dynamic in nature than
organisms. Indeed organisms are systems on the
analysis we shall defend.
Examining our list of systems above, we see that
each of them consists of a certain organized or somehow connected group of objects – including bodily
organs and also certain associated tissues and
populations of cells – to which some complex
function is ascribed. Unfortunately there are very
many organized collections of bodily parts, including
every single cell of the body, with which functions
can be associated. To make an analysis along these
lines work, therefore, we need to provide a more
precise specification of the specific notion of
‘function’ that is at issue here.
THE BODY’S MODULAR HIERARCHY
A toolbox is sold in the hardware store as ‘a system
for keeping your tools safe.’ Why is the toolbox a
system, rather than merely an object – a part of inert
reality? Could we designate a rock we find in the
forest as ‘a system for cracking open walnuts’? One
reason why the toolbox deserves the name system is
its complexity: the box is divided into compartments
of varying sizes and shapes. Each bodily system, too,
enjoys a certain complexity, and its parts are
interconnected in certain ways – but the same is true
also of the rock, which may manifest an elaborate
internal structure of crystal forms and cleavage
planes.
Every complex organism has parts at many levels
of granularity. The brain contains neurons, the neur-
ons contain organelles, etc., the organelles contain
molecules which are composed of atoms which are
composed in turn of subatomic particles. We can, in
other words, partition complex organisms into
causally relevant portions (organs, cells, macromolecules, and so forth) by employing grids of
different sizes and levels of granularity.11 We can
partition bodily functions, too, on a number of
different levels. Thus the function of the kidney is to
excrete urine, but the execution of this function is a
composite process that consists of smaller interrelated
processes that occur on lower levels of granularity
(the excretion of urea and creatinine, absorption of
ions and water, and so forth). As the philosopher
Roman Ingarden expressed the matter, each multicellular organism is
a relatively isolated system of a very high order,
and as such contains in itself very numerous, likewise relatively isolated, systems of lower and lower
levels, which are hierarchically ordered and
variously situated within the organism, and are at
the same time both partially interconnected and also partially segregated, as a consequence of which
they can exercise the specific functions which are
characteristic to them relatively undisturbed.12
Our task here is to provide the beginnings of an
account of this modular hierarchy and of the successsive granular layers from out of which it is built, from
macromolecules via cells and organs through to the
whole organism. To anticipate somewhat we can say
that the highest level of this modular organization
immediately beneath that of the whole organism is
provided precisely by the body’s complement of
bodily systems.
ELEMENTS AND FUNCTIONS
When we make an assay of the parts of the body on
any given level of granularity then we can distinguish
certain special sorts of parts, which we shall call
elements, which are marked out by the fact that they
are relatively causally isolated from the surrounding
parts (for example as a result of their possession of
some membrane or covering which at the same time
allows certain kinds of influences and substances to
encroach into their interiors). The body as a whole is
then organized in modular fashion out of the assemblages of elements arrayed on each distinct level of
granularity.
We can now define:
X is an element of Y if and only if:
(i) X is a proper part of Y and Y exists on a higher
level of granularity than X;
(ii) X is causally relatively isolated from the surrounding parts of Y;
(iii) one or more specific functions are ascribed to X;
(iv) X is maximal, in the sense that X is not a proper
part of any item on the same level of granularity
satisfying conditions (i) to (iii).
Thus the heart and kidneys are elements, but the
upper hemisphere of the heart is not an element,
because it is not maximal. In bodily systems we can
distinguish many levels of elements. The coarsegrained elements of the digestive system include the
esophagus and stomach; finer grained elements are
the specific glands in the stomach wall, the serous
membrane, the layers of smooth muscular tissue.
Assigned functions are: constricting, producing
hydrochloric acid and pepsin.
One problem with our definition is that the notion
of our ‘ascribing’ a function to an element seems to
involve an element of subjectivity which conflicts
with our goal of contributing to the formulation of
causally predictive theories. To solve this problem we
need to have some notion of the function which an
object, for example a mechanism, realizes when it is
doing what it is supposed to do. The toolbox exists
only because it has been designed to perform a
certain function. Something similar can be said about
bodily systems, though we must here speak not of
design but rather of the workings of evolutionary processes. Each bodily system has an internal structure
which is such that (1) there are various interconnected elements on different levels of granularity
within the system as a whole and (2) these
interconnected elements perform certain specialized
functions which contribute to the functioning of the
system as a whole and (3) these elements and the
whole which they form exist and have the structure
they do in order to allow for this functioning.
A DEFINITION OF ‘BODILY SYSTEM’
In order to understand this last phrase we need to exploit the notion of proper function introduced by
Ruth Millikan.13 The proper function of the heart is to
pump blood. This is so even though, due to some defect, a given heart may fail to perform this function
because each heart exists in virtue of the fact that its
immediate evolutionary predecessors were successful
in carrying out this function. The proper function of a
sperm’s tail is to propel the sperm to an egg, and this
is so even though only a small fraction of sperm tails
realise this function to completion. Technically, we
can say that for products of evolution in mature
species such as ourselves:
An item X has proper function F if and only if:
(i) X is a reproduction of some prior item that,
because of the possession of certain reproduced
properties, actually performed F in the past
(ii) X exists because of this performance.
What, now, are the proper functions performed by
bodily systems? Before we answer this question we
must note one apparent difference between bodily
systems on the one hand and those elements of the
body’s modular hierarchy which we have distinguished at lower levels of granularity. Macromolecules, cells and organs are separated from each
other by real physical discontinuities; they are
analogous to the body as a whole in manifesting a
high degree of (topological) connectedness and selfcontainedness. The body’s systems, in contrast, may
be topologically highly complex and they may even,
as in the case of the endocrine system, consist of
disconnected parts. One crucial difference between
the toolbox and our bodily systems is this: the
toolbox is a single substance in its own right in
relation to which no demarcation problem arises. A
toolbox is a connected whole, with its own bona fide
boundary. The demarcation lines between bodily
systems, in contrast, are to a degree a matter of fiat;14
they are boundaries inserted by human beings – like
the boundaries between the midbrain, pons, medulla
and spinal cord – for the purposes of constructing
predictively powerful causal theories.
Why, then, do we partition the body into its
maximal elements in just the way that we do? To
answer this question we need to introduce a further
notion, that of criticality (a term which we use in a
somewhat non-standard sense). The human body has
a great deal of redundancy; this means that many of
its elements can cease to function for longer or
shorter periods and yet the human being still survive.
Some elements, however, are critical; if they are not
present, or if their functions are not executed, then
the body dies. We can define this notion more precisely as follows:
An item X is a critical element for an organism Y if
and only if:
(i) X is an element of Y
(ii) there is a proper function F of X;
(iii) X performs F and no other part of Y performs F;
(iv) the continuing to exist of the organism Y is
causally dependent on the continued performance by
X of F.
Of course there are critical functions performed also
by single organs of the body (for example the
maintenance of acid base by the kidney). Note,
however, that each single kidney is not itself in
normal circumstances a critical element of the human
organism. This is because of the presence of a second
kidney. More generally, we can assert that all
performance of critical functions by single organs
and other subsystem elements are contributions to the
performance of critical functions on a higher level of
granularity. Eventually we reach some maximal level,
where we are dealing with critical functions
performed by parts of the organism that are such as to
make a contribution to the functioning of no larger
part except the organism as a whole. We can then
define:
X is a bodily system for organism Y if and only if:
(i) X is a critical element for Y;
(ii) X is not a proper part of any larger critical
element for Y.
Of course, the body’s systems are, in spite of being
relatively causally isolated, still also massively causally interconnected. Thus if one system ceases to function then so also, by virtue of the ensuing death of
the whole organism, do all the other systems. Experience shows, however, that there is a sequentiality to
this interdependence, so that the pathologist is normally able to establish which system was responsible
for causing the organism’s life processes to cease.
CONCLUSION
The first piece of evidence for the correctness of our
account is that it yields a roster of bodily systems
which corresponds very well to those given in the
standard reference sources. Such sources do not, for
example, classify the visual and other perceptual
systems as bodily systems alongside those given in
our list above, and the majority do not separate out
the (male and female) reproductive systems at all.
The former are classified as modules of the nervous
system; the latter as modules of the urogenital system. This corresponds to the fact that the functioning
of the perceptual and reproductive systems are not
critical to the existence of the human organism
(though reproduction – and indeed perception – are
critical to the existence of the species as a whole).
Our approach suggests also how we might formulate
an explanation of the reason why some textbooks of
anatomy include both bones and joints in the skeletal
system, while others, including both the Nomina15
and the Terminologia Anatomica4 represent bones
and joints as two separate systems – and it may even
perhaps give us a means to determine which classification is correct. As we saw, there is a certain
sequentiality to the interdependence of bodily systems. If one system ceases to function, then others
will follow in its train and in a certain order. If two
putatively distinct systems always cease to function
simultaneously – as in the case of the pulmonary and
the systemic components of the circulatory system,
for example – then they are for this reason parts of
the same system rather than systems in their own
right.
As Rosse points out, ‘The practical benefit of explicitly defining a “system” in a knowledge source,
which is organized according to systems, is that the
definition can provide the logical basis for consistently assigning to the appropriate system those anatomical entities which share a set of inherent properties.’4 We have sought to set out some ontological
tools for providing an analysis of the needed sort, in a
way that will do justice to the way the term ‘system’
is used in existing standard sources while at the same
time providing the necessary degree of formal precision to provide the basis for an anatomical domain
ontology of the future.
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Acknowledgements: This work was supported by
the Alexander von Humboldt Foundation under the
auspices of its Wolfgang Paul Program. Our thanks
go also to David Hershenov, Anand Kumar, Ingvar
Johansson and Rainer Schubert.