From Achille Varzi and Laure Vieu (eds.), Proceedings of FOIS 2004.

International Conference on Formal Ontology and Information Systems, Turin, 4-6 November 2004

Beyond Concepts:
Ontology as Reality Representation
Barry Smith
Department of Philosophy, University at Buffalo, NY 14260, USA
Institute for Formal Ontology and Medical Information Science,
Saarland University, 66041 Saarbrücken, Germany

Abstract. There is an assumption commonly embraced by ontological engineers, an

assumption which has its roots in the discipline of knowledge representation, to the
effect that it is concepts which form the subject-matter of ontology. The term ‘con-
cept’ is hereby rarely precisely defined, and the intended role of concepts within on-
tology is itself subject to a variety of conflicting (and sometimes intrinsically inco-
herent) interpretations. It seems, however, to be widely accepted that concepts are in
some sense the products of human cognition.
The present essay is devoted to the application of ontology in
support of research in the natural sciences. It defends the thesis that ontologies de-
veloped for such purposes should be understood as having as their subject matter,
not concepts, but rather the universals and particulars which exist in reality and are
captured in scientific laws. We outline the benefits of a view along these lines by
showing how it yields rigorous formal definitions of the foundational relations used
in many influential ontologies, illustrating our results by reference to examples
drawn from the domain of the life sciences.

1 Idealism
It is a matter of considerable astonishment to ontology-minded philosophers that many
thoughtful members of the knowledge representation and related communities, including
many of those involved in the development of ontologies, have embraced one or other form
of idealist, skeptical, or constructionist philosophy. This means for example:
a) a view according to which there is no such thing as objective reality to which the
concepts or general terms in our knowledge representation systems would corre-
spond;
b) a view according to which we cannot know what objective reality is like, so that
there is no practical benefit to be gained from the attempt to establish such a corre-
spondence;
c) a view according to which the term ‘reality’ in any case signifies nothing more than
a construction built out of concepts, so that every concept-system would in principle
have an equal claim to constituting its own ‘reality’ or ‘possible world’.
Doctrines under all three headings nowadays appear commonly in the wider world under
the guise of postmodernism or cultural relativism, where they amount to a thesis according
to which the theories of objective reality developed by the natural sciences are nothing
more than cultural constructs, comparable to astrology or witchcraft. In the AI world they
are often associated with constructivist ideas, for example as propounded by Maturana [1],
who holds that even biology and physics do not reflect any objective reality but are de-
signed, rather, to help us adapt to a world which we ourselves create through our subjective
experiences.
Gruber notoriously defines ‘ontology’ as ‘a specification of a conceptualization’ [2],
and definitions in Gruberian spirit have been and still are accepted by most ontological en-
gineers. A recent example is provided by the website owlseek.com, which provides the fol-
lowing definition of ontology:
We can never know reality in its purest form; we can only interpret it through our senses and experi-
ences. Therefore, everyone has their own perspective of reality. An ontology is a formal specification of
a perspective. If two people agree to use the same ontology when communicating, then there should be
no ambiguity in the communication. To enable this, an ontology codifies the semantics used to represent
and reason with a body of knowledge.
Such views have become entrenched not least because much work in ontology rests on
practices predominant in the field of knowledge representation, where it is assumed as a
matter of course that knowledge representation has to do not with reality but rather with
concepts conceived as human creations.
A first argument for this assumption might be formulated as follows. Knowledge exists
in the minds of human subjects. Hence we can have knowledge of things in reality only in-
sofar as they are brought under the conditions which are the presuppositions of their being
taken up into our minds. Hence we can have knowledge not of entities as they are in them-
selves but only of our own concepts.
As David Stove points out, this argument has the same form as:
We can eat oysters only insofar as they are brought under the physiological and chemical conditions
which are the presuppositions of the possibility of being eaten. Hence we cannot eat oysters as they
are in themselves. [3]

A second argument starts out from the premise that what we now know to be errors
were in the past counted as belonging to knowledge. There are certainly among our current
beliefs some that are misclassified in just this way. Hence knowledge must be allowed to
comprehend also false beliefs, including false beliefs expressed by means of sentences in-
volving general terms (such as ‘phlogiston’ or ‘ether’) which refer to nothing in reality but
rather only to our own concepts.
The fallacious character of this argument rests on its failure to take careful account of
time. Certainly we know that false beliefs were once erroneously counted as belonging to
knowledge. But this does not prove that knowledge once comprehended false beliefs.
Rather it shows only that false beliefs were sometimes erroneously misclassified as knowl-
edge. Certainly part of what we currently count as knowledge is also mistakenly so classi-
fied. Yet the striking progress of science and technology (and its prodigiously cumulative
character) gives us every reason to believe that the broad mass of what we count as knowl-
edge today is classified correctly and that ‘ether’ and ‘phlogiston’ represent exceptions
rather than the general rule. The appropriate response to the problem of error is thus to cor-
rect our errors as we find them, and this is so whether we are building ontologies or are en-
gaged in any other type of scientific endeavor.
The response to the problem of empty general terms from the side of the concept-
centered view has been, in contrast, to guarantee that every term has a referent effectively
by insisting that all general terms refer in any case only to our concepts. Thus they abandon
the goal of coming to grips with reality and substitute instead the much more easily attained
goal of grasping conceptual entities that we ourselves have created.
In many contexts, of course, ontologists still deal with concepts, correctly, as analo-
gous to, though as more abstract than, the linguistic expressions with which they are asso-
ciated. Thus they talk of ‘defining’ concepts and of ‘mapping’ the concepts of different on-
tologies – understanding concepts effectively as tools (analogous to telescopes or micro-
scopes) which we can use in order to gain cognitive access to corresponding entities in real-
ity. Too often, however, there occurs an insidious shift in focus: concepts themselves be-
come the very subject-matter of ontology. The ontologist’s tools become transformed into
the very focus of his inquiries.
The influence of the concept-centered view is a product not merely of the roots of in-
formation systems ontology in the field of knowledge representation. It has become en-
trenched also in virtue of the fact that much work of ontology has been concerned with rep-
resentations of domains, such as commerce, law, or public administration, where we are
dealing with the products of human convention and agreement – and thus with entities
which are in some sense merely ‘conceptual’. [4]
Today, however, we are facing a situation where ontologies are increasingly being de-
veloped in close cooperation with those working at the interface between the informatics
disciplines and the empirical sciences, and under these conditions the concept-centered
view is exerting a damaging influence on the progress of ontology. In what follows I pre-
sent an analysis of the view and a sampling of some the problems which it brings in its
wake. I then sketch an alternative view of ontology as a discipline rooted in the representa-
tion of universals and particulars in reality.

2 On Defining ‘Concept’

That there are few convincing attempts to define the term ‘concept’ (and related terms such
as ‘conceptualization’ or ‘conceptual entity’) in the current literature of ontology follows in
part from the fact that these terms deal with matters so fundamental to our cognitive archi-
tecture (comparable in this respect to terms like ‘identity’ or ‘object’) that attempts to de-
fine them are characteristically marked by the feature of circularity. Such circularity is il-
lustrated for example by the Semantic Network of the Unified Medical Language System
(UMLS) [5], which defines idea or concept as: ‘An abstract concept, such as a social, reli-
gious or philosophical concept.’
Occasionally more elaborate definitions are offered:
Concepts, also known as classes, are used in a broad sense. They can be abstract or concrete, elementary
or composite, real or fict[it]ious. In short, a concept can be anything about which something is said, and,
therefore, could also be the description of a task, function, action, strategy, reasoning process, etc. [6]
This passage illustrates the way in which, in much of the relevant literature, concepts are
not clearly distinguished from either entities in reality or names or descriptions on the side
of language.
Another (randomly selected) example of this same confusion is provided by the Bio-
logical Pathways Exchange Ontology (BIOPAX), which defines ‘four basic concepts’: the
‘top-level entity class’ and ‘three subclasses: pathway, interaction and physicalEntity’. It
then provides for the top-level class entity the following definition: ‘Any concept that we
will refer to as a discrete unit when describing biological pathways, e.g. a pathway, interac-
tion or physicalEntity.’ [7]
The tendency to run together concepts and entities is found also in linguistics; for ex-
ample in passages like the following:
we are capable of constructing conceptual worlds of arbitrary complexity involving entities and phe-
nomena that have no direct counterpart in peripherally connected experience. Such are the worlds of
dreams, stories, mythology, mathematics, predictions about the future, flights of the imagination, and
linguistic theories. All of us have constructed many conceptual worlds that differ in genre, complexity,
conventionality, abstractness, degree of entrenchment, and so on. For many linguistic purposes all of
these worlds are on a par with the one we distinguish as “reality”. [8] (Emphasis added)
But where it may be acceptable for linguists’ purposes to run together cells and molecules
with whatever might be the ontological correlates of myths and fairy tales, such a distinc-
tion is indispensable when we embark on the development of ontologies in support of natu-
ral science.

3 The Linguistic Reading of ‘Concept’

The core reading of the term ‘concept’ in the knowledge representation and related litera-
tures starts out from the recognition that different terms – for example terms in different
languages such as ‘dog’, ‘chien’, and ‘Hund’ – may have the same meaning. ‘Concept’ is
then used in place of ‘name’ or ‘word’ as a device which allows us to abstract away from
incidental syntactic differences and focus instead on those sorts of relations between terms
which are important for reasoning. Sometimes the concept is explicitly identified with the
meaning that is shared in common by the relevant terms. Sometimes it is seen rather as
something psychological – something like an idea shared in common in the minds of those
who use these terms. Sometimes the concept is seen as a logical construct, for example as a
‘synset’ in WordNet terminology, i.e. as a set of words which can be exchanged for each
other salva veritate in given sentential contexts. [9]
One obvious problem with the concept-centered view of ontology is that it is difficult
to understand how ontologies could be evaluated on its basis. Intuitively, a good ontology is
one which corresponds to reality as it exists beyond our concepts. If, however, knowledge
itself is identified with knowledge of our concepts, and if an ontology is a mere specifica-
tion of a conceptualization, then the distinction between good and bad ontologies seems to
lose its foothold.
This problem would in other disciplines rightly be regarded as grievous. How, then, is
the linguistic reading able to retain its grip on its adherents? Only, I believe, because this
reading is rarely wielded without alien admixtures. ‘Concept’ is for example used in such a
way that it is assumed to carry also connotations normally associated with terms such as
‘property’, ‘kind’ or ‘universal’ – terms which in normal usage do not denote entities which
are the products of human cognition. It is this additional baggage which is responsible for
the preponderance of confused interpretations of ‘concept’ adverted to already above.
Could we, then, reform the literature of knowledge representation by enforcing the lin-
guistic reading in consistent fashion? Unfortunately not. For this would have the effect of
collapsing KR into a branch of psychology or anthropology, a discipline whose claim to the
effect that it is modeling the knowledge possessed by human subjects – rather than their
mere beliefs – would lose its force. For uses of language to express both true and false be-
liefs are, after all, from the linguistic perspective cut of one cloth. One is not capturing
knowledge when one describes the beliefs widely distributed in certain cultures pertaining
to concepts such as alien implant removal or Chios energy healing.

4 Is_a and the Linguistic Reading

On the linguistic reading the assertions of is_a and other relations between concepts are
assertions about meanings or ideas. A sentence like
lytic vacuole is_a vacuole
is, appearances notwithstanding, not an assertion about lytic vacuoles; rather it is an asser-
tion about language use. It tells us that the meaning associated with the name ‘lytic vacuole’
is narrower or more specific than the meaning associated with the name ‘vacuole’ by this or
that group of subjects.
 This interpretation is, as we would anticipate, especially common in work on terminol-
ogies and thesauri. There we are interested not in is_a relations in the strict sense (and not
in scientific laws), but rather only in various kinds of relations of ‘association’ between
concepts and in the networks which these form. Statistics-based pattern recognition tech-
niques can be applied to such networks in support of a range of information retrieval and
extraction tasks – and for these purposes it may be of no account that the concepts of which
such networks are formed fail to correspond to any external reality.
Note that matters are not essentially changed when the linguistic reading is given a pre-
cise technical specification, as for example in the Standard Upper Ontology, which defines
a SUO_concept as a tuple (p, t, d, [s]), in which
p is a predicate defined by a definition or axioms in KIF;
t is an English term (word or multiword phrase);
d is an English documentation which attempts to precisely define the term;
s is an optional English syntactic category represented by one of the following character strings:
“noun”, “intransitive verb”, “transitive verb”, [etc.] [10]
Here, too, sentences like ‘lytic vacuole is_a vacuole’ turn out to be transformed into sen-
tences which are not about vacuoles at all, but rather (somewhat implausibly) about set-
theoretic objects built out of syntactic strings as urelements.
Something similar applies also in the context of Description Logic (DL), where ‘con-
cept’ is standardly used as an abbreviation for ‘concept description’ (which – again some-
what confusingly – is not in its turn to be interpreted as meaning ‘description of a con-
cept’). [11] This means that in DL circles talk of concepts is talk of certain syntactic enti-
ties. Such talk is, to be sure, semantically motivated (in the sense of ‘semantics’ that we
know from Tarski and from set-theoretic model theory). Each DL concept description repre-
sents, with respect to any given interpretation, a collection of objects that are postulated as
sharing the property that is specified by the description. Even this does not provide an an-
chor for concepts in external reality, however, for the objects in question may be (and stan-
dardly are) merely abstract mathematical postulates. Thus when it is said that DL provides
the terms we use in ontologies with a ‘precise semantics’, then we should bear in mind that
the sense of ‘semantics’ at issue here involves recourse to a mathematical abstraction that is
far removed from our normal understanding of semantics as relating to the interplay be-
tween terms, meanings and corresponding entities in reality.

5 The Engineering Reading of ‘Concept’

The difficulties with the linguistic reading have led to the crystallization of a second, engi-
neering reading of ‘concept’, a reading best exemplified in the use of the term ‘conceptual
model’.
Sometimes conceptual modelers, even conceptual modelers developing applications in
support of research in the natural sciences, talk as though their business were modeling
data or information. [12] Were this to be the case, then the models themselves would be at
one remove from the underlying reality with which the scientists themselves have to deal.
Against this, however, we can note that the term ‘information’ – like the term ‘model’ (and
like the term ‘semantics’) – is itself subject to many of the same confusions that have be-
come associated with the term ‘concept’ in the KR and related literatures. Closer inspection
of actual modeling practice then reveals that the modelers in question are in fact concerned
with building models of entities in reality, thus for example with building models of the or-
ganization of the genome and not just of information about this organization contained in
this or that database.
 The term ‘concept’ itself, on the engineering reading, refers to entities that are created
by modelers. Concepts are creatures of the computational realm which exist (in some sense
hard to explain) through their representations in software, in UML diagrams, XML repre-
sentations, in systems of axioms, or what one will. Such creation of concepts need not be a
trivial matter. Not every collection of lines of code is interpretable as being associated with
a conceptual model. To count as thus interpretable the code must pass what we might call a
simulation test. This means that the code on execution must be such that there are relations
between inputs and outputs which match relations between corresponding entities in reality.
The relevant input- and output-concepts as joined together functionally by the software
must in this sense model, which means (we presume): stand in some sort of isomorphism to,
corresponding entities in reality. To the extent that the engineering reading of concepts
makes sense at all, therefore, it, too, must make appeal to reality as its exists outside our
minds.

6 An Ontological Turn

Good ontology and good modeling in support of the natural sciences can, we conclude, be
advanced by the cultivation of a discipline that is devoted precisely to the representation of
entities as they exist in reality.
In the framework of such a discipline – which would look very much like the discipline
of ontology as practiced by philosophers such as Aristotle [13], Ingarden [14], Chisholm
[15], Johansson [16] or Lowe [17] – we would talk not of concepts as linguistic or com-
puter artefacts but rather of universals, conceived as that in reality to which the general
terms used in making scientific assertions correspond. The particulars or tokens with which
we have to deal, for example when carrying out experiments in natural science, are the in-
stances of such universals which exist in the real world of space and time. The term ‘uni-
versal’ then signifies what the corresponding instances – for instance all whales, all en-
zymes – have in common. Universals are invariants in reality.
Universals and their instances enjoy hereby a symbiotic relationship: the one cannot
exist without the other. Statements like:
human is_a mammal
metabolism is_a physiological process
nucleus part_of cell
cell part_of eukaryotic organism
can be interpreted both as statements about universals and as abbreviated versions of state-
ments about the corresponding instances.
Statements like ‘whale is_a mammal’ or ‘regulation of protein kinase activity part_of
protein amino acid phosphorylation’ convey knowledge precisely because they represent
relations between entities in reality, relations to which the advance of science has given us
cognitive access but which themselves obtain independently of our cognitive activities.
They convey not extensional relations analogous to that of set-theoretic inclusion, but
rather law-like relations between universals of the sort that are discovered through scien-
tific research. [18]
Taking the reality of universals into account also gives us a means of coming to grips
with what constitutes the difference between good and bad ontologies:
Bad ontologies are (inter alia) those whose general terms lack the relation to corre-
sponding universals in reality, and thereby also to corresponding instances.
 Good ontologies are reality representations, and the fact that such representations
are possible is shown by the fact that, as is documented in our scientific textbooks,
very many of them have already been achieved, though of course always only at
some specific level of granularity and to some specific degree of precision, detail
and completeness. [19]
It seems, now, to be a presupposition of much work in the field of knowledge represen-
tation that something changes in this respect when we bring computers into play (when sci-
entific texts are supplemented by data stored electronically) – as if terms stored in com-
puters were for some reason incapable of relating to entities in reality in the same way as do
terms printed in scientific texts. When challenged to defend their assumption that computer
representations must be representations of special artefacts (‘concepts’, ‘models’, ‘strings’),
the adherents of such views – if I am understanding them correctly – defend themselves by
pointing out that real physical entities (cells, organisms, diseases) cannot be stored inside
the computer. This, however, is to reveal a simple misunderstanding of the nature of repre-
sentation. It is to make a mistake that is equal and opposite to that made by the academi-
cians of Lagago, who held that
since Words are only Names for Things, it would be more convenient for all Men to carry about them,
such Things as were necessary to express the particular Business they are to discourse on … which hath
only this Inconvenience attending it, that if a Man’s Business be very great, and of various kinds, he
must be obliged in Proportion to carry a greater bundle of Things upon his Back. [20]

7 Is_a as a Relation between Universals

A view of ontology as reality representation does not merely resolve certain broadly phi-
losophical confusions common on the part of information systems ontologists. It can also
provide a quite specific kind of practical help to those involved in building ontologies in
support of empirical science by offering the resources to provide formally rigorous defini-
tions of basic ontological relations.
Universals, we said, are instantiated by instances in space and time. A formal theory of
this instantiation relation is advanced in [21], [22] and [23]. It begins by drawing a primi-
tive distinction, within the realm of entities in general, between particulars and non-
particulars. Examples of particulars (individuals, tokens) are: you and me, the planet Earth,
this piece of cheese, your eating of this piece of cheese. Examples of non-particulars are
universals such as: human being, enzyme, butterfly, heptolysis, death. Universals (kinds,
types) thus come in different categories. Above all we can distinguish universals instanti-
ated by continuant objects (things, substances and their parts), and universals instantiated
by occurrent processes (activities, events). We shall confine ourselves in what follows to
the former.
A universal is defined as anything that is instantiated, and an instance as anything that
instantiates some universal. The relation of instantiation is hereby taken as primitive, and it
is specified axiomatically that it holds exclusively between instances and universals (in that
order). Note that it is not the case that all particulars are instances. This is because there are
what we might call junk particulars (for example the mereological sum of Bush’s right knee
and the pain in Clinton’s left leg) which instantiate no universal (or at least no universal
standing to other universals in relations captured by scientific laws).
We can now apply these ideas to the formal treatment of the is_a relation as this is used
for example in biomedical ontologies such as the Foundational Model of Anatomy [24], the
Gene Ontology [25], and other ontologies curated under the auspices of the Open Biologi-
cal Ontologies consortium [26].
 Standard definitions of ‘is_a’ conceive it in broadly set-theoretic terms: ‘A is_a B’ is
held to mean that the set of instances of A is a subset of the set of instances of B. The prob-
lem with this definition is, first of all, that it makes it difficult for us to do justice to the
temporal complexities of the relation between instances and universals and thus to take care
of false positives such as ‘adult is_a child ’. It makes it difficult also to take care of situa-
tions (for example in the area of embryology) where one and the same individual – for ex-
ample as larva and as butterfly – may be held to instantiate different universals at different
times. A second problem with the set-theoretic reading is that it admits of purely contingent
cases of class subsumption, as illustrated in:
dog owned by me is_a mammal weighing less than 200 Kg
dog in Leipzig is_a dog
and also of logically constructed cases of class subsumption, such as:
dog is_a dog or apple
dog and mammal is_a dog or apple
dog is_a non-cat
Cases of these sorts are surely not admissible as genuine is_a relations where we are at-
tempting to develop ontologies for purposes of supporting inquiry in disciplines like the life
sciences. For the task of such ontologies is to capture not contingent classifications (ef-
fected, for example, for administrative purposes) but rather scientific laws.
We can, however, by calling in aid the theory of universals and instantiation, formulate
a better definition of the ‘is_a’ relation which will exclude such spurious cases:
A is_a B if and only if: (1) A and B are universals, and (2) for all times t, if anything in-
stantiates universal A at t then that same thing must instantiate also the universal B at t.
The phrase ‘must instantiate’ here connotes: in virtue of a scientific law. Our proposed defi-
nition thus involves an essential departure not only from the concept-centered view but also
from the extensionalism of set-theory-based approaches, and thus also from the familiar
DL-based formalisms founded thereon.

8 Part_of as a Relation between Universals

The power of the universals-based methodology becomes still clearer when we turn to the
relation part_of, another relation widely used in current biomedical ontologies. For this
relation can be given no coherent interpretation at all when considered as a relation be-
tween concepts on either the linguistic or the engineering reading. What would it mean, af-
ter all, to say that ‘coccyx part_of vertebral column’ expresses a relation of the same type as
the is_narrower_than relation conceived as a relation between meanings? And what would
it mean to say that this statement expresses a relation between artefacts of a computer
model?
To understand ‘A part_of B’ we need first of all to call in aid the familiar mereological
parthood relation understood as a relation among particulars and illustrated by: ‘Jane’s
heart is part of Jane’s body’. We can then establish that assertions of the form ‘A part_of B’
in fact signify a variety of different sorts of relations among the instances of the corre-
sponding universals – relations which are often confusedly run together when understood
as relations between concepts. [27] Thus (and least interestingly for scientific purposes) it
can mean:
some instances of A are parts of some instances of B,
as in roof part_of car (WordNet), or acquired abnormality part_of bird (UMLS). More sig-
nificantly, for the purposes of ontologies designed to support the needs of scientific re-
search, A part_of B can express relations between universals such as:
A part_ for B, which asserts (i) that if an instance of A exists at a given time, then an
instance of B exists at this same time and (ii) that the former is an instance-level
part of the latter. A part_ for B thus provides information primarily about the As; it
tells us that As do not exist except as instance-level parts of Bs. Examples: nucleus
part_ for cell; human testis part_ for human being.
B has_ part A, which asserts (i) that if an instance of B exists at a given time, then
an instance of A exists at this same time and (ii) the latter is an instance-level part of
the former. B has_part A thus provides information primarily about the Bs; it tells us
that Bs do not exist except with As as instance-level parts. Examples: woman has_
part heart; cell has_ part membrane.
A reading of part_of as a relation between universals which suggests itself against this
background would see this relation as a combination of part_ for with has_ part. Thus:
A part_of B obtains if and only if, (i) for any instance x of A existing at some time t,
there is some simultaneously existing instance y of B which is such that x stands to y
in the instance-level part relation, and (ii) vice versa for any instance y of B.
This implies a strong structural tie between the universals A and B: the one can be instanti-
ated only hand in hand with the other. Examples: cell membrane part_of cell; human brain
part_of human being.
The resultant framework gives us the resources to formulate definitions also of time-
dependent part-relations between universals for example of the type expressed in a state-
ment to the effect that a notochord is part of a mammal only in the embryonic state. Thus it
allows us also to add improvements to existing lexical resources in other fields, for example
by adding to WordNet the facility to deal with what one might call ‘optional’ body parts
such as warts and freckles, and with ‘temporary optional’ body parts such as fetuses or five-
o’clock shadow.

9 Relations in the UMLS Semantic Network

The framework outlined above illustrates the degree to which, when we move beyond the
domain of concepts to the realm of universals and particulars in a changing reality, formal
distinctions become apparent which have been too often glossed over. It also provides us
with a guiding thread as to the approach that needs to be adopted to provide formally rigor-
ous definitions also of those other relations – such as ‘causes’, ‘is_a_realization_of ’, ‘par-
ticipates_in’, ‘develops_ from’, ‘derives_ from’, and so on – which are standardly employed
in the construction of ontologies in the life sciences. To see why a coherent formal treat-
ment of such foundational relations is needed if ontologies are to be developed which are
capable of supporting scientific inquiry in an area such as biomedicine, consider the treat-
ment which they currently receive in the UMLS Semantic Network (SN), described as an
‘upper level ontology for the biomedical domain’ [5].
SN is a graph-theoretic structure that is designed to unify the 975,354 ‘concepts’ and
2.4 million ‘concept names’ of the UMLS Metathesaurus, itself one of the most important
tools of inquiry in the domain of biomedical informatics. Inspection reveals that the major-
ity of the 54 relations contained in SN are subject to problems even more serious than those
affecting traditional treatments of ‘part_of ’.
 Table 1 consists of randomly selected examples of the 6000 or so edges which form the
SN conceived as graph-theoretical structure. These examples nicely illustrate the dubious
assertions which arise when one adopts a purely linguistic reading of ‘concept’, and at the
same time they reveal that great difficulties will be set in the way of anyone who attempts
to establish what it is, in reality, to which SN’s relation-types correspond. In what sense
does a mental process precede a genetic function? In what sense does an antibiotic cause an
experimental model of a disease?

Table 1. Semantic Relations from the UMLS Semantic Network, with definitions and selected examples

precedes: occurs earlier in time

Cell Function precedes Cell Function Mental Process precedes Genetic Function
Mental Process precedes Molecular Function Experimental Model of Disease precedes Cell or Molecu-
lar Dysfunction
Molecular Function precedes Mental Process

affects: produces a direct effect on. Implied here is the altering or influencing of an existing condition,
state, situation, or entity

Acquired Abnormality affects Fish Experimental Model of Disease affects Fungus

Physiologic Function affects Reptile Experimental Model of Disease affects Genetic Function

causes: brings about a condition or an effect. Implied here is that an agent, such as for example a
pharmacologic substance or an organism, has brought about the effect

Food causes Experimental Model of Disease Manufactured Object causes Disease or Syndrome
Biomedical or Dental Material causes Mental Vitamin causes Injury or Poisoning
or Behavioral Dysfunction
Bacterium causes Pathologic Function

location_of: the position, site, or region of an entity or the site of a process

Gene or Genome location_of Fungus Organization location_of Diagnostic Procedure

Fungus location_of Vitamin Tissue location_of Mental or Behavioral Dysfunction

10 From Names to Objects

Such questions are not otiose. They cut to the very heart of ontology as a tool of contempo-
rary biomedical informatics. Consider, for example, what the molecular biologist Sydney
Brenner has to say in his critical comments on the Gene Ontology, published under the title
“Ontology Recapitulates Philology”. [28] Brenner first of all accepts that we ‘need a theo-
retical framework in which to embed biological data’ so that the endless streams of data
currently being assembled through biomedical research ‘can be sifted and abstracted.’ He
then goes on to insist, rightly, that ‘the network we should be interested in is not the net-
work of names but the network of the objects themselves.’ (Emphasis added.)
At the same time, however, he asserts that it is only when exploring reality at the
granularity of molecules that one has to do with objects. Only there, he tells us, do objects
‘have their own names: they are chemical names written in the language of DNA se-
quences’. Brenner unfortunately reveals hereby that (like the academicians of Lagago) he,
too, has a very weak understanding of the relation between a name and its denotatum. At
the same time he denies what the Gene Ontology correctly recognizes, namely that biologi-
cal reality can be grasped in adequate fashion only by taking entities at a multiplicity of dif-
ferent granularities into account.
Where the Gene Ontology goes wrong is in its failure to provide even the beginnings
of a formal architecture for its is_a and part_of relations and thus also – since granular hi-
erarchies are structured via part_of relations – for its treatment of the different granular lev-
els which fall within its scope. [29] And if the argument presented above is correct, then
this lack of an adequate formal treatment of relations, which is manifested also by the
UMLS SN, flows precisely from a failure to penetrate beyond the realm of concepts lin-
guistically conceived to the world of universals and their instances in spatiotemporal real-
ity. It is thus especially poignant that Lawrence Hunter, in his response to Brenner on behalf
of GO [30], asserts that ‘the essence of the Gene Ontology project ... and of other knowl-
edge-bases of molecular biology [such as] the Unified Medical Language System, is not in
the list of names they embody, but in the relationships they represent’. For as has been re-
peatedly pointed out, it is these very relationships which are currently dealt with so inco-
herently in the knowledge-bases mentioned.
As Hunter points out, ontologies are designed primarily for use not by human beings
but rather by computer programs in order to accomplish complex inference tasks. This
however, as he also points out, ‘requires the presence of a well represented knowledge-base
of molecular biological entities.’ If neither the Gene Ontology nor the UMLS as a whole yet
comprehends a well-represented knowledge-base of the needed sort, then this is at least in
part because they have been constructed within an ontological framework in which the nec-
essary coming to grips with entities in reality has been blocked by the focus on their lin-
guistic surrogates in the realm of concepts.

Acknowledgements
Work on this paper was carried out under the auspices of the Wolfgang Paul Program of the Alexander von
Humboldt Foundation, the EU Network of Excellence in Medical Informatics and Semantic Data Mining, and
the Project “Forms of Life” sponsored by the Volkswagen Foundation. Thanks go also to Bill Andersen,
Sebastian Brandt, James Cimino, Dirk Siebart and Leo Zaibert for helpful comments.

References

[1] Humberto R. Maturana and Francisco J. Varela, The Tree of Knowledge: The Biological Roots of Human
Understanding, 1998, Shambhala Publications, Boston MA
[2] T. R. Gruber, A Translation Approach to Portable Ontologies, Knowledge Acquisition, 5: 199-220, 1993.
[3] James Franklin, Stove’s Discovery of the Worst Argument in the World, Philosophy, 77: 615-24, 2002.
[4] Andrew Frank, Ontology: A Consumer’s Point of View, Spatial and Temporal Reasoning, ed. Oliviero
Stock, Kluwer, Dordrecht, 1996.
[5] Alexa T. McCray, Representing biomedical knowledge in the UMLS semantic network, High perform-
ance medical libraries: Advances in information management for the virtual era, 45-55, 1993.
[6] Oscar Corcho and Asuncion Gomez-Perez, A Roadmap to Ontology Specification Languages, in Rose
Dieng and Olivier Corby (eds.), Knowledge Engineering and Knowledge Management. Methods, Mod-
els and Tools, Springer, Berlin, 80-96, 2000.
[7] http://www.biopax.org/Downloads/Level1v0.5.2/biopax-level1-v0.5.2_Ontology_Documentation.pdf.
[8] Ronald Langacker, Foundations of Cognitive Grammar, Stanford University Press, 1987/1991.
[9] Christiane Fellbaum, ed., WordNet: An Electronic Lexical Database, Cambridge, MA: MIT Press, 1998.
[10] http://suo.ieee.org/email/msg01175.html
[11] Franz Baader, Diego Calvanese, Deborah McGuinness, Daniele Nardi, and Peter Patel-Schneider, Edi-
tors, The Description Logic Handbook: Theory, Implementation and Applications, Cambridge Univer-
 sity Press, Cambridge, 2003.
[12] Norman S. Paton, et al., Conceptual Modelling of Genomic Information, Bioinformatics, 16: 6, 548–
557.
[13] S. Marc Cohen, Aristotle’s Metaphysics, Stanford Encyclopedia of Philosophy, http://plato.stanford.-
edu/entries/aristotle-metaphysics.
[14] Roman Ingarden, Der Streit um die Existenz der Welt, Tübingen: Niemeyer, 3 volumes, 1964/1965/1974.
[15] Roderick M. Chisholm, A Realistic Theory of Categories: An Essay on Ontology, Cambridge: Cam-
bridge University Press, 1996.
[16] Ingvar Johansson, Ontological Investigations. An Inquiry into the Categories of Nature, Man and Soci-
ety, Frankfurt: Ontos, 2004.
[17] E. J. Lowe, A Survey of Metaphysics, Oxford: Oxford University Press, 2002.
[18] David M. Armstrong, Universals and Scientific Realism, Volume 1: Nominalism and Realism, Volume
2: A Theory of Universals, Cambridge: Cambridge University Press, 1978.
[19] Thomas Bittner and Barry Smith, A Theory of Granular Partitions, in: M. Duckham, et al. (eds.), Foun-
dations of Geographic Information Science, Taylor & Francis, London, 117-151, 2003.
[20] Jonathan Swift, Gulliver’s Travels, Part III, A Voyage to Laputa, Balnibarbi, Luggnagg, Glubbdubdrib
and Japan, Chapter V, 1726/1735.
[21] Jan Berg, Aristotle’s Theory of Definition, ATTI del Convegno Internazionale di Storia della Logica,
San Gimignano, 4–8 December 1982, Bologna: CLUEB, 1983, 19–30.
[22] Barry Smith, The Logic of Biological Classification and the Foundations of Biomedical Ontology, in:
Dag Westerstahl (ed.): Invited Papers from the 10th International Conference in Logic, Methodology
and Philosophy of Science, Oviedo, Spain, 2003.
[23] Fabian Neuhaus, Pierre Grenon and Barry Smith, A Formal Theory of Substances, Qualities, and Uni-
versals, in this volume.
[24] C. Rosse and J. L. V. Mejino, A Reference Ontology for Bioinformatics: The Foundational Model of
Anatomy. Journal of Biomedical Informatics, 36: 478-500, 2003.
[25] http://www.geneontology.org/
[26] http://obo.sourceforge.net/
[27] Barry Smith and Cornelius Rosse, The Role of Foundational Relations in the Alignment of Biomedical
Ontologies, Proceedings of Medinfo, 2004.
[28] Sydney Brenner Life Sentences: Ontology Recapitulates Philology, Genome Biology 3 (4):1006.1-
1006.2, 2002.
[29] Barry Smith, Jacob Köhler and Anand Kumar, On the Application of Formal Principles to Life Science
Data: A Case Study in the Gene Ontology, Proceedings of DILS 2004. Data Integration in the Life Sci-
ences (Lecture Notes in Computer Science 2994). Springer, Berlin, 124-139, 2004.
[30] Lawrence Hunter, Ontologies for Programs, Not People, Genome Biology 3 (6): 1002.1–1002.2, 2002.