=Paper=
{{Paper
|id=Vol-3939/paper3
|storemode=property
|title=Grounding Realizable Entities
|pdfUrl=https://ceur-ws.org/Vol-3939/paper3.pdf
|volume=Vol-3939
|authors=Michael Rabenberg,Carter Benson,Federico Donato,Yongqun He,Anthony Huffman,Shane Babcock,John Beverley
|dblpUrl=https://dblp.org/rec/conf/icbo/RabenbergBDHHBB24
}}
==Grounding Realizable Entities==
https://ceur-ws.org/Vol-3939/paper3.pdf
Grounding Realizable Entities
Michael Rabenberg,1,2* Carter Benson,1,3 Federico Donato,1,3 Yongqun He,4 Anthony
Huffman,4 Shane Babcock1,5, John Beverley1,3,6
1 National Center for Ontological Research, USA
2 University at Buffalo Department of Biomedical informatics, USA
3 University at Buffalo Department of Philosophy, USA
4 University of Michigan Medical School, USA.
5 KadSci LLC, USA
6 Institute for Artificial Intelligence and Data Science, USA
Abstract
Ontological representations of qualities, dispositions, and roles have been refined over the past
decade, clarifying subtle distinctions in life science research. After articulating a widely-used
characterization of these entities within the context of Basic Formal Ontology (BFO), we identify gaps
in this treatment and motivate the need for supplementing the BFO characterization. By way of
supplement, we propose definitions for grounding relations holding between qualities and
dispositions, and dispositions and roles, illustrating our proposal by representing subtle aspects of
host-pathogen interactions.
Keywords
Basic Formal Ontology, realizable entity, disposition, role, grounding 1
1. Introduction
The prevalence of “roles” in contemporary life science literature is hard to overstate. Molecules
are said to play roles in molecular transitions; enzymes play roles in metabolism; pacemakers
play roles in heart rhythm regulation. Despite such prevalence, “role” is used in widely different
ways across and within life science domains [1]. Some treat “role” as something a function can
play, e.g. “role of mitochondria function” [2]. Others treat “role” as a type of function, e.g.
“causal role function” [3]. Still others claim “role” refers to an ahistorical description of how an
entity contributes to a complex system [4]. Varied uses of the same term run the risk of creating
confusion when there is a need for researchers to communicate across disciplines or indeed
within a single discipline. The risk of confusion is exacerbated given the sheer volume of data
across life science domains, more than can be mastered by a single individual in a lifetime. And
while advances in computing, artificial intelligence (AI), machine learning, and so on, may hold
the promise of automating detection of semantic differences and similarities in life science
domains, training algorithms employed on training sets using the same label for semantically
15th International Conference on Biological and Biomedical Ontology, July 17–19, 2024, Enschede, The Netherlands
∗ Corresponding author.
† These authors contributed equally.
rabenbergm@gmail.com (M. Rabenberg); carterbe@buffalo.edu (C. Benson); fdonato@buffalo.edu (F. Donato);
yongqunh@med.umich.edu (Y. He); huffmaar@umich.edu (A. Huffman); sbabcock@kadsci.com (S. Babcock);
johnbeve@buffalo.edu (J. Beverley)
0000-0001-9004-5322 (M. Rabenberg); 0009-0006-5880-7503 (C. Benson); 0009-0001-6600-240X (F. Donato); 0000-
0001-9189-9661 (Y. He); 0000-0002-0576-550X (A. Huffman); 0000-0003-0798-114X (S. Babcock); 0000-0002-1118-
1738 (J. Beverley)
© 2024 Copyright for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
CEUR
ceur-ws.org
Workshop ISSN 1613-0073
Proceedings
different phenomenon can only do so much [5]. Further advances must leverage, we maintain,
knowledge representation methodologies in general, and ontology engineering in particular.
Ontologies are widely used in bioinformatics and biomedical data standardization, supporting
data integration, sharing, reproducibility, and automated reasoning [6]. Thus, in the interest of
promoting clarity, AI-ready life science data, and semantic interoperability, we aim to improve
on an ontological characterization of “role” and nearby phenomena.
More specifically, our goal in this piece is to cut through existing ambiguity in life
science research and debates in ontological circles over the use of “roles” by supplementing
what we take to be the best candidate interpretation of this term within the context of the widely
used Basic Formal Ontology (BFO) [7]. Despite the virtues of the BFO characterization, we argue
the treatment of roles and related entities in BFO leaves several important questions
unanswered, and in doing so, obscures the - sometimes - subtle value offered by the BFO’s
definitions. To bring this value to light, we propose introducing grounding relations holding
between roles and other dependent entities, such as dispositions and qualities. In defining
precise ontological relationships among these terms, we will illustrate to stakeholders how they
are intended to relate, providing guardrails for the use of both the terms and relationships
among them. To illustrate the value of our proposal, we apply our results to one rather
complicated modeling task: host-pathogen interactions.2 Our application demonstrates how
appealing to grounding relations holding between properties can provide clarity when
modeling even the most complex phenomena ontologists and researchers face.
1.1 Basic Formal Ontology
The Open Biomedical and Biological Ontologies (OBO) Foundry was created to provide
guidance for ontology developers and promote alignment and interoperability while structuring
life science data [7]. Basic Formal Ontology (BFO) has, for decades, been the designated OBO
top-level ontology, providing life science researchers a highly general terms, such as quality,3
process, function, and role, and relations, such as participates in and member of, which
form a common starting point from which to extend to more specific terms and relations [7, 8].
At present count, BFO is used by over 600 open-source ontology projects [9], many of which
aim to conform to OBO principles. Additionally, BFO is the first ISO/IEC approved top-level
ontology standard 21838-2 [10], provides the foundation for the Industrial Ontologies Foundry
[11], the Common Core Ontologies [12] suite, and is the “baseline standard” for ontology
development across U.S. defense and intelligence agencies [13]. Given its wide use,
standardization, and well-developed ontological structure, and existing characterization of roles
and nearby phenomena, BFO is a natural starting point for exploring a more robust ontological
characterization of these entities.
2 In future work we anticipate applying our results to additional modeling tasks, including ones in quantum
biology. An earlier version of this paper contained some such applications; space limitations prevent us from
including them in the present article. The earlier version is accessible here: https://osf.io/preprints/osf/cbqyj.
3We adopt the convention of signifying BFO terms and relations in bold. Class names in BFO are always singular,
i.e. “material entity” rather than “material entities”. Plural class names in the text should be understood as
shorthand for “instances of class X”.
Figure 1: Basic Formal Ontology Hierarchy
BFO divides reality into disjoint categories of continuant and occurrent [8].
Continuants lack temporal parts and exist entirely at any time at which they exist at all.
Occurrents, in contrast, have temporal parts and so are often stretched along a temporal axis.
BFO adopts several further subclasses of continuant and occurrent. Figure 1 displays the
complete BFO hierarchy where “A is_a B” means “instances of class A are instances of class B”.
This paraphrase, moreover, reflects BFO’s distinguishing between instances, e.g. red on this
apple, and classes, e.g. the class of red things. In this paper we focus on only those BFO entities
relevant to the discussion of role.
1.2 Realizable Entities
In BFO, all instances of specifically dependent continuant, including instances of quality
and realizable entity, depend for their existence on other entities. Instances of quality are
distinguished from those of realizable entity, however, in that while instances of the former
are fully manifested whenever they exist, the latter are not. For example, a red apple bears a
quality, an instance of the color red. This color will manifest in its entirety whenever it
manifests at all. Qualities need not be of single bearers; the class relational quality covers,
for example, instances that depend on more than one bearer, such as a relational quality of love
that depends on the lovers, or some contractual relationship that depends on the people
involved in it.
An apple plausibly also bears a tendency to decay if left in the heat, but this feature of
the apple need not manifest for the apple to bear it. In BFO, what the apple also then bears, is
an instance of realizable entity [14]. When investigating the natural world, identifying
whether an apple might decay often involves attention to what similar types of entity have done
in the past under similar environmental conditions, and prediction about what similar types of
entity will do in the future. Instances of realizable entity can be understood as underwriting
connections between what has happened and what may happen. Identifying instances of
realizable entity thus requires attention to empirical evidence and inference to the best
candidate explanatory mechanism. Instances of realizable entity always have some bearer on
which they depend, which may participate in processes which realize the realizable entity.
Instances of realizable entity may thus remain, in a sense, dormant. For example, a piece of
sodium chloride need not ever dissolve if placed in unsaturated water. Instances of realizable
entity are, in this respect, how BFO characterizes apparent modal and probabilistic features of
reality.
There are further divisions to be drawn within the class. A student, for example, appears
to bear a realizable entity insofar as they may or may not participate in processes associated
with being a student. The sense in which a student bears a realizable entity is distinct from
the sense in which salt is soluble. In the interest of capturing this distinction, BFO divides
realizable entity into subclasses of disposition and role. The former is captured as [8]:4
d is a disposition =def (i) d is a realizable entity & (ii) d’s bearer is some material
entity & (iii) d is such that, if it ceases to exist, then its bearer is physically changed &
(iv) d’s realization occurs because this bearer is in some special physical circumstances
& (v) this realization occurs in virtue of the bearer’s physical make-up.
Instances of disposition are said to be “internally grounded”, which reflects the fact that were
the instance to cease to exist, then its bearer would be materially changed in some manner. For
example, if a piece of sodium chloride is soluble at some time, then not soluble at another, there
must be some change to its physical structure. In this sense, instances of disposition are not
optional for bearers. Realizations of instances of disposition occur, moreover, owing to the
physical structure of the bearer – determined by its qualities - and the fact that the bearer is in
some special environment, where “special” means an environment the material bearer is not
always in [8]. Turning again to the solubility of a piece of sodium chloride, the realization of its
disposition occurs owing to the lattice structure and bonding forces of the material entity
when placed in unsaturated water, which has its own bonding forces. Figure 2 illustrates these
features of sodium chloride solubility using the resources of BFO.
Figure 2: A portion of NaCl manifesting its solubility disposition in a portion of H2O5
Role is a disjoint sibling class of disposition, and so a realizable entity, but one with
characteristics sharply distinguishing it from its sibling [13]:6
4Talk of dispositions is also quite common in life science research. Brønsted-Lowry acids are said to be “disposed” to
donate protons, infected patients are “disposed” to manifest symptoms of disease, and so on. Parallel to debates
over “roles”, there are persistent debates over “disposition,” both in terms of ambiguity in the life science literature
and extant debates among ontologists [15].
5This diagram emphasizes one dimension of the chemical interaction, namely, the electronegativity of H2O and
electropositivity of NaCl. A more detailed picture would have electropositive dispositions inhering in instances of
Na+, and H+, and electronegative dispositions inhering in Cl- and O-.
6We note in passing that there remain debates among ontologists as to how understand “role” [16, 17].
r is a role =def (i) r is a realizable entity & (ii) r exists because there is some single bearer
that is in some special physical, social, or institutional set of circumstances in which this
bearer does not have to be & (iii) r is not such that, if it ceases to exist, then the physical
make-up of the bearer is thereby changed.
In contrast to disposition, instances of role are thus optional in the sense that bearers may
gain or lose them without alteration to their physical structure. A student, for example, who
graduates from a university no longer bears the role of student at that institution. That does
not, however, imply any physical change in the student. The individual, moreover, need not
have been involved in that social circumstance at all. Put another way, whether an entity bears
a role or not depends largely on what happens external to the entity. Related, roles may be
borne by entities that do not have material matter as parts, i.e. immaterial entities, such as
boundaries and sites. For example, the northern border between the U.S. and Canada plays a
role in economic, immigration, and political policy for respective nations. The border itself is,
however, not to be identified with any material entity, though its location may be determined
by, say, geographical features between these countries. Dispositions cannot be borne by
immaterial entities since immaterial entities do not have physical bases.
1.3 The BFO Treatment
The BFO characterization of disposition and its disjoint sibling class role tracks the following
important distinctions (inter alia): (i) non-optional vs. optional; (ii) physical basis vs. non-
physical basis; (iii) internally-grounded vs. externally-grounded. Call this the BFO Treatment.
While the BFO Treatment provides classes and relations reflecting many aspects of these
distinctions, there are noticeable gaps.
At a high level, little has been said about relationships among instances within each
BFO class, such as the relationship between an employee role and a teacher role in a university
[18] or the dispositional relationship between polar molecules [8]. Second, little has been said
concerning relationships across classes, e.g. the relationship between a student role and the
student’s disposition to participate in coursework. Third, little has been said about
relationships among instances – either within or across each class – at different levels of
granularity, e.g. the relationship between the solubility of a molecule and the qualities born by
its atomic structure [19]. This last point is worth elaborating as the dispositions a material
entity bears are determined by some collection of qualities inhering in the bearer [14].7
Although BFO adopts the inheres in relation holding between – among other things –
instances of quality and instances of material entity, there is no corresponding relation
holding between a given disposition and qualities in which it is grounded.
Ontology developers may be susceptible to – at best – ignoring these gaps or – at worst
– modeling errors in specific domains. It is our position that supplementing the BFO Treatment
with additional relationships among these classes, will help minimize user confusion and
ontological errors. To sharpen our focus, we turn to explications of challenging modeling cases
involving roles and related phenomena, to further motivate and highlight gaps in the BFO
Treatment.
7There is no “bare matter” which lacks qualities in BFO [20, 21].
2. Methods
Development of the needed grounding relations proceeds by reflection on examples relevant to
life science researchers. Careful analysis of entities which should be modeled ontologically in
such cases, provides insight into features that these grounding relations must have. In general,
such relationships may be quite complex. Realization of, say, the disposition of sodium chloride
to dissolve, affects the material structure of the system, and depends on realizations of
dispositions borne by the other constituents.
Case 1: Sodium chloride is soluble because of its lattice structure, a specific quality
that it may lose at a time while remaining soluble, assuming the new structure
it exhibits permits solubility. Sufficient changes to the lattice structure may
result in sodium chloride no longer being soluble.
Properties may exhibit determinate-determinable structure [22, 23]. For example, an entity
bearing color (determinable) may bear different colors over time (determinate). Dispositions
also appear to exhibit determinate-determinable structure. Sodium chloride bearing a solubility
disposition (determinable) may bear different degrees of solubility over time (determinate).
Notably, in this example the determinable solubility appears to depend on determinate shapes,
i.e. lattice structures, borne by the sodium chloride over time. Sufficient change in determinate
shape may result in the loss of determinable or determinate solubility dispositions. As with
other determinate properties, where cutoffs exist between one determinate disposition, and
another is an empirical question. That there may be no sharp cutoff is a feature of determinates
[23]. Most importantly for our purposes, some collection of qualities makes it possible for a
disposition to inhere in the bearer.
Case 2: A university comprises, as mereological parts, administrative staff, educators,
students, etc. each of which bears roles as member of the university, and these
roles are correlated with various duties. A student, say, graduating from a
university is no longer mereological part of the university. That is, a
departing student results in material change of the university but may also
lead to a change in the role the university has towards the student.
Universities can be understood as instances of BFO object aggregate, a material entity
consisting solely of object member parts. Consequently, universities plausibly bear instances
of quality and realizable entity, much like other material entities. Individuals gain and lose
student roles – and so membership as part of a university – without material change to
themselves. The loss of students, however, results in material change to a university. Sufficient
loss of students, additionally, may even result in loss of realizable entities borne by the
university itself, such as the role of a degree-granting institution. This suggests there are
scenarios in which a university may lose a role while exhibiting change of physical basis
through the loss of material parts. This parallels the dependence of dispositions on their
physical basis,8 suggesting a nuanced relationship between mereological parts of aggregates,
roles, and dispositions that has as of present not been explored. From another direction, there
is plausibly an instance of BFO’s relational quality holding between the student and the
university, which underwrites the role the former has. Once the individual is no longer a
8 It is compatible with the BFO Treatment that entities bear both a disposition and a role. The heart of a gazelle
might bear a disposition to pump blood, but in other circumstances may play the role of dinner for a carnivore.
student, the relation between the individual and the university is eliminated. That is, there is a
qualitative change to the university. Indeed, in any case of a student leaving university there
will be such qualitative change.
Case 3: In commensal relationships, like the one between a small baitfish swimming
under the protection of a larger manta ray, one organism benefits while the
other is neither benefitted nor harmed. If one organism leaves the
relationship, it need not be physically changed, but the aggregate of the pair
will lose a physical part.
This case is similar in structure to Case 2. But where students are mereological parts of
a larger whole that exists after they depart, in this case the commensal aggregate no longer
exists after a member departs. Each member of the pair bears a commensal role realized in
commensal processes, which in our marine example is that of being protected and that of being
a protector. The pair comprises an object aggregate, and each bears a respective commensal
role insofar as they are members of the aggregate, which is easy to see when the baitfish departs
from the manta ray and loses its protection, while no material part in its body or in that of the
manta ray is necessarily changed. Though each may lose their respective role without being
physically changed, the aggregate losing a mereological part results in a physical change, both
in terms of matter and dispositions borne by the aggregate. As before, the grounds of each role
might be understood in terms of relational qualities holding between the organisms. The
organisms together comprise an object aggregate in which the relational quality, the relation
of protecting, for example, inheres. Thus, when we describe an organism as bearing a
commensal role, this is to say it bears a realizable entity grounded externally, in the sense that
it is a proper part of some aggregate and other members of that aggregate partially ground the
realizable entity.
These cases illustrate a variety of relationships involving disposition, role, and
quality classes. Our characterizations of these cases highlight lines along which we may
address gaps in the BFO Treatment of these entities. Case 1 illustrates the need for analyzing the
relationship between dispositions and the qualities on which they depend. Case 2 and Case 3
highlight the need for clarifying relationships between aggregates, properties which they bear,
properties borne by and among constituents. From our perspective, these cases illustrate a need
for precise explication of varieties of grounding at play in these examples. We turn next to
regimenting talk of grounding to supplement the BFO Treatment.
3. Results
Given the definitions of role and disposition in BFO, it seems clear that the latter can exist
without the former. This, at least, seems intuitive when we restrict our attention to material
entity bearers. A portion of water, for instance, bears many dispositions, but may not bear
any role at a given time. That said, any given instance of role does seem to depend on some
instance of disposition. It seems, moreover, that any instance of disposition must ultimately
depend on some instance of quality or collection of qualities. This observation is motivated
by the plausible assumption that entities bearing qualities can causally affect the world in some
manner, which would be understood as the realization of some instance of disposition. Indeed,
what would it mean to say some entity bears instances of quality but no instance of
disposition? Much like we are hard-pressed to come up with an example of a bearer lacking
all instances of quality, so too are we hard-pressed to come up with an example of a bearer
lacking all instances of disposition.
1.1. Regimenting Grounding
Case 1 illustrates how a realizable entity inhering in a material entity depends on the
presence of a quality inhering in that material entity. More specifically:
x dependence grounded in y =def x is a realizable entity and y is some specifically
dependent continuant of type T and x inheres in b at t because determinates of y inhere
in b at t.
Dependence grounding captures Case 1. For example, a piece of sodium chloride is an instance
of material entity which bears an instance of disposition, which may manifest in dissolving
processes. There is, moreover, some instance of a determinate shape quality inhering in the
molecule of sodium chloride, on which the sodium chloride’s disposition to dissolve depends.
Were there no such instances of determinate shape quality of the relevant sort, then the portion
of sodium chloride would not bear a disposition to dissolve.
Case 2 and Case 3 appear to exhibit a distinct variety of mereological dependence, in
which the mereological parts of entities influence the presence or absence of realizable entities:
x mereologically grounded in y at t1 =def x is a realizable entity inhering in material entity
y with proper part z at a time t1 and were y to become disjoint from z at some t2 later than
t1 then x does not inhere in y at t2
Mereological grounding applied to Case 2 makes sense of the fact that the loss of a sufficient
number of students as mereological parts of the university may be accompanied by loss of some
role inhering in the university. Similarly, mereological grounding makes sense of Case 3 as the
commensal aggregate loses both dispositions and mereological parts following dissolution of
the commensal relationship. We highlight roles given the lacuna in the literature, but it is worth
observing mereological grounding can equally make sense of aggregates losing parts which bear
instances of disposition, resulting in the aggregate losing a distinct instance of disposition.
For example, a heart valve is disposed to expand and contract based on its elasticity, the loss of
which, would undermine the heart of which it is mereological part, and which bears be a blood
pumping disposition.
Mereological grounding can be explained in terms of dependence grounding. A
university bearing a disposition that depends on maintaining a mereological part, bears some
specifically dependent continuant on which this disposition depends. A pair of commensal
organisms exhibit some manner of material structure in their pairing, which is a specifically
dependent continuant on which dispositions borne by the pair depend. Loss of a
mereological part often results in loss of a specifically dependent continuant, which in many
cases brings loss of a disposition or role as well. Each of the three cases can be explained, it
seems, by appealing ultimately to dependence grounding alone.
Dependence grounding also provides explication of the BFO Treatment for dispositions
as “internally grounded” and roles as “externally grounded”. We maintain that in Case 1, the
disposition of the portion of sodium chloride to dissolve is grounded in the qualities inhering
in the material entity. The grounding of roles, in contrast, must refer to more than simply the
bearer of the role, its dispositions, and qualities. A student bears a role that is grounded
partially in the relevant person and partially in – for simplicity – the university. The aggregate
itself bears dispositions which themselves depend on qualities of the aggregate, as discussed
above. For example, the university is disposed to enroll new students each year, which depends
on the quantity of students enrolled already and the financial resources of the university, among
other things, many of which are in fact relational qualities. A student role is externally
grounded in the university because it is grounded in instances of relational quality inhering
in the university.
These remarks suggest the following: dispositions are internally grounded because
they exhibit dependence grounding with respect to qualities that are not relational qualities
while roles are externally grounded because they exhibit dependence grounding with respect
to relational qualities. We thus have two species of dependence grounding:
x is internally grounded in y =def x is a realizable entity and y is some quality of type T
that is not a relational quality and x inheres in material entity b at a time t because
determinates of y inhere in b at t.
x is externally grounded in y =def x is a realizable entity and y is some relational quality
of type T and x inheres in material entity b at a time t because determinates of y inhere
in b at t.
The former applies to dispositions; the latter applies to roles.
3.1 Application to Host-Pathogen Interactions
To illustrate how our proposal may aid researchers, we turn to the phenomena of host-pathogen
interactions so important to contemporary infectious disease research. Until recently,
microbiologists, immunologists, virologists, and others studying pathogenesis have engaged in
either host-centered or pathogen-centered pathogenesis research. Each approach has its merits
and has led to impressive research results. Nevertheless, emphasizing one aspect of host-
pathogen interactions at the expense of the other may leave valuable questions unanswered.
Emphasis, for example, solely on pathogenic factors of SARS-CoV-2 provide only a partial
explanation of various pathogenesis pathways observed in clinical settings; focusing solely on
host immune response is similarly limiting. These observations have not gone unnoticed by life
science researchers and have motivated development of the Damage Response Framework [24]
to explain host and pathogen contributions to pathogenesis. Defenders of the framework adopt
the following principles, which guide our discussion:
(1) Pathogenesis results from interactions between host and pathogen and is attributable
to neither alone.
(2) Hosts and pathogens interact primarily through damage to the host.
(3) Host damage is a function of the intensity and degree of host response and pathogen
factors, each determined by genetic and phenotypic profiles.
Host and pathogen engage in – metaphorically – a tug of war, the results of which influence
manifestations of signs, symptoms, and disease [25].
Even with such guidance we should take care to describe pathogens and hosts
accurately, as these terms are used ambiguously in extant literature. For our purposes,
“pathogen” should be understood as indexed either to a species or to stages in the
developmental cycle of a species [26]. Motivation for the former stems from the fact that some
viruses may engage in mutual symbiosis with one species, while exhibiting pathogenic
behavior towards others. With respect to the latter, mature plants are often susceptible to
different pathogens than developing plants. We reuse terms from the Infectious Disease
Ontology for this illustration [26]:
x is a pathogenic disposition =def Disposition borne by a material entity to establish
localization in or produce toxins that can be transmitted to an organism or acellular
structure, either of which may form disorder in the entity or immunocompetent members
of the entity’s species.
Pathogens bear such dispositions and so may establish localization in some host. Consider, s.
aureus is an opportunistic pathogen in humans, becoming harmful to its host under changes in
its environment. S. aureus is a pathogen, even when it does not realize disorder in a host, since
it is nevertheless disposed to localize in a human host and generate disorder, if given the
opportunity. This is a disposition of s. aureus – following BFO – because it is an “internally-
grounded” property of the entity. That is, it is part of the material basis of s. aureus to generate
disorder in human hosts if given the chance.
To characterize relationships between pathogens and hosts, IDO introduces:
x is a host role =def Role borne by an acellular structure containing a distinct material
entity, or organism whose extended organism contains a distinct material entity, realized
in use of that structure or organism as a site of reproduction or replication.
Hosts thus bear externally-grounded realizable entities, namely, to be sites of reproduction
or replication for pathogens. Figure 3 illustrates various relationships emerging from host-
pathogen interactions, using BFO conformant terminology and relations.
Figure 3: Host Roles and Pathogen Dispositions
An additional strength of our proposal is that we can reflect further subtleties arising from host-
pathogen interactions. Figure 4 illustrates the symmetry we find when focusing on the
replication cycle of pathogens like SARS-CoV-2, which realizes an externally grounded
pathogen role inhering in the virus. Similarly, host organisms bear host dispositions internally
grounded in the quality of susceptibility inhering in the organism.
Figure 4: Host Dispositions and Pathogen Roles
4. Discussion
Our proposal clarifies relationships among dispositions, roles, and qualities within the BFO
Treatment. We thus provide a supplement to ontologists using these terms to model such
phenomena in various domains. Our proposal, moreover, provides precision to commonly used
metaphors that make these terms obscure to those unfamiliar with the philosophical literature
underwriting relevant definitions. Roles are realizable entities inhering in some member of
an aggregate which bears a relational quality in which it is grounded; dispositions are
realizable entities inhering in some entity which bears a quality or qualities that provide
the grounds for the disposition.
There are of course limitations to our proposal worth noting. For example,
implementing our proposal would require the inclusion of a new relation to BFO. BFO has
undergone several changes in the past decade, moving from BFO 1.0 and 1.1 to BFO 2.0 to the
present BFO-2020 specification. Presently, updates to BFO are handled locally. That is,
ontologists importing versions of BFO are expected to conform to the most recent version, often
requiring manual inspection and revision of domain-level ontological classes. Given the labor
involved, version updates are not always completed quickly, and there is concern that users
may experience “update fatigue” with new additions to downstream ontologies. We respect
such concerns, but we note that while our supplement would require updating ontologies that
import BFO, this update would require minimal effort. Our proposed changes do not change,
for example, the hierarchy of BFO or alter existing relations associated with BFO. Our proposal
is a simple additional resource which users can take advantage of when specifying complex
relationships among roles, dispositions, and qualities.
5. Concluding Remarks
We have identified and defended a supplement to the BFO Treatment of qualities, dispositions,
and roles. Gaps in this standard treatment can be filled by the introduction of grounding
relations holding between qualities and dispositions, and relational qualities and roles.
Among our goals in this proposal has been to lift any obscurity in the use of these entities
among ontology developers and life science researchers. In the interest of showing developers
how these relations can be applied, we provide ontological representations of subtle aspects of
host-pathogen interactions.
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