=Paper=
{{Paper
|id=Vol-3603/Paper3
|storemode=property
|title=An Extendible Realism-Based Ontology for Kinship
|pdfUrl=https://ceur-ws.org/Vol-3603/Paper3.pdf
|volume=Vol-3603
|authors=Michael Rabenberg,Anuwat Pengput,Werner Ceusters
|dblpUrl=https://dblp.org/rec/conf/icbo/RabenbergPC23
}}
==An Extendible Realism-Based Ontology for Kinship==
https://ceur-ws.org/Vol-3603/Paper3.pdf
An Extendible Realism-Based Ontology for Kinship
Michael Rabenberg 1, Anuwat Pengput 1 and Werner Ceusters 1
1
University at Buffalo, 77 Goodell Street, Buffalo NY, 14203, USA
Abstract
Adequately representing kinship relations is crucial for a variety of medical and biomedical
applications. Several kinship ontologies have been proposed but none of them have been
designed thus far in line with the Basic Formal Ontology. In this paper, we propose a novel
kinship ontology that exhibits the following characteristics: (1) it is fully axiomatized in First
Order Logic following the rules governing predicate formation as proposed in BFO2020-FOL,
(2) it is modularized in 6 separate files written in the Common Logic Interface Format (CLIF)
each one of which can be imported based on specific needs, (3) it provides bridging axioms to
and from SNOMED CT, and (4) it contains an extra module with axioms which would not be
literally true when phrased naively but are crafted in such a way that they highlight the unusual
kinship relations they represent and can be used to generate alerts on possible data entry
mistakes. We describe design considerations and challenges encountered.
Keywords 1
Kinship ontology, SNOMED CT, BFO2020
1. Introduction
Ontologies are rarely developed completely from scratch these days, even if they don’t make use of
any of the few upper ontologies that are around. Re-using ontologies, primarily parts thereof, has even
become standard practice, specifically for ontologies rendered in OWL. However, it is not free of risks.
Several issues with re-used content have been reported in BioPortal ontologies such as duplicated
classes and object properties, inconsistent utilization of reused properties and redundant class
hierarchies [1]. Tools such as ROBOT can detect certain syntactic errors in source ontologies used for
import [2], and reasoners can detect logical errors within the boundaries of the logic they are designed
for. Neither, however, can prevent the most common types of representation errors. One such type is
caused by ‘using OWL just as a syntax and ignoring its open-world semantics’ [3, p11]. That is for
instance the case with the majority of assertions of the form ‘disease - has symptom - some - symptom’
in the Disease Ontology [4]: the OWL semantics requires such statement to be true for ALL instances
of the named disease, which is rarely the case. Although some recommend competency question-driven
ontology authoring as a means to test the internal quality of an ontology before its release [5], doing so
may result in ‘tweaking the axioms so that the reasoner “gets the right answer” ignoring what else the
axioms might entail’ [3, p11]. Another form of tweaking is simply removing the axioms that otherwise
would come with imported classes or object-properties, or creating axiom-less classes and object-
properties with vague textual definitions and names that are slightly altered from what is found in
reference ontologies.
Unfortunately, it is not only representation errors that hamper ontology reuse, but also differing
perspectives in otherwise similar domains, as well as the contexts and applications for which they have
been developed. Simply importing terms and axioms from domain- and application ontologies that are
claimed to be internally coherent and consistent – even logically – is therefore not enough. In many
cases, a thorough manual inspection on top of semi-automated procedures is therefore required. In this
Proceedings of the International Conference on Biomedical Ontologies 2023, August 28th-September 1st, 2023, Brasilia, Brazil
EMAIL: rabenbergm@gmail.com (A. 1); anuwatpe@buffalo.edu (A. 2); wceusters@gmail.com (A. 3)
ORCID: 0000-0001-9004-5322 (A. 1); 0000-0002-0273-1531 (A. 2); 0000-0002-2676-8689 (A. 3)
©️ 2023 Copyright for this paper by its authors.
Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
CEUR Workshop Proceedings (CEUR-WS.org)
CEUR
ceur-ws.org
Workshop ISSN 1613-0073
Proceedings
25
paper, we demonstrate the dilemmas that had to be faced in developing a realism-based kinship ontology
for a specific use case while trying to maximally reuse what has already been developed. In Section 2,
we explain realism-based ontology. In Section 3, we describe a use-case for our ontology, from which
some of the relations in our ontology are derived. Section 4 contains a review of several extant kinship
ontologies, including the one from which ours is primarily adapted. We describe our methodology in
Section 5 and detail the results of our project in Section 6. Further discussion, including some of the
more important design choices we made, appears in Section 7. Section 8 contains concluding remarks.
2. Realism-based ontology design
For something to be a realism-based ontology is for it (1) to be a representation of what is generically
the case for a plurality of entities in reality, and (2) to be built out of smaller representations each one
of which must be faithful to reality. If such a representation is expressed in terms of one or more
representation languages, then at least two requirements must be met for all assertions that are part of
the representation: (1) the symbols intended to denote entities denote only entities that exist or have
existed and (2) the symbols which express relationships between these entities do so equally veridically,
i.e. all posited relationships must obtain in reality. This means that the ontology must have a very
precisely defined ontological commitment that is anchored in an ontological theory based on one or
other form of realism. A requirement for high-quality ontologies – whether realism-based or not – is
that the veridicality of all assertions made therein is verifiable. When part of the representation is
expressed in a logical language, then the logical coherence and consistency of that part can be checked
algorithmically. This is because logical connectors and quantifiers, if any at all, of such languages are
precisely defined, as well as how they may be combined and what sorts of operations and
transformations can be applied to them. Both of these requirements are satisfied by the Basic Formal
Ontology (BFO): it is a domain-independent upper ontology [6] which is based on Ontological Realism
[7]. Its most recent version, BFO2020-FOL, has recently been accepted as an ISO standard [8]. This
includes an axiomatization in First Order Logic (FOL) for a fair part of its underlying philosophical
principles and theories, enough to allow for sound spatial and temporal reasoning on top of the mere
classification as offered by description logics.
3. Use case: history of cholangiocarcinoma in ‘relatives’
Cholangiocarcinoma (CCA) is a significant public health problem in Thailand, especially in the
northeastern region [9, 10]. CCA is a lethal bile duct cancer which in countries of Southeast Asia is
associated with Opisthorchis viverrini (OV) infection [11]. Roughly 5,000 new cases of CCA are
diagnosed annually, and at least 8 million people are infected with OV in Thailand. In 2013, the Khon
Kaen University (KKU) developed a prospective cohort study called the Cholangiocarcinoma
Screening and Care Program (CASCAP) to eliminate OV and CCA. This led in collaboration with the
National Health Security Office and the Ministry of Public Health to a national policy to improve
diagnosis and treatment for CCA, covering all primary, secondary, and tertiary cares [12]. Subjects
enter the CASCAP program in one of two ways [13]. One is through screening performed in high-risk
areas on the basis of voluntary enrollment. This includes a structured interview followed by an
ultrasound screening for CCA. Patients suspected of having a CCA may obtain a confirmation diagnosis
through Computerized Tomography (CT) or magnetic resonance imaging (MRI) [14]. Subjects can also
enter when they are diagnosed as having a CCA in hospitals from the CASCAP network.
The CASCAP administration maintains a data repository about subjects exhibiting the following
inclusion criteria: (1) living in northeastern Thailand, (2) being at least 40 years old, and (3) either of
the following: (3a) ever having been infected with or treated for liver fluke, or (3b) ever having
consumed raw freshwater fish with scales. Data in the repository is collected by means of six forms
[15]. One of them is the Demographic Information and Enrollment form CCA-01, which researchers
and public health officers use to register participants and collect from them demographic information
as well as certain risk factors for CCA, amongst which is having a family history of CCA [16, 17]. It is
the latter topic that inspired us as a demonstration use case for ontology re-use and adaptation in line
with realism-based principles. Family history is in the CCA-01 form determined by means of a yes/no
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response to the question ‘Do you have any relatives diagnosed with cholangiocarcinoma?’. When this
question is positively answered, the following options are offered as categories: (1) paternal grandfather
or mother, (2) maternal grandfather or mother, (3) older aunt or uncle, (4) younger aunt or uncle, (5)
father or mother, (6) son or daughter, (7) brother or sister, (8) nephew or niece, and (9) spouse. In this
paper, we discuss the development methodology of our kinship ontology as well as the challenges
encountered. In a companion paper, we elaborate on how to use it for quality control of the CASCAP
data-repository.
4. Existing kinship ontologies
Chui et al. propose a kinship ontology that they call ‘Tkinship’ [18]. The ontology is axiomatized in
First Order Logic (FOL) and consists of 13 axioms. Axioms (1)–(8) are concerned with natural-
ancestor-of, (9)–(12) with spouse-of, and axiom 13 with both. Chui et al. use the phrase ‘ancestor’ rather
than the more specific term ‘natural ancestor’ and in general do not append ‘natural’ to terms that admit
of ‘non-natural’ readings (e.g., ‘grandparent’), but it is clear that when they use such terms they mean
them to carry their blood-relative senses. Chui et al. also elaborate on how they think their axioms can
be exploited so as to define some additional familial relations, such as the has-natural-grandparent
relation.
Stevens et al. propose a different kinship ontology, the Family History Knowledge Database
(FHKD), written in OWL 2 DL [19]. The FHKD was designed as a way of demonstrating OWL 2’s
features and testing automated reasoners. As they admit, some of the axioms in their ontology, if
interpreted as genuine claims about reality, are seriously questionable; for example, some of their
axioms concerning siblinghood imply that a given person, S, is sibling of S [19, p5]. But in light of the
educational and testing purposes for which the FHKD was designed, it seems charitable to interpret
such axioms not as genuine claims about reality. The work also demonstrates that even the expressive
DL SROIQ(D) is not expressive enough to represent kinship.
KIN, a DL kinship ontology produced as a part of the Global Alliance for Genomics and Health
Pedigree Standard project [20], contains a fairly small number of defined classes, with person and sex
subsuming the rest, and a larger hierarchy of object properties, at the top of which are hasSex and
isRelativeOf, and further down relations such as isGestationalCarrierOf and isMitochondrialDonorOf.
KIN is said to allow using an OWL reasoner to automatically validate a family history graph and infer
new relations, while the expansiveness of its object properties would allow for detailed descriptions and
inferences concerning individuals. However, like FHKD, KIN contains some axioms that yield
implausible results if interpreted as genuine claims about reality. For example, KIN holds that
isRelativeOf is symmetric and transitive, thus implying (implausibly) that a given person, S, is relative
of S. Furthermore, KIN’s sex class-hierarchy is a bit peculiar. In addition to Female and Male, KIN
contains OtherSex and UnknownSex, but OtherSex is a subclass of Female or Male (implying that it is
not another sex, as might be had by some organism of an imaginable sexually ternary species); and KIN
specifies that OtherSex is meant to cover cases in which ‘It is not possible to accurately assess the
applicability of male or female’ (making one wonder what its difference from UnknownSex is supposed
to be) [21].
Cantone et al. present several DL kinship ontologies, some for SROIQ and one for EL++ [22]. They
explicitly note (as mentioned above) that FHKB treats isSiblingOf as reflexive, and they appear to treat
avoidance of such results as a side-constraint on the development of an acceptable kinship ontology.
Among their goals, however, are to show some of the limitations of SROIQ and EL++, by showing that
the SROIQ and EL++ ontologies that they consider are logically weaker than a different plausible set
of kinship axioms that they call ‘KL.’ For example, KL contains an axiom to the following effect: x is
relative of y iff (a) x and y are non-identical and (b) there is a sequence x…y every member of which
with an immediate successor is relative of its immediate successor. As Cantone et al. point out, this
axiom allows KL to yield inferences that are unavailable to SROIQ and EL++ ontologies.
Although not itself a kinship ontology, SNOMED CT has a large number of kinship concepts, which
are not classified as relations – in SNOMED CT called ‘attributes’ – but as ‘person’, a subhierarchy of
‘social entity’. In what follows, we reference SNOMED CT concepts through the concatenation of
‘sct_’, the fully specified name (with the first letter of the fully specified name capitalized as in
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SNOMED CT itself and spaces replaced by hyphens), a second underscore, and finally the concept’s
semantic tag. Two broad classes of kinship concepts are worth noting. First, there is the concept
sct_Blood-relative_person and all the concepts falling under it. These concepts, unsurprisingly,
specifically correspond to blood-relative categories of which individuals can be members. Examples
include, in addition to sct_Blood-relative_person itself, sct_Natural-sibling_person and sct_Natural-
child_person. Second, there are familial concepts in SNOMED CT that do not specifically correspond
to blood-relative categories. Examples include sct_Niece_person and sct_Maternal-
grandparent_person; one can be a niece or maternal grandparent of someone else without being a blood
relative of that person.
5. Methodology
We built our ontology following a number of steps, thereby reiterating over previous steps whenever
deemed necessary. These steps were taken to satisfy the following requirements for our ontology: (1)
maximally re-use what is available and be maximally re-usable itself, (2) be able to represent all kinship
relations required for the CCA-01 form, (3) be fully BFO2020-compatible and (4) fit in the logical
framework set up to combine realism-based ontologies with concept-based ontologies such as
SNOMED CT [23].
Step 1 consisted of manually inspecting the axioms in the existing kinship ontologies to assess the
degree to which they can be read literally, i.e. the extent to which they are faithful to the aspects of
reality to which they pertain. For example, consider axiom (A1) from the Tkinship ontology:
(A1) x(ancestorOf(x,x))
If we thought there were counterexamples to this axiom – involving backwards time-travel and
causal loops or some other such exotic phenomena – then we would not import it in our ontology. This
step included the identification of axioms that are most often satisfied, yet not in general. An example
is axiom (A2) as found in Tkinship.
(A2) xy (hasChild(x,y)
(ancestorOf (x,y) ∧
(z (ancestorOf (x, z) ∧
ancestorOf (z,y)))))
The sort of situation that counterexamples (A2) is indeed highly unusual: people do not ordinarily
have natural children who are natural descendants of their own natural descendants. Readers familiar
with the classic 1974 film Chinatown might recall that one of the big revelations toward the end of the
movie is that one of the characters had fathered a child with his own daughter. This would be a situation
of the sort at issue. Such axioms were however not excluded from our ontology but turned into related
axioms in such a way as to mark the peculiarity of the situation.
Step 2 was to rewrite the accepted axioms so as to be fully compatible with the BFO2020-FOL
axiomatization. Several transformations were to be considered. One was to rewrite predicates which for
BFO are considered ‘fantologically conceived’ [24]. Examples appear in axiom (A3) from Tkinship.
(A3) xy (ancestorOf(x,y)
→ (person(x) & person(y)))
In FOL as used in Tkinship, ‘ancestorOf’ and ‘person’ are relations – binary and unary resp. – that hold
for certain individuals in the domain of discourse. FOL allows one to predicate something about
individuals in its domain without being bothered by any ontological commitment. While BFO might
commit to ‘ancestorOf’ representing an instance-level formal relation [25], it would not commit to
‘person’ representing a formal relation but rather a universal instantiated by а particular at a time. A
BFO-compatible FOL translation of (A3) would therefore be:
28
(A4) xy (ancestorOf(x,y)
→ (t1t2((instance-of(x, person, t1) &
instance-of(y, person, t2)))))
In general, any axiom in a source ontology that describes an individual as timelessly standing in
some unary relation (as in FOL ‘fantologically conceived’ [24]) or as timelessly being a member of a
class (as in OWL) required revision for BFO2020-compatibility during Step 2. This is because under a
realism-based perspective, such an individual is very likely a particular which instantiates at a time a
universal. Such revision was also needed for cases expressing some individual’s timelessly standing in
some relation to some class member when such а relation would require time-indexing as per BFO’s
ontological commitment.
Step 3 consisted of replacing terms for relations and universals with terms that express better what
is intended. Examples included replacing occurrences of ‘ancestorOf’ with occurrences of ‘natural-
ancestor-of’ to make explicit that our axioms containing this expression are concerned with natural
ancestry and not with some broader notion of ancestry, and replacing occurrences of ‘person’ with
occurrences of ‘human-being’.
Step 4 consisted in formulating axioms detailing relations between the kinship relations referenced
on the CCA-01 form to the kinship relations completed thus far. Only one relation referenced on the
form, the has-spouse relation, we did not address at this stage, because it already appeared in our
collection. The other relations referenced on the form are all blood relations, despite the fact that the
English version of this form confusingly contains some non–blood-relation-specific terms such as ‘son’,
‘daughter’, and ‘sibling’; the Thai terms carry specifically blood-relation senses only.
We devised in Step 5 bridging axioms from the relations and universals referenced in the axioms
produced thus far to corresponding kinship terms found in SNOMED CT and vice versa, as exemplified
by (A6) and (A5) respectively. Although many of these axiom pairs can be written as biconditionals,
we refrained from doing so for reason of modularization towards re-usability on a needs basis.
(A5) x (individual-of(x, sct_Natural-child_person)
→ (y (has-natural-child(y, x))))
(A6) x ((y (has-natural-child(y, x))
→ individual-of(x, sct_Natural-child_person)))
In Step 6, we devised a set of axioms specifying certain highly unusual ancestry and spousal
situations as unusual. These axioms are inspired by axioms from Tkinship that we have rejected because
they admit of counterexamples. An example is the rejected axiom (A2) (discussed above), from which
we derived (A7).
(A7) xyz((has-natural-child(x,y)
& natural-ancestor-of(x,z)
& natural-ancestor-of(z,y))
→ occupy-unusual-ancestry-situation(x,y,z))
We note that we do not mean by ‘unusual’ ‘counterintuitive’. For example, a spousehood relation
between first cousins is not, in our view, counterintuitive, though we mark such a relation as unusual.
A better gloss on ‘unusual’ is ‘atypical’. Spousehood relations between first cousins are atypical—they
just don’t happen very often. Furthermore, they happen sufficiently infrequently that an unusualness
axiom pertaining to them seems to serve valuable data-entry and -inspection purposes, as we explain in
Section 6. We also emphasize that ‘unusual’, as we use it, is not meant to carry any normative weight.
In calling a relation ‘unusual’, we do not mean to imply that it is bad, that it ought to be illegal, or that
any other such normative fact obtains.
As a last step, we translated all axioms in CLIF following the schema of the BFO2020-FOL
axiomatization in CLIF, used a parser-generator to transform the axiom collection in a Kowalski-rule
base, and the latter as input for a reasoner for satisfiability testing [26]. Kowalski rules are a further
29
transformation of FOL axioms after they have been translated into clausal normal form. Kowalski rules
are logical implications of which the antecedent is formed by conjoining the atoms of the negative
literals in a clause, and the consequent from the disjunction of the positive literals [27].
6. Results
Our kinship ontology consists of six modules. Some modules contain axioms whose definientia refer
to relations or entities defined in other modules. However, some modules can be ignored when
irrelevant for certain applications. That is for instance the case for the bridging axioms to and from
SNOMED CT when SNOMED CT is not used in an application the ontology intends to serve.
Each axiom comes with a short textual description terminated by an index which is unique within
and across all modules. This index can be used to import individual axioms as well as to create
additional documentation containing detailed textual definitions and elucidations. It can also be used to
link the ontology to a terminology.
The core module, ancestry.clif, consists of 56 axioms, each one of which belongs to one of the
following categories: (1) replacements of the Tkinship axioms, subindexed ‘tkr’; (2) axioms for ordinary
kinship relations requested on the CCA-01 form, subindexed ‘cca’; (3) a recursive definition of the
natural-ancestor-of relation, split into two axioms each subindexed ‘nao’; (4) additional axioms for
ordinary kinship relations, subindexed ‘ak’; and (5) axioms linking universals referenced in this module
to BFO categories, subindexed ‘u’. Most of these relations are fairly ‘ordinary’ ones, such as the
natural-maternal-grandparent-of relation and the natural-sibling-of relation: they are ordinary in the
sense that they are to be interpreted as literal in all contexts. But a few ‘extraordinary’ relations, not
commonly treated in kinship ontologies, appear on the CCA-01 form as well, including the natural-
older-uncle-of relation. The Thai expression which appears on CCA-01 for this relation refers to a
person who is an older biological brother of one of one’s biological parents. These and other unusual
relations we axiomatized in the separate module, cca01-ground.clif. The axioms therein are also to be
interpreted literally – i.e. they represent universal ground truth – but are not useful in an environment
in which such relations are not considered.
Three modules provide a bridge to and from SNOMED CT. Axioms linking from relations and
universals to SNOMED CT concepts are in ancestry-sct.clif; those linking from SNOMED CT concepts
to relations and universals are in sct-ancestry.clif. For example, ancestry-sct.clif contains an axiom to
the effect that if x is natural parent of someone, then x is an individual of sct_Natural-parent_person;
and sct-ancestry.clif contains an axiom to the effect that if x is an individual of sct_Natural-
parent_person, then x is natural parent of someone. Whenever one of these modules is imported, the
axioms in sct-declaration.clif also need to be imported. This module contains a collection of axioms,
the first member of which states that if x is an individual of y, then x is a particular and y is a class, and
the other members of which state about each term taken from SNOMED CT that it is a class. For
example, one of the axioms in sct-declarations.clif states that sct_Natural-parent_person is a class.
The module unusual.clif contains 4 axioms pertaining to highly unusual situations, in which (1) a
person z has a natural descendant which has as parent a natural ancestor of z; (2) a pair of close blood
relatives are co-natural-parents of someone; (3) a pair of close blood relatives are spouses; and (4) some
people are in a plural spousal situation. These unusual-case axioms can serve valuable data-checking
purposes. If someone enters into an electronic medical record data that trigger one of these axioms (by,
say, entering data to the effect that Fred and Sally are spouses while a contemporaneous spousal relation
between Fred and Catherine is already on record), then a warning message can be devised
recommending that the entered data be double-checked for accuracy. Given how unusual the situations
in question are, the triggering data-entry will often have been erroneous.
For the sake of convenience, we also compiled a file, inspiration.clif, containing Tkinship translated
into CLIF but otherwise left untouched. This file is not to be considered part of our kinship ontology.
All axiom files as well as certain additional documentation is available via the following link:
https://buffalo.box.com/s/pn9rv6m0i7wkcfow48f9270c4jh3kp6c
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7. Discussion
Crucial to our ontology is the has-natural-child relation; the natural-ancestor-of relation is defined
recursively partly in terms of it. Other blood relations are defined in our ontology partly in terms of one
or the other of these two relations. By ‘partly’, we mean that additional information is needed to fully
grasp the intended meaning. Although such information can be axiomatized as well, and should be done
for other purposes extending kinship between individuals, it would not lead to useful reasoning in the
context of CASCAP. By ‘has-natural-child(Amy, Bob)’, for example, we mean that among the gametes
from which Bob originates is a gamete of Amy. By ‘of Amy’ in this context, we do not mean (say)
owned by Amy or controlled by Amy, but rather having its biological origin in Amy. If Amy has sold
one of her ova, O, to Clair, then O is in a loose sense a gamete of Clair but is not of Clair in the sense
relevant here. The expression ‘natural’ is thus to be understood throughout our ontology as helping to
designate blood relations. We use the term ‘natural’ in this context, as opposed to (say) ‘biological’ or
‘blood’, simply because ‘natural’ is also the term used in most SNOMED CT blood-relation concepts,
and relevant modules in our ontology function as a bridge between SNOMED CT and BFO.
Many relations in our ontology, as in many kinship ontologies, are also partly defined in terms of
sexes. In our axioms, the expression ‘male-sex’ picks out the sex had by males qua males, and ‘female-
sex’ picks out the sex had by females qua females. We insist that ‘male-sex’ picks out the sex had by
males qua males, not the sex had by males simpliciter (and similarly, mutatis mutandis, for ‘female-
sex’ and females). Simultaneous hermaphrodites (e.g., great pond snails) are male and female at the
same time. It follows that there is no such thing as the sex had by males simpliciter, for some males
have multiple sexes. But even a simultaneous hermaphrodite has the male sex, and only the male sex,
qua male. Hence our insistence on the “qua” restriction.
We also use the term ‘spouse’ to pick out a marriage-partner, and the expression ‘has-spouse(x,y)’
to mean that x has a marriage partnership with y. We take a rather minimal stand on the metaphysics of
marriage – concerning who can enter into it, how many individuals can enter into a given marriage,
whether marriage is ‘purely legal’ and so on. Our stand is not utterly neutral, though. For example, one
axiom of ours entails that the has-spouse relation is irreflexive: you can’t be married to yourself. We
also assume that if x has spouse y, then there is a marriage bond that inheres in x and y and that exists
at a time at which x and y exist. This assumption secures the intuitively correct verdict that spousehood
is a temporal matter; people are not simply atemporally spouses of one another, even if natural-ancestry
relations are simply atemporal. At present, our ontology says nothing about other non-blood relations
beyond spousehood, such as domestic partnerships, close friendships, and so on; though it could be
extended to comprehend such relations.
7.1. Time indexing
Because time-indexing plays such an extremely important role in BFO, a package of questions
guiding our project was which elements of our ontology required time-indexing, which did not, and
how the appropriate time-indexings would be best accomplished. The axioms in the ontologies
discussed in Section 4, including Tkinship, treat (say) being a person as a matter of timelessly bearing
some property, or as a matter of timelessly being, or being related in some way, to a member of some
class. One feature of our ontology that makes it different from those discussed in Section 4 is thus that
all such talk is replaced by talk of individuals’ being instances of universals at times, as in, for example,
the following axiom:
(A8) xy(natural-father-of(x,y)
(natural-parent-of(x,y)
& qt(instance-of(q,male-sex,t)
& inheres-in(q,x))))
Relations between individuals included in our ontology were a somewhat trickier matter than
universals, because for some of these relations time-indexing seems appropriate but for others it does
not. For example, it is plausible that natural-ancestor-of is non–time-indexed: it seems atemporally true
31
that, for example, Abraham Lincoln’s maternal grandfather is among Lincoln’s ancestors. By contrast,
consider has-spouse. Some form of time-indexing seems appropriate for this relation, for people are
married to one another for specific time periods, and a given person can be married to different people
at different times. One way to accommodate an element of time-indexing concerning has-spouse is to
time-index has-spouse itself; another is to attach time-indexing to something that one’s ontology holds
to be inextricable from spousal relations. As mentioned above, we took the latter approach, by
maintaining that x has spouse y if and only if there is a marriage bond – a specialization of BFO2020’s
relational quality – that exists when x and y do and that inheres in x and y.
7.2. Bridging to SNOMED CT
The meaning of each SNOMED CT term is provided either through an individual concept or by at
least one axiom expressed in the description logic EL++ [28]. Some of us have described elsewhere
some of the potential benefits of using bridge axioms to attach the terminological richness of SNOMED
CT to the ontological foundation supplied by BFO [23, 29]. The approach defended in [23, 29] is to let
SNOMED CT’s view and BFO’s view happily co-exist, not in one ontological framework, but in one
logical model-theoretic framework capable of exploiting what SNOMED CT offers terminologically
and realism-based ontologies offer ontologically. We developed the modules sct-ancestry.clif, ancestry-
sct.clif and sct-declarations.clif of our kinship ontology partly as a proof of concept of this general
bridging strategy.
While devising our ontology, we encountered a number of challenges. For example, some of the
relations at issue in ancestry.clif and cca01-ground.clif do not have precisely corresponding SNOMED
CT concepts. For instance, one relation defined in cca01-ground.clif is the natural-older-uncle-of
relation. Unsurprisingly, sct_Natural-older-uncle_person does not exist in the international version of
SNOMED CT. Perhaps a bit more surprisingly, there is also no SNOMED CT concept precisely
corresponding to the natural-ancestor-of relation. In these cases, bridging axioms cannot be proposed.
When, however, a relation in our ontology lacked a precisely corresponding SNOMED CT concept, but
there was a SNOMED CT concept that nearly precisely corresponded to the relation and a true bridge
axiom connecting them could be imagined, we chose to include such an axiom. For example, because
natural-niece-of and sct_Niece_person nearly precisely correspond and sct_Natural-niece_person does
not exist, we included in our ontology the following bridging axiom:
(A9) x(y(natural-niece-of(x,y)) → individual-of(x,sct_Niece_person))
A related issue concerned the question when bridging axioms could be formulated in both directions
and when they could not be. In situations involving precisely corresponding kinship relations and
SNOMED CT concepts, axioms in both directions were warranted; in situations not involving such
precise correspondence, this was not the case. Hence the axioms (A10) and (A11), for example, both
appear in our ontology, because natural-sibling-of and sct_Natural-sibling_person precisely
correspond:
(A10) x(y(natural-sibling-of(x,y))
→ individual-of(x,sct_Natural-sibling_person))
(A11) x(individual-of(x,sct_Natural-sibling_person)
→ y(natural-sibling-of(x,y)))
By contrast, the right-to-left analogue of (A9) does not appear in our ontology.
At present, our kinship ontology focuses primarily (though not exclusively) on blood-relations, and
we have accordingly focused up to now on linking SNOMED CT blood-relative concepts to our
ontology and proposing axioms defining relations corresponding to such concepts. However, there are
a great many SNOMED CT blood-relative concepts, some of them highly specific, and we have not
thus far tried to link every SNOMED CT blood-relative concept to our ontology or to propose axioms
defining relations corresponding to every such concept. For example, sct_Identical-twin-
32
brother_person falls under sct_Blood-relative_person, but we have not yet linked this concept to our
ontology, we have not proposed an axiom defining the identical-twin-brother-of relation, and so on.
Still, the work we have done thus far could be extended so as to cover all SNOMED CT blood-relative
concepts, and indeed we hope in future work to do that.
7.3. Unusual kinship relations
A different stage of our project that required judgment calls on our part was the production of
unusual.clif. Consider, for example, the following axiom in unusual.clif:
(A12) xyz((has-natural-child(x,z) & has-natural-child(y,z) & (natural-parent-of(x,y)
natural-sibling-of(x,y) natural-grandparent-of(x,y) natural-aunt-of(y,x) natural-
uncle-of (y,x) natural-first-cousin-of(x,y)))
→ occupy-unusual-ancestry-situation(x,y,z))
The intuitive idea behind (A12) is that if two people are co-natural-parents of a common person and
are themselves close blood relatives, then they and their child occupy an unusual ancestry situation. The
long disjunctive clause specifies a range of blood-relations that clearly qualify as close. But, of course,
there are other close relations not covered by the clause (e.g., natural-second-cousin-of). Adding
additional such relations to the disjunctive clause would allow for the generation of additional data-
entry warnings, and so would probably flag some incorrect data-entries that would otherwise go
undetected. However, expanding the disjunctive clause in certain imaginable ways might also generate
enough warnings in cases of correct data-entry that doing so would not be all-things-considered
prudent. For example, if one were to revise (A12) in such a way that co-natural-parenting natural
seventh cousins count as occupying an atypical ancestry situation, then one would perhaps thereby
revise (A12) in such a way that it yielded a counterproductively large number of false positives.
We suggest that (A12) be read as an example of a warning-case axiom relevant to the situations to
which it pertains, not as the best possible version of such an axiom. This axiom and the others in
unusual.clif could be revised to suit particular data-entry contexts, or even rejected altogether. For
example, the axiom (A13) is in unusual.clif, we hope for obvious reasons:
(A13) xyz(tm1m2(instance-of(m1,marriage-bond,t) & instance-of(m2,marriage-
bond,t) & inheres-in(m1,x) & inheres-in(m1,y) & inheres-in(m2,x) & inheres-in(m2,z)
& ~y=z) → occupy-unusual-spousal-situation(x,y,z))
However, if one lives in a polygamous society, then it might be a good idea for one not to adopt
axiom (A13) at all. Though even this is not obviously right: if one lives in a society in which some but
very few people practice polygamy, then (A13) might be worth adopting after all.
8. Conclusion
We have developed a novel kinship ontology in First Order Logic following the representational
principles of BFO2020-FOL. The ontology comes in separate CLIF-modules each one of which can be
imported based on specific needs, for example, mapping to and from SNOMED CT, or exploiting
axioms which would not be literally true when phrased naively but are crafted in a way that allows the
generation of alerts on possible data entry mistakes. The ontology can be used directly by CLIF-
reasoners, or translated into much weaker versions of the axioms for OWL-DL reasoners. In future
work, we intend to expand on this project by adding SNOMED CT kinship concepts that we have not
yet wedded to our kinship ontology, either through definitions of corresponding relations or through
production of relevant bridge axioms. Further expansion following the same bridging strategy might
happen when other relevant kinship terminologies become prominently used.
33
Acknowledgements
This work was supported in part by Clinical and Translational Science Award UL1 TR001412 from
the National Institutes of Health and a T15 grant awarded by the National Library of Medicine. We
would like to thank Dr. Kavin Thinkhamrop for providing valuable information about CASCAP.
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