=Paper=
{{Paper
|id=Vol-2050/foust-paper5
|storemode=property
|title=A Note on the Compatibility of Part-Whole Relations with Foundational Ontologies
|pdfUrl=https://ceur-ws.org/Vol-2050/FOUST_paper_5.pdf
|volume=Vol-2050
|authors=C. Maria Keet
|dblpUrl=https://dblp.org/rec/conf/jowo/Keet17a
}}
==A Note on the Compatibility of Part-Whole Relations with Foundational Ontologies
==
https://ceur-ws.org/Vol-2050/FOUST_paper_5.pdf
A Note on the Compatibility of
Part-Whole Relations with Foundational
Ontologies
C. Maria KEET 1
Department of Computer Science, University of Cape Town, South Africa
Abstract. Parthood in mereology is one relation, and typically is included
in foundational ontologies. Some of these foundational ontologies and
many domain ontologies use a plethora of parthood and part-whole re-
lations, such as ‘sub process’ and ‘portion’. This poses requirements on
the foundational ontologies and, perhaps, Ontology, on what to do with
these two different approaches to part-whole relations. We present an
analysis of DOLCE, BFO, GFO, SUMO, GIST, and YAMATO on their
inclusion and use of part-whole relations. It demonstrates there is no
perfect fit with either for various reasons. We then aim to bridge this
gap with an orchestration of ontologies of part-whole relations that are
aligned to several foundational ontologies and such that they can be
imported into other ontologies.
Keywords. Mereology, part-whole relations, ontology engineering
1. Introduction
Foundational ontologies (FOs) differ in their inclusion of part-whole relations. For
instance, DOLCE [12] and GFO [4] have only mereological parthood and proper
parthood, and one or two meronymic relations, such as participation and mem-
bership. However, even in ontology literature, more specific parthood relations
are recognised [8], notably portions [2,6], relating processes [12,20], and, more
generally, the ‘multitude’ approach to part-whole relations as first proposed com-
prehensively in [24]. SUMO [17] has many part-whole relations, including having
them tailored to what might be considered domain entities, such as a sub plan for
stating that one plan is a proper part of another plan, and parts with a temporal
flavour, like initially contains part. Domain ontologies also use a plethora of varia-
tions, with the medical terminology GALEN a case in point with 23 part-whole
relations [19]. Note that this does not yet even concern inclusion of various for-
malisations of mereological theories in FOs, which is assessed in [3], but at most
the bare minimum of ground mereology together with all those variants, such as
sub-processes, portions, and pieces and so on, which is what we focus on here.
1 Corresponding Author: C. Maria Keet, Department of Computer Science, University of Cape
Town, Cape Town, South Africa; E-mail: mkeet@cs.uct.ac.za.
From a minimalist perspective, the choice to include in one’s FO the one
single mereological parthood relation may sound appealing (and may be the only
option according to an ontologist), but it is not workable in domain ontologies, for
it permits many modelling errors and can cause many undesirable deductions as
a result, which should be prevented. For instance, relating an object to a process
with a parthood relation would violate mereology—an object participates in a
process instead—but can be declared in an ontology if the domain and range are
declared to be just any entity (or owl:Thing in an OWL ontology). Then the
reasoner will not detect it as a mistake and instead return undesirable deductions;
e.g., if an atom is part of a protein (both objects) that is part of a catalytic
reaction (a process), then it would undesirably infer that the atom is part of the
catalytic reaction. At the other end of the spectrum is the proliferation of part-
whole relations such that it becomes hard to obtain any inferences at all. If there
is a ‘part of X’ way of naming relations (e.g., hasHand, hasArm), then one cannot
obtain deductions from a partonomy thanks to part of’s transitivity (e.g., that the
hand is part of the human).
The questions these issues raise thus concern 1) how to bridge the Ontolog-
ical ‘cleanliness’ of mereological theories with the practicalities of domain ontol-
ogy development were multiple part-whole relations are used, and 2) where, or
when, to stop proliferating naming part-whole relations. In this paper we aim to
contribute to resolving such a balancing act toward a ‘sweet spot’ for part-whole
relations. Because those more specialised part-whole and parthood relations dis-
tinguish themselves by their domain and range, we conduct a feature comparison
among six FOs. First, we zoom in on their inclusion of mereological parthood and
other part-whole relations, and, second, assess their coverage of top-level cate-
gories used to specify the meaning of part-whole relations. Based on the outcome
of the comparison, we take an engineering approach by developing ontology mod-
ules that can be imported into FOs and thus be used for practical ontology devel-
opment. These modules contain the taxonomy of part-whole relations proposed
in [8], stuff relations [6], and mereotopological ones [9] and are linked to DOLCE
and SUMO (manually) and to BFO and GFO (automatically).
The remainder of the paper is structured as follows. Section 2 summarises
part-whole relations. Section 3 discusses the comparison and Section 4 presents
the orchestration of the OWL files. We conclude in Section 5.
2. Part-whole relations beyond just part-of
The notion of a ‘multitude’ of part-whole relations started in earnest with Win-
ston, Chaffin, and Herrmann’s paper [24], which deviates from the notion of a
single mereological parthood relation. Over time, it has been elucidated that there
are distinctions in that some relations are parthood indeed in the sense of mereol-
ogy (as in, e.g., [22]), and in other cases they are just meronymic part-whole rela-
tions (in natural language language, but not necessarily ontologically), and that
for the purpose of modelling in ontologies and conceptual models—as opposed
to analytic philosophy—it serves to use different names when the part-whole re-
lation relates objects of different categories. Specification of a relation’s domain
and range results in a more precise representation of its intended meaning, as
also noted in, among others, [8,18,23]. This ‘multitude’ approach resulted in a
common list of part-whole relations. The scope of the paper is not to argue for
which ones are there, but accepts that there are several and that that has to be
interoperable with FOs. We take the one of [8] extended with its stuff relations
and portions [6] and mereotopological ones [9], which are based on extensive lit-
erature reviews. The basic set of part-whole relations has been relatively stable,
and is shown informally in Fig. 1 and annotated with the domain and range types.
Needing to declare the domain and range poses the question which categories
from which FO should be used. For instance: (a) Are involved-in’s ‘processes’ in
Fig. 1 processes-as-in-BFO or processes-as-in-DOLCE (or whichever other FO)?
(b) Is there a FO that has all the necessary domain and range categories? If a FO
does not have a particular category, like portion-of’s ‘stuff’ (amounts of matter,
indicated typically with mass nouns), then what can, or should, be done? We will
answer these questions in the next sections.
Part-whole relation
part-of mpart-of
member-of constitutes
s-part-of spatial-part-of involved-in (object/role-collective) (stuff-object)
(objects) (processes) participates-in
contained-in located-in stuff-part-of portion-of (object-process)
(3D/region objects) (2D/region objects) (different stuffs) (same stuff)
tangentially non-tangentially tangentially non-tangentially
contained-in contained-in located-in located-in
Figure 1. Summarised sketch of the part-whole taxonomy with mereotopological extension, with
mpart-of merely a stub for grouping the meronymic part-whole relations together.
3. FO content comparison for part-whole relations
We conduct a brief analysis and comparison of selected FOs on their suitability
for being used in, or have incorporated, part-whole relations. For this content
comparison, we selected six FOs, which are:
DOLCE: The Descriptive Ontology for Linguistic and Cognitive Engineering [12]
is selected because the original part-whole relations taxonomy was already
aligned to it [8];
BFO: The Basic Formal Ontology [1] enjoys great uptake in the biological and
biomedical domains as part of the OBO Foundry efforts [21];
GFO: The General Formal Ontology [4] is already aligned to DOLCE and BFO
[11] and therewith making the comparison exercises easier;
SUMO: The Standard Upper Merged Ontology [17] was an early FO and it has
relatively many relations.
GIST: The GIST minimalist upper ontology [13] was updated in 2017, and is
therefore included;
YAMATO: The Yet Another More Advanced Top-level Ontology, which empha-
sises qualities and processes and events [14].
The UFO was not included, because we could not find an OWL file of it. Con-
cretely, the file DOLCE-Lite.owl in DLP397.zip was used for DOLCE, as that is
what most ontology developers will use if they use it (cf. the axiomatisation in
[12]), bfo.owl (v2), the full GFO (cf. basic) in gfo.owl, the SUMO.owl file from
2010, gistCore7.5.owl, and YAMATO20120714.owl.
The respective OWL files were examined on two aspects: 1) content pertaining
to the relations themselves, being:
i) whether they include the basic parthood (P) and proper parthood (PP);
ii) their respective use of the usual characteristics in ground mereology [22],
where part-of is reflexive (Ref.), antisymmetric (Anti.), and transitive (Trans.)
and proper part of is irreflexive (Irr.), asymmetric (Asym.), and transitive;
iii) inclusion in the OWL file (anywhere) of property chains (Chain), qualified
cardinality (Qual.), and object property hierarchies (H), because they are
‘interesting’ computationally, in that not all languages have those features
and no Description Logics-based OWL species can have them all together
with the parthood characteristics [16];
iv) which other part-whole relations they include, if any;
and 2) their main categories (classes/concepts/kinds/types) of entities, which may
be more or less applicable as domain or range for the part-whole relations. The
results are discussed in the next two subsections.
3.1. Part-whole relations in FOs
First, we compare the FOs’ contents regarding part-whole relations, which is en-
coded in Table 1. There are several observations to make. First, the DOLCE and
GFO releases were before OWL 2 was standardised in 2008 and they have not
been updated accordingly. This means that reflexivity, irreflexivity, asymmetry,
property chains, and qualified cardinality could not have been used and thus nec-
essarily have a “–” in the table. The other four FOs have later release dates, and
thus could have, with caution, more or other ‘object property characteristics’ than
just transitivity. For instance, irreflexivity could have been asserted on parthood,
at the cost of omitting transitivity2 . Also, antisymmetry is not available in OWL
2 [16]3 , hence it necessarily has a “–” for all FOs. Both issues also explain why
one cannot even represent ground mereology fully in OWL 2 DL; if a modeller
wants them all, one could use, e.g., the Distributed Ontology Language [15].
The second obvious observation is that BFO v2.0 has “–” everywhere: it is
a bare taxonomy. While BFO v2.0 is richly annotated, this does not count from
a formal (logic-based) perspective. There are three close alternatives one could
consider: the BFO-associated Relation Ontology (RO) [20], the ROcore4 , and the
draft release of BFO v2.15 . The RO’s informal domains and ranges are not taken
from a specific FO [20], though this is likely to be BFO; we shall return to this
aspect in the next section. The more recent ROcore does indeed contain
2 irreflexivity can be declared on ‘simple’ relations, but a transitive relation is not ‘simple’ [16]
3 ‘antisymmetry of the irreflexive kind’, what the original SROIQ paper claims [5], amounts
to asymmetry
4 https://github.com/oborel/obo-relations/wiki/ROCore
5 https://raw.githubusercontent.com/BFO-ontology/BFO/releases/2014-05-03/
owl-group/bfo.owl
Table 1. Main characteristics of part-whole relations in the selected FOs;
FO P PP Ref. Anti. Trans. Asym. Irr. H Chain Qual. Other part-whole relations
DOLCE + + – – + – – + – – participant, temporary part (for endurants)
BFO 2.0 – – – – – – – – – – –
GFO + + – – + – – + – – participant, member
SUMO + + – – – – – + – – geometric part, subprocess, member, sub plan, ...
GIST + – – – + – – + – + direct part, member, made up of
YAMATO + – – – – – – + – – very many, including ‘has X’ [as part]
Table 2. Alignments of the domain and range categories used in defining part-whole relations.
Domain/range DOLCE BFO GFO SUMO GIST YAMATO
none owl:Thing owl:Thing owl:Thing owl:Thing owl:Thing owl:Thing
Particular Particular Entity Individual Entity – Particular
Endurant Endurant Independent Continuant Presential Object – ± continuant
Perdurant Perdurant Occurrent Occurrent Process ± Event occurrent
Physical Object Physical Ob- Object Material Object ± Self-connec- Physical identifiable ± object
ject ted object item
Social Object Social Object – ± Social role Group – –
Stuff Amount of – Amount of Sub- Substance Physical substance amount of
matter strate matter
Region Region ± union of Spatial, Temporal, ± Spatial and ± Region – space
and Spatio-temporal region Temporal region
Collective – ± object aggregate – Collection Collection –
the relevant BFO classes, it has a transitive part-of, property hierarchies, and also
location (subsuming both the contained-in and located-in of [8]), participates in
with domain continuant and range occurrent, and an irreflexive has-member for
items and collections. Thus, while it does not include all proposed part-whole
relation variants, there is a notable commonality. BFO v2.1 is problematic in
that its relations have no compatibility with either the RO or ROcore, and very
limitedly with or any other ontology, due to the fact that most names of the
relation would suggest temporality, yet OWL is atemporal. The part of occurrent
matches involved-in of the aforementioned part-whole taxonomy, but any other
part-whole relation in v2.1 is ‘temporalised’ in its name, such as part of continu-
ant at some time, and as such different in intended meaning. This is similar for
DOLCE’s temporary-part-of between endurants that was a time-indexed part in
[12] (DOLCE’s parthood between perdurants in [12], the same as involved-in in
[8], is not included as such in DOLCE-Lite).
SUMO, GIST, and YAMATO stand in stark contrast to DOLCE, BFO, and
GFO, for they do contain multiple part-whole relations. For instance, SUMO’s
subProcess matches with the taxonomy’s involved-in, member with member-of,
and material with constitutes. The case is similar for GIST, such as its made up
of matching constituted-of (the inverse of constitutes). While both SUMO and
GIST are FOs, they also contain a substantial amount of knowledge that would
typically not be considered within the realm of FOs but of domain ontologies, such
as types of organisations, manufacturer, types of groups, or a building address.
YAMATO lies at the other extreme for part-whole relations. It essentially has
introduced relations for each part-whole relation between distinct domain objects;
e.g. has-arm, has-brain, and has-mouth are subproperties of hasPart. It is clear that
these domains and ranges are domain entities rather than categories in FOs, such
as ‘process’ or ‘object’. However, the boundary between what a subject domain
entity is and what a FO one is probably not crisp. In the interest of reusability
of FOs with some part-whole relations, one would assume that only the domain-
independent ones should be included.
Overall, based on just the analysis of the contents on part-whole relations,
one could argue for aligning the part-whole relations with SUMO, for there is the
most overlap, or BFO, for it would not need any alignment of the relations.
3.2. Possible domain and range categories in FOs
The second step is to examine whether the common part-whole relations could
perhaps be easily slotted in—i.e., the FOs extended—or be designed as an im-
portable ‘foundational ontology module of part-whole relations’ that would eas-
ily align with the FO. To assess this, we list first which domains and ranges are
needed in the first column in Table 2. The first eight categories follow trivially
from the literature and Fig. 1. The last one, collective, was added because it came
afore in the assessment of verbalising part-whole relations in isiZulu, the largest
language by first language speakers in South Africa, and its subsequent ontological
analysis [7]. In short: while participates-in is understood as relating any endurant
participating in a perdurant, in isiZulu (the Zulu language) or by the amaZulu
(the Zulu people), it has that general notion of ‘participates in’ as well as one
for collectives specifically (-hlanganyele), such as an electorate participating in an
election (cf., e.g., a voter participating in an election) [7].
We availed of the FO comparison of [11] for DOLCE, BFO, and GFO, and
added a tentative alignment for the others. The outcome is listed in Table 2,
where a “±” indicates that we deemed it ‘roughly the same’ based on the available
information (documentation, annotations, and use), but not fully, and a “–” that
no match could be found. Among the latter, two refinements might be made, in
the sense of ‘some of it is there’ vs. ‘nothing of the like is there’. For instance,
endurant, social object, and region do have a very limited presence in GIST: there
are several classes that, when joined and asserted as subclass, would approximate
it. This is in contrast to not having collective in DOLCE and no stuff in BFO.
From a pedantic stance, one may assume that the DOLCE and BFO authors
intentionally excluded it, i.e., the foundational ontological choice was made to, by
their absence, assert that those kind of entities do not exist. Extending the FO
with such entities would violate those principles. But, perhaps, it was an oversight
or the FO is considered still under construction.
Based on the comparison in the table, SUMO seems a good candidate. Zoom-
ing in on the two “±”s, a SelfConnectedObject is “any Object that does not
consist of two or more disconnected parts”, which is not the same as a physi-
cal object in DOLCE that is an “... endurant[s] with unity. However, [it has] no
common unity criterion...”. To illustrate: a bikini is a physical object, but not a
self-connected one. SUMO’s Region is “A topographic location”, i.e., just the ‘2D’
part of space and is a subclass of Object, whereas DOLCE’s Region is subsumed
by Abstract and subsumes, among others, any physical region, hence, also the
‘3D’ space. Logically, they could be aligned through subsumption because SUMO
does not have a disjointness axiom between Physical (the parent of Object) and
Abstract. However, ontologically by their parent categories, they cannot. Whether
that distinction is a disagreement among the Ontology of the developers or just
some artefact of modelling remains to be seen. From a user-based perspective to
FOs, as is the case here, one cannot ignore such distinctions.
Overall, there is no exact match for either FO regarding declaring domains
and ranges for the part-whole relations, but DOLCE and SUMO come closest.
4. Operationalising part-whole relations in OWL files
The assessment in the previous section indicates that it will be easier to align the
part-whole relations to DOLCE, BFO, or SUMO than the others. The orchestra-
tion of the ontology modules is depicted in Fig. 2. Their basic statistics are listed in
Table 3. All files are available at http://www.meteck.org/files/ontologies/.
We commenced with the alignment with DOLCE, for it existed in part al-
ready. First, the file named PW was created and the part-whole taxonomy ([8]
updated with stuff relations [6]), their inverses (has-part etc.), the relevant proper
part versions of them (with inverses), transitivity, and annotations were added. A
module of DOLCE, called, dolcemini, was then imported, domains and ranges
declared according to Table 2, where applicable, and equivalences to some DOLCE
relations were asserted, constituting the complete PW.owl file. We did not use the
PWzu.owl PWzuPWbridge.owl
Dolce-Lite.owl
dolcemini.owl
PW.owl PWwithSUMO.owl
PWMT.owl
SUMOmini.owl
PWbfo.owl PWgfo.owl
SUMO.owl
Figure 2. Orchestration of OWL files, where the solid arrow denotes ‘imported into’, the arrow
with dashed shaft denotes a ‘conceptual’ import (in essence, but implemented differently), and
the dotted arrow stands for automated generation with SUGOI.
full DOLCE mainly because of performance reasons. DOLCE-Lite was modularised
by manually removing unnecessary classes and axioms, and social object and agen-
tive and non-agentive physical objects were added, for they are in the DOLCE
documentation [12] and social object is needed for the part-whole relations (recall
Table 2), resulting in dolcemini. Subsequently, we used the SUGOI tool [10] to
interchange DOLCE automatically for BFO and GFO, resulting in PWbfo and
PWgfo, respectively. In turn, PW was imported into PWMT for the mereotopologi-
cal extension. This was done rather than adding the basic mere topological rela-
tions to PW, because they may be used less often, and there were relatively many
relations in PW already.
The alignment of the part-whole relations with SUMO was carried out man-
ually as follows. First, a small module was created, because the 35MB OWL file6
from 2010 is practically unworkable. We deleted all instances and most classes
and object properties that were subject domain entities; the resultant module
is SUMOmini. Then, to ensure correct IRIs and avoiding unintentional original
file loading, PW was saved as PWwithSUMO and sumomini imported. The swap of
dolcemini for sumomini was carried out following SUGOI’s algorithm [10].
Finally, PWzu is the part-whole taxonomy informed by isiZulu culture and
language [7] and it was aligned to PW in the PWzuPWbridge file. The main distinc-
tions are some non-1:1 alignments and transitivity was not asserted for its generic
parthood (-ingxenye), because it does not hold always (see [7] for a discussion).
The notable differences in number of relations and logical axioms for the
ontologies in the orchestration are listed in the last two columns of Table 3: just
declaring the part-whole relations already count for a third of the axioms in the
PW ontology and a quarter in PWwithSUMO, and between 25-100% of the relations
in the ontology files. The largest difference is between PWMT and dolcemini: it has
a total of 103 relations, of which 59 domain-independent part-whole relations, 1
deprecated, and 43 from DOLCE. This may seem off-putting to use, but effective
tooling to help selecting the right relation is possible with OntoPartS [9].
6 http://www.adampease.org/OP/SUMO.owl
Table 3. Basic statistics of the OWL files and notable changes; |Ax|: ‘logical axiom count’ as
measured in Protégé 5.x (i.e., excluding annotations); Other: other property characteristics,
such as functional and inverses; δ: number of additions cf. its predecessor.
prev. prev.
File |Ax| |C| |OP| |SubOP| |Trans| |Other| δax δrel
Dolce-Lite 349 37 70 70 6 39
dolcemini (dm) 243 40 43 42 4 21
PW 364 40 92 98 23 47 dm
δ121 dm
δ49
PWMT 380 40 103 109 23 52 PW
δ16 PW
δ11
PWbfo 224 48 55 56 19 26
PWgfo 341 53 92 78 27 68
SUMO 175208 4558 778 5330 51 144
SUMOmini (sm) 363 104 138 0 31 32
PWwithSUMO 489 104 187 64 50 57 sm
δ126 sm
δ49
PWzu 272 40 60 57 4 27 dm
δ29 dm
δ17
PWzuPWBridge 405 40 109 121 23 57
5. Conclusions and future work
The comparison of six foundational ontologies showed that neither is a perfect
fit for typical part-whole relations found in domain ontologies and conceptual
models. This is due to language limitations, the stance of relational parsimony vs
abundance as fundamental modelling choice for the ontology, and limited coverage
of categories of entities (classes/universals) that are needed for most part-whole
relations to specify their meaning. Informed by the analysis, several Ontology and
FO-informed ontology modules of part-whole relations were created and aligned
to four foundational ontologies.
These files solve some issues in ontology development—extending a FO and
reaching out to a domain ontology—and indicate a cut-off point for generic part-
whole relations. The predominantly engineering approach taken in this paper,
however, still leaves much to be investigated. Ontologically, it will be useful to
examine whether the mereological theories should be extended in some way to
take into account domain and range declarations and therewith accommodate the
‘multitude’ approach rather that offering just a single parthood relation. That is,
perhaps no separate spatial theories with parthood relating regions and theories of
portions relating stuff parts to wholes, but all that within one connected network
of theories. Extending beyond the current scope of part-whole relations, a more
precise specification of the borderline of FO vs top-domain and domain ontology
may be of use, as would be revisiting the FOs on inclusion of certain categories.
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