=Paper=
{{Paper
|id=Vol-3805/ICBO-2022_paper_9687
|storemode=property
|title=Exploring the Ontology of Pandemic
|pdfUrl=https://ceur-ws.org/Vol-3805/ICBO-2022_paper_9687.pdf
|volume=Vol-3805
|authors=C. Maria Keet
|dblpUrl=https://dblp.org/rec/conf/icbo/Keet22
}}
==Exploring the Ontology of Pandemic==
https://ceur-ws.org/Vol-3805/ICBO-2022_paper_9687.pdf
Exploring the Ontology of Pandemic
C. Maria Keet
Department of Computer Science, University of Cape Town, South Africa
Abstract
Pandemics do take place. When exactly they begin and end, and why, is harder to determine, as also demonstrated in early
2020 at the start of the Covid pandemic and the many debates in 2022 on calling it over. To determine these points, one has
to know which criteria have to be satisfied and which not, respectively. This requires a clear definition of what a pandemic
is, with at least its necessary and sufficient characteristics. There is no such crisp and clear definition, neither in the expert
documentation nor in domain ontologies. In this paper, we assess mentions of ‘pandemic’ in domain ontologies, evaluate
the argument that foundational ontologies may provide guidance, and examine the characteristics that domain experts have
put forward for pandemics. The guidance from foundational ontologies is underwhelming when taken together, but tooling
greatly simplified the alignment. The assessment of characteristics show that pandemic is not bearer of them all but they are
of attendant entities, elucidates which ones are dependent and which essential, and it demonstrates why one may compute
more than one unique start and end of a pandemic. Considering the complexities, it may be of use to develop an ontology
of pandemics.
Keywords
Pandemic, Foundational Ontology, Ontology comparison, Covid-19
1. Introduction independent practical alignment guidance for two of the
multitude of the FOs [3, 4], in the sense of not having to
Pandemics have taken place throughout the millennia rely on human services [5] to accomplish the task.
[1] and they have been investigated by scientists in many In taking steps toward the ontology of pandemic, we
disciplines, but not ontology. Pandemics somehow start are guided by the following questions. What is a pan-
and end; e.g., the 1918 influenza pandemic ended in 1920. demic, ontologically? What properties does it have? To
This raises the questions as to what the criteria are such which entity in a FO should it be aligned or categorised
that something is an instance of Pandemic and which into, and as part of that: how to align and how to know
criteria would have to be not met to determine the end one has done that alignment correctly? Methodologically,
of the pandemic. And, practically at present: how does it we first examine related work with the 9 relevant domain
apply to the current Covid-19 pandemic? ontologies and summarise the key advances from the
They are simple questions without easy answers. The domain experts. We then proceed toward an ontological
informal short description of ‘pandemic’ is that it is a characterisation, by, first, assessing 7 FOs and seek to
large epidemic [2] and, by the WHO’s guidelines, the align pandemic to it, and subsequently we examine the
pandemic is over when it is alike a seasonal influenza asserted characteristics of pandemics (notably [2], but
epidemic (“post-pandemic phase 6”)1 . While the former also [6]) as an ongoing process of modelling refinements.
is easy to communicate to the public and the latter is The tooling support for FO alignment was found to be
operationally clear, scientifically, it is an unsatisfying very helpful and increased confidence that the alignment
answer. The key issues are that, ontologically, there is is as precise as it can be. The assessment of asserted
no clear definition of pandemic in such a way as to un- characteristics of pandemics are, in some cases, actually
ambiguously classify something as being a pandemic or properties of intricately related entities (e.g., the disease),
not being a pandemic. This holds for both the scientific some turned out to be dependent or implied, others are
literature of the subject domain and, as we shall see, the essential. Crucial for classifying something as (not) a
domain ontologies that have ‘pandemic’ in their vocab- pandemic, is that several properties are vague and thus
ulary. In this unclear situation, foundational ontologies there can be multiple start and end points for a single
(FOs) should be able to be of assistance somehow, to pandemic. To be able to classify things as a pandemic,
help determine at least the category that a domain entity a separate ontology of pandemics may be needed and
such as ‘pandemic’ is. There is only limited published perhaps a rule-based decision table as well.
ICBO 2022, September 25-28 Ann Arbor, MI, USA In the remainder of the paper, the related work is pre-
mkeet@cs.uct.ac.za (C. M. Keet) sented in Section 2 and the assessment with FOs (Sec-
0000-0002-8281-0853 (C. M. Keet) tion 3) and pandemic’s claimed characteristics (Section 4)
© 2022 Copyright for this paper by its authors. Use permitted under Creative
Commons License Attribution 4.0 International (CC BY 4.0). follow afterward. We discuss in Section 5 and conclude
CEUR
CEUR Workshop Proceedings (CEUR-WS.org)
Workshop
http://ceur-ws.org
ISSN 1613-0073
in Section 6.
"
Proceedings
1
https://www.who.int/influenza/resources/documents/
_
pandemic_phase_descriptions_and_actions.pdf
CEUR
ceur-ws.org
Workshop ISSN 1613-0073
Proceedings
Table 1
Summary of where ‘pandemic’ is positioned in the ontology that has it (VIDO and CIDO import the IDO; hence, pandemic is
also a process there), with ID where applicable. Ontology references: prefix https://bioportal.bioontology.org/ontologies/ and
then their abbreviation as listed.
Ontology Pandemic wrt Parent type in the subject do- Top-level Category
or model Epidemic main
AURA is a infection event
CRISP the same medicine (4000-0244) –
GSSO is a – event (EFO_0009629)
IDO sibling – process (sensu BFO, so not an event) (BFO_0000015)
IOBC sibling infection (200906067292879338) ‘Biological phenomenon, process, and state’ (Sys-
tem_cat)
NCIT is a ‘disease or disorder’ (C2991) –
MESH is a ‘public health’ (D011634) –
2. Related work collectives, aggregates) of individuals, be they processes
or objects, are categorically different kind of entities from
We consider first the domain ontologies that contain ‘pan- single individuals and from the individuals that are mem-
demic’ and subsequently summarise domain literature ber of it—both ontologically (e.g., [7]) and in FOs such as
that, overall, have it ill-defined as well. BFO with its object aggregate (and, in BFO v1, process
aggregate)—but epidemic and pandemic are not categor-
2.1. Domain ontologies ically different kinds of things. There is a fiat boundary
between an epidemic evolving into becoming a pandemic
Domain ontologies that have something to do with pan- and then subsiding into one or more epidemics, as the
demics were collected by means of a BioPortal search recent IDO documentation also indicates (see figure 4
using the search string “pandemic” (without quotation in [8]). A secondary issue that the IDO approach faces
marks), which returned 17 hits2 . Of those, 9 refer to the in particular, is how to determine the boundary of one
entity (of which 3 with the same IDO entry), 1 is a list epidemic from another (of the same disease with same
rather than an ontology (the ELD) once it was added as causative agent) to be able to construct a collective, if it
a top category afterthought (in LOINC), once as instance indeed is one, and, more fundamentally, what the respec-
for just the pandemic in 1918 (in OMIT), and once the tive identities of those co-occurring epidemics are. This
organism (in SNOMED CT), rather, and 4 hits are related is unclear; among others: is it one epidemic in two places
things, such as ‘Product delay due to pandemic’ in MED- that it jumped to—e.g., from Italy to South Africa—or do
DRA. The 9 were analysed further and their respective they count as two? How to count two purportedly sep-
key points are summarised in Table 1. We shall discuss arate ones when they touch: do they merge to become
each in turn, on i) how pandemic relates to epidemic (and one large one or are they presumed to be overlapping
outbreak), ii) what its parent is within the subject domain distinct entities (that may not be identifiable as such)? A
scope, and iii) what its domain-independent ancestor is third issue, and minor for the current scope, is the def-
within the realm of top-level entities typically in FOs. inition for epidemic in the ontology’s annotation field,
Regarding how pandemic relates to epidemic, a key mentioning “statistically significant increase in the in-
difference across the 9 ontologies is to have it either as fectious disease incidence” as determiner, but actually it
subsumption, the same, or sibling, which cannot be all is based on a threshold that is based on a moving epi-
correct. The subsumption rationale is based on the notion demic method that relies on historic data for the country
that a pandemic is a large epidemic, having spread over [9], for influenza at least. If epidemic and pandemic are
more or larger regions and affecting more people, i.e., siblings rather than the former subsuming the latter, a
that that is an extra feature meriting the subsumption. better argument has to be put forward. At this stage
The sibling approach of the IDO and its related on- of the analysis, the argument for subsumption is more
tologies is based on the premise that a pandemic is an plausible.
aggregate or collection of “multiple infectious disease Regarding pandemic’s parent in the subject domain
epidemics”, as indicated by the natural language defini- of the selected ontologies (see Table 1), it cannot be ei-
tions in the ontology (it lacks an axiomatisation). There ther of them. In particular, public health in MeSH and
are three problems with this approach. The first, and key, medicine in CRISP are merely intended as broad group-
problem is the ‘collection’ of epidemics: collections (i.e., ings of context, not ontologically a superclass, despite
that the ontology formally asserts the latter. The infec-
2
https://bioportal.bioontology.org/; last checked d.d. 2-3-2022
tion in AURA and IOBC and disease or disorder in NCI country regularly calculates it by comparing it to their
are all more specific as superclass than the previous two, own historical data over the preceding years [9]3 . In-
but are attendant topics, rather. A particular infection, an formally, an epidemic is an occurrence where there are
instance of a disease (or disease course in an organism) or multiple instances of an infectious disease in organisms,
disorder each are a single thing, as an intrinsic whole, in for a limited duration of time, and that affects a commu-
an individual organism, whereas from outbreaks onward nity of said organisms living in a region, and the number
to pandemic, there are multiple related infections in mul- organisms it affects exceeds the agreed-upon threshold
tiple organisms in at least one region. Pandemics need compared to average historical data for that region.
infections to happen, but that does not make them infec- Also within the WHO there used to be a lot of debate
tions. Similarly, there is a disease that causes a pandemic, about defining and describing a pandemic [11, 6, 2], and
but that does not make the pandemic a disease. several national centres of (infectious) diseases made at-
Lastly, the top-level category, for those that had one. tempts as well. The lowest common denominator, and
The IOBC category ‘Biological phenomenon, process, and oft-repeated phrase, is still that it is a large epidemic.
state’ is too imprecise for ontological analysis, although itMinor additions or refinements of features include that it
does provide a general indication that pandemic is some- is spread over the world, or at least multiple regions and
thing that is happening, or occurring or perduring, in continents, and that it usually affects many people4 , that
ontological terms. For the others, the key distinction be- it has to involve a new disease5 , and that there are out-of-
tween process and event—however it may be formalised season infections [6]. Morens, Folkers and Fauci’s litera-
in one’s preferred logic—is that processes, at least in the- ture review on pandemics [2] resulted in a list of eight
ory, can go on forever whereas events necessarily have characteristics, which are: wide geographic extension,
both start and an end, i.e., they have a limited duration by disease movement, high attack rates and explosiveness;
definition whereas processes do not. We know from his- minimal population immunity, novelty, infectiousness,
tory that pandemics indeed do have an end, even though contagiousness, and, with some caution since it is not
it may not be trivial to determine and have fiat bound- often added explicitly, also severity. We shall analyse
aries. them further in Section 4.
In sum, the domain ontologies have been mostly help- Overall, there is a tendency to oversimplify the defini-
ful in indicating what a pandemic is not, and a possible tion of a pandemic for the wider population—as a large
avenue for the direction for FO alignment. epidemic—and leave it for the experts to debate the fea-
tures, which features really count most, and at least for
2.2. Domain literature some of them, what a threshold would be for declaring
something an outbreak or an epidemic, and to keep it
Domain experts have had multiple debates about defining that way to avoid public confusion [2]. This approach of
what a pandemic is and they assessed it from multiple an- outward underspecification seems to have carried over to
gles, including infectious diseases, immunology, epidemi- the domain ontologies. While an underspecification may
ology, and health policy. In the literature, most debate suffice for some tasks, e.g., literature annotation, to be
occurred from around 2009 during the H1N1 influenza able to determine whether we have a pandemic at hand,
pandemic (‘swine flu’) to about 2011. when a pandemic can be called over, and to compare
WHO’s eventual pandemic phases document consists pandemics, a higher level of precision is required.
of descriptions of the phases, but steers clear of a defini-
tion of pandemic (see fn. 1). Its first phase is where an
animal influenza circulates but is not reported to jump 3. Categorising Pandemic
over to humans and it goes up to phase 6 (where we
still are with Covid-19 at the time of writing), where Before assessing the possible characteristic properties
there are sustained community outbreaks in two or more of a pandemic, it first has to be established what sort of
countries in one region and at least one other country generic entity it is. Two FOs have an assistive method
in another WHO region. It also has a “post-peak” phase to categorise an entity, therewith contributing to filling
that is still pandemic but the worst is deemed to be over, the tool gap in the ontology-as-a-service approach [5],
and a “post-pandemic” phase when there are “levels seen which we therefore commence with. Afterward, we will
for seasonal influenza in most countries with adequate
surveillance”, revealing also that these phases were spec- 3
The interested reader may consult such a surveillance re-
ified either with the expectation that the next pandemic port for an impression, e.g., https://www.nicd.ac.za/wp-content/
would be an influenza pandemic or on the basis that uploads/2022/02/NICD-Private-Consultations-Surveillance-Epide-
seasonal influenza is acceptable loss. Seasonal influenza mic-Threshold-Report-Week-5-2022.pdf
4
https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section11.
surveillance is well-established and, knowing that those
html
values vary by country for a range of reasons [10], each 5
https://www.healthdirect.gov.au/what-is-a-pandemic
consider a selection of other FOs to examine whether it a perdurant and bfo:occurrent aligns to dolce:perdurant
will shed any further light on the matter. [15].
3.1. FOs with decision diagrams: DOLCE 3.2. Other FOs
and BFO A recent inclusive survey lists 37 resources as FOs and
There is a “D3” decision diagram to guide entity align- candidate top-level categorisations [16]. We created a se-
ment [3] to DOLCE [12]. The question trail is as follows: lection based on the following considerations: commonly
• Is [pandemic] something that is happening or oc- considered foundational or top-level, ample documenta-
curring? Yes (perdurant). tion, ideally there is also a file to inspect with the formali-
• Are you able to be present or participate in [a pan- sation, diverse in ontological commitments, and the final
demic]? Yes (event). selection represents a wide geographic distribution just
• Is [a pandemic] atomic, i.e., has no subdivisions of in case that matters. This reduced the selection to BORO,
it and has a definite end point? No (accomplish- GFO, SUMO, UFO, and Yamato, which will be discussed
ment). in alphabetical order. The outcomes are summarised in
From the viewpoint of the affected population, it may be Table 2.
unpleasant to state that pandemic is an accomplishment,
but it is one from the perspective of the infectious agent. BORO The Business Objects Reference Ontology [17]
Regardless, it confirms that a pandemic unfolds in time has the distinguishing metaphysical commitment of per-
and is a temporal entity with a limited lifespan. It will durantism. Since Type is the most specific for types, it
cease to be a pandemic at some point in time and evolve does not reveal any category for Pandemic. BORO may
back to epidemic6 . This does not help determining when be more useful for representing a pandemic’s components
it starts or ends, just that it does. or stages that have boundaries and parts, such as a wave
We developed the BFO Classifier7 [4] for BFO v2 [14], of infections with a variant or a flare-up of infections due
as a tool wrapping around the new decision diagram. to lapsing prevention measures.
Pandemic is a process, as follows:
• Does [pandemic] persist in time or unfold in time? GFO The General Formal Ontology [18] differentiates
Unfold in time (occurrent). between universals and individuals, where the Individual
• What is [pandemic]’s relation to the universal spa- branch is where universals are placed for representing
tiotemporal region? Inhabits (occurrent, still) instances. By elimination of options, Pandemic has to be
• Does [pandemic] have a proper temporal part? Yes a Concrete and among those subclasses, an Occurrent
(process) that has temporal parts. Based on the descriptions in
• Is [pandemic] the sum of the totality of processes the ontology, in the documentation, and knowledge of
in a material entity’s spatiotemporal region? No pandemic, it is not possible to be certain of the appro-
(process, still) priateness of Occurrent’s subclasses, partially because 1)
• Is [pandemic] a collection of disjoint part-processes? the descriptions are not easily accessible to casual users,
None of the above (remains a process) in turn partially due to the incomplete characterisation
Regarding the last question, which is optional since ‘pro- in the OWL file and partially because the documenta-
cess’ may be a leaf category (or: its subclasses are not tion is out of lockstep with the content of the ontology,
exhaustive): a pandemic is not a collection of disjoint part- and 2) Pandemic meets several criteria among the sib-
processes if the part-processes all have to be instances of lings. Notably, Actions “are occurents which are caused
different types of processes. BFO’s process need not have by some presential (the agent) at every (inner and outer)
an end, however, whereas pandemics do. So one may ar- time-boundary of the chronoid framing the occurent.”:
gue that bfo:process is not as precise as could be for a gen- there is an agent (the SARS-CoV-2 virus), so it may fit.
eral high-level category. For now, most relevant is that And processes “are a special kind of occurrent. Processes
pandemic is in the occurrent branch of BFO, which is in are directly in time, they have characteristics which can-
agreement with DOLCE since dolce:accomplishment is not be captured by a collection of time boundaries.”, and
where discrete processes “are made up of alternating se-
quences of extrinsic changes and states or continuous
6
It might be that it evolves from pandemic to endemic, but even processes”, which does not sound necessarily inapplica-
then it is expected to evolve via epidemic. Pandemic to endemic has ble either. Process and Action are not declared disjoint,
not happened with any of the previous pandemics. HIV/AIDS is still
so a multiple inheritance is permitted if needed. An ar-
categorised as a pandemic [13], not endemic. To not overcomplicate
the analysis, any possible endemicity of an infectious disease after gument in favour of action is that it has that agent for
a pandemic is assumed to occur via an epidemic stage. the duration of the action that the process does not have
7
https://bfo-classifier.github.io/
Table 2
Summary of what ‘pandemic’ would likely be aligned to (or categorise as) for a selection of foundational ontologies.
Foundational Alignment (con- Comment
Ontology servative)
BFO Process An occurrent. Lacks the specification of definite end
BORO Type Only few options available. Perdurantist foundation
DOLCE Accomplishment It is an event that is a perdurant
GFO Occurrent Likely one or more of its subtypes: action or process
SUMO Process Likely one or more of its subtypes: causing unhappiness and natural process
UFO Situation?? Based on elimination and no observed conflicts; disjoint from endurant and event
YAMATO ordinary event A refinement to intrinsic or extrinsic accomplishment depends on more insight
into pandemic
explicitly, and so it may capture pandemic somewhat ticular configuration of a part of reality which can be
more precisely. understood as a whole and in which entities stand in re-
The reference article for GFO [18] also includes event, lations.”) and the gUFO does not have Perdurant. There
which “is a right boundary of a process”, rather, and thus is gufo:Event that is a “A gufo:ConcreteIndividual that
inapplicable. ’occurs’ or ’happens’ in time. They may be instantaneous
or long-running.”, without the baggage of dispositions.
SUMO The Suggested Upper Merged Ontology [19] Regarding pandemic, then: 1) they clearly also exist
would have pandemic to be at least a process, which may in the now and not only in the past, and they will occur
be of the continuing variety and those with a sure end in the future, thus it cannot be a perdurant, 2) if indeed
to it (i.e., events). Process has 10 direct subclasses and the “nature of events as manifestations of objects’ dis-
further subclasses, and it may satisfy more than one of positions” [20] holds, then it is not at all certain that
them. For instance, the subclass causing unhappiness pandemics would be events, since there is no inherent
“Any Process whose result is that the patient of the pro- disposition in an infectious agent of ‘pandemic-causing’
cess is unhappy.”: if ‘patient’ includes the infected organ- to be manifesting itself. Perhaps a population of organ-
isms, pandemics surely qualify, but Natural process as isms, under the assumption it would be an individual,
“A Process that take place in nature spontanously.” fits may have a disposition of, say, ‘propensity to suffer from
as well. These sibling classes are not declared disjoint. a pandemic’ that is being manifested. On dispositions,
Biological process sounds potentially applicable too, but two papers from 2016 by the main proposers of UFO are
it is a subclass of internal process that happens within referenced, that in turn pass the bucket of clarification to
a single object, which is not the case with a pandemic a book by Molnar and Powers from 2006, at which time I
that happens to many organisms simultaneously. Regard- categorised this line to be a dead end.
ing natural process’s subclasses, there are electrical and Two more directions were pursued. First, contrary
mechanical processes and resonance, neither of which to other FOs where Walk is an example of process or
applies to pandemic, and so it remains at being a natural event, it is a Mode in UFO (which is the parent of Dis-
process as best fit among the options in the ontology. position), which is a Moment that is an Endurant [21].
Moment in the documentation is gufo:Aspect, and the
UFO The Unified Foundational Ontology has several match to the mode is gufo:IntrinsicMode that is described
versions. We consider its OWL version gUFO and both as “A gufo:IntrinsicAspect that is not measurable.”, which
the UFO-B for events [20] and the recent UFO overview does not rhyme with the Walk, and so this direction
[21]. These recent key sources are not in agreement with was abandoned as well. Second, pandemic as a Situation
each other, which hampers alignment of pandemic to may be plausible, and the slight differences across the
something; a selection follows. sources do not fundamentally contradict Situation in [20],
The latest UFO reference paper [21] describes very cf gUFO:Situation, above (that is disjoint from Event and
little about UFO-B. Presumably, Pandemic would be a Endurant); it is mentioned in [21] but not used in any for-
Perdurant and UFO-B slotted in there, but it cannot. “Per- malisation. What the disposition and atomic event are is
durants are individuals that unfold in time accumulating to be determined. Having roughly checked the Situation
temporal parts. They are manifestations of dispositions axioms in [20], which are richer than in gUFO, it does not
and only exist in the past.” [21] where a disposition “in- seem to contradict. There is no example in either [20]
heresIn a unique ConcreteIndividual” [20]. That contra- or gufo.owl as a way to further check understanding. In
dicts with gUFO:Situation that is not a manifestation of conclusion, if something had to be chosen for alignment
a disposition (“A gufo:ConcreteIndividual that is a par- of pandemic, it might be Situation in UFO-B.
YAMATO Lastly, the Yet Another More Advanced Top- modelling style [23]. They are presented and discussed in
level Ontology [22], with YAMATO20120714.owl. It is the remainder of this section in the sequence they were
definitely an event, since it mentions the start and end presented in Morens et al.’s article.
and has unity and wholeness. Among that, it is an or-
dinary_event (cf. instant), but any more precise is dif- 1. Wide geographic extension This refers to the ge-
ficult to determine at this stage, with its subclasses in- ographic region where the organisms that are infected
trinsic_accomplishment and extrinsic_accomplishment. with the disease-causing infectious agent are living. ‘Wide’
For the extrinsic one, there is a process and start and end, is vague, which may be fuzzy in the mathematical sense
with as example ‘a walk in the park’; the intrinsic one or be estimated by other means. It is the statement that
“is an accomplishment by itself alone”, such as ‘a confer- indicates there is no crisp threshold when ‘wide’ starts
ence, a game, or a trip’. If we were to know whether a (1/yes) or ends (0/no), but either with a gradual mem-
pandemic always ends by itself or that that is superseded bership function between 0 and 1 or there are ranges of
by humans deciding it is over, we would be able to say values based on some arbitrary scale. This could be pre-
for certain which of the two it is. Either way, for sure cisiated by consensus at least in theory, but practically
pandemic is an ordinary_event in YAMATO. will still run into issues. For instance, ‘if on 1 continent,
then Localised’, ‘if 2 continents, then Wide’, and ‘if all
In closing, without any aid to help aligning or cate- or 𝑛-1 continents, then Global’: not all continents are
gorising a subject domain entity to a FO, it is nontrivial equal in size and population density (hence, disruptive
to do so and that with less certainty, largely due to insuffi- effects of a growing epidemic), such rules are yet to be
cient detail that may not be consistent across the sources. defined, and there are several different continent models,
For the alignments themselves, they are split along a di- counting between 4 and 7 continents on earth. If there
vide of either something that possibly can go on forever is scientific consensus on those aspects as well, then the
(process) where there is no entity in the ontology that has vagueness can be eliminated.
something that unfolds and with an end to it, and ones For an ontology, three possible short-hand representa-
that do have such type of entity (event, accomplishment). tions for the wide geographic extent are as a binary, say,
Whether it is an intentional act of omission of the former geo_extent ↦→ Pandemic × {local, wide, global}, where
group (at least: BFO, GFO, and SUMO), is unknown; their that range consists of either classes or values, or an ob-
documentation does not indicate intentional exclusion. ject property geographic region and a suitable cardinality
constraint, such as ≥ 4 for the 6 or 7-continent model.
Alternatively, one may opt for including all components
4. Further domain analysis of the complex property—inclusive of the species, disease,
So far, based on domain and foundational ontologies, and causative agent—for which we first need to address
pandemic is a subtype of epidemic, and it an occurrent some of the other characteristics, further below.
(perdurant) that unfolds in time and, if available in the Kelly’s “out of season” feature [6] implies wide geo-
foundational ontology, an event or accomplishment. This graphic extension and may be more useful than simply
is still at a very high level. In this section, we zoom in on counting continents. Kelly focussed on influenza, which
what the properties of pandemic are claimed to be, what is seasonal, and many infectious diseases are seasonal
they may be ontologically, and to assess how, if at all, it [24], but it does not imply that any pandemic-causing
may assist refining the ontological status of pandemic to infectious agent would otherwise be seasonal. A more
determine when some thing is one or not. accurate term may be nonseasonal; either way, this is a
The pandemic feature most often mentioned is the clear yes/no attribute of the disease. This is illustrated
‘large’. Etymologically, the ‘pan-’ in pandemic means with the COVID-19 pandemic, where countries record in-
‘all’, in that it is happening across the world or, prac- fections throughout the year and have waves in multiple
tically, at least multiple regions and continents. For this seasons.
to happen, it suggests that there must be an almost si-
multaneous transmission taking place, which entails that 2. Disease movement This means that there is trans-
infections are happening out of season. Other proposed mission from one place to another place and it can be
features include that it usually affects many people and traced. This implies a comparison of geographic extents
that it has to involve a new disease. Morens, Folkers and across time points, which has a known solution in infor-
Fauci collated eight characteristics of pandemics [2] and mation systems. Ontologically, at the type (TBox) level,
it is, to date, still the most comprehensive list. From however, it is computationally costly to represent and
an ontological and modelling viewpoint, ‘characteristics’ reason with temporal and spatial information. Depend-
is to be understood informally, since there are multiple ing on the purpose of the ontology, one could choose to
ways to represent them in an ontology, depending on the represent those details nonetheless, e.g., using the DOL
Table 3
Summary of the properties of pandemics proposed by domain experts, whether it is an essential/necessary or mandatory
property (“Req.?”) or not, proxy terminology for somehow computed estimated values (in single quotation marks), the key
bearer of that property, and any further comments.
Characteristic Req.? Value Key bearer Comment
Geographic extension Y ‘wide’ Disease Prevalence of the disease
Disease movement Y yes Disease Measured over time and space
High attack rate Y ‘high’ Infectious agent
Minimal population im- Y ‘yes’ Population and immune sys- Implies at least partial novelty
munity tem
Novelty Y yes Infectious agent and organ- Implies minimal population im-
ism’s immune system munity
Infectiousness Y yes Infectious agent
Contagiousness N any type Transmission mode Implies infectiousness
Severity N ‘severe’ Disease and Pandemic As compound property for both
and computed in different ways
Out-of-season N yes Disease Implicit through wide geographic
extension
framework to tie in a first order predicate logic [25], or an inherently fuzzy feature without crisp boundaries
to delegate that to an external system to merely record other than the two extremes of 100% immunity and 0%
yes/no disease movement with a data property and a where no-one is, which is the case when the agent is so
Boolean data type, or refine that into a categorical vari- novel that not even partial cross-immunity—i.e., the im-
able or with ranges how slow or fast it moves for more munity to another agent protects at least a little from the
detailed analysis, where a ‘yes’ suffices for pandemic. Dis- novel one—applies. To add this to a data model, one again
ease moment may not be an essential primary property of can take the ‘easy’ way by introducing, e.g., a categorical
pandemics, but rather a secondary one related to arriving variable alike a populationImmunity with possible val-
at, and maintaining, a wide geographic distribution. ues {minimal,partial,high,full}. Also this prop-
erty can be unpacked to bring it more into the realm of
3. High attack rates and explosiveness Many peo- ontologies. As a minimum, population, organism, and in-
ple are affected in a short amount of time. The notions of fectious agent are involved and, second, an agreed-upon
‘many’, ‘short’, and ‘high’ all indicate vagueness, which definition of population immunity [27] is needed that, in
can be made specific in different ways either with a turn relies on the 𝑅0 estimate (and thus relates to the
membership function or thresholds by consensus. A attackRate). A higher 𝑅0 entails a higher population
shortcut with an attribute attackRate ↦→ Pandemic × immunity threshold, as do imperfect vaccines when they
{low,medium,high} (or, noncommittal, to anyType) do not prevent against infection [27]. While this latter
is useful for information systems, but not a scientific on- aspect is less relevant for declaring a pandemic—minimal
tology. Attack rate relies on components to determine immunity is easy to determine—it is more relevant for
the rate, such as that there is a disease, an infectious when to declare a pandemic over, because it requires a
agent, and the reproduction (R) number of the agent. certain adjustable level of immunity.
The R number with all its variants, in turn, uses notions
such as population, susceptibility to infection (or: level 5. Novelty The species’ immune system has never
of immunity; see below), social dynamics of a population been exposed to it or, in the case of a localised epidemic, a
(i.e., how people behave), ability to measure infections subset of the population of a species has not been exposed
and mortality figures, and a dispersion parameter (how to the infectious agent. This can be a yes/no attribute
(un)evenly an infected organisms passes on the agent to in its simplest form. One maybe could add ‘partial’ to
other individuals in the population)8 . make it three-valued, either in the sense of those sub-
populations or a strain may be new but not the disease
4. Minimal population immunity Immunity to an more broadly (as with influenza and SARS). This relates
infectious agent is relative, in that an organism has it to to immunity insofar as that novelty implies that there will
a degree to some or all of the variants of the infectious be minimal population immunity. Entities underpinning
agent, and likewise for the whole population. This is also novelty are that it is a property of the infectious agent
in relation to the organisms of the species it infects, and
8
A brief overview about the R number and in the context of therewith it is only secondary to pandemic itself.
COVID-19 and the pandemic can be found in [26].
6. Infectiousness It has to involve an infectious dis- WHO’s Pandemic Influenza Severity Assessment uses
ease and thus excludes non-infectious states, disorders, as attendant properties the transmissibility, impact (e.g.,
or diseases such as obesity, heart attacks, and smoking. effect on hospitalisations), and disease severity as input
Thus, there has to be an infectious agent that causes the to compute severity [28], which has been successfully
disease, excluding all non-communicable diseases. This adapted to Covid-19 recently as well (e.g., [29]). The
may be a straight-forward notion for which a ‘yes’ is es- details are actively being investigated and therefore an
sential to pandemics, alike infectiousness ↦→ Pandemic attempt to formally characterise it would be part of ongo-
× {yes} as a shortcut. Whose property it really is, is less ing research rather than only a representation challenge
straight-forward, however: a pandemic is not infectious, for ontologies, and thus, as temporary representation, a
but the causative agent of the infectious disease that, in single property with an output value may be the least-
turn, gets a species into a pandemic, is the one that bears worst option.
the infectiousness property, i.e., a chain of relations from,
e.g., Pandemic ⊑ ∃causedBy.InfectiousDisease to Infec- In sum, there seem to be nine properties, of which six
tiousDisease ⊑ ∃causedBy.InfectiousAgent and only are at least mandatory, if not also the necessary and suf-
then InfectiousAgent ≡ Agent ⊓ ∃infects.Organism, un- ficient conditions for something to be a pandemic. They
der the assumption of clear definitions of causation and are summarised in Table 3. There are indeed vague prop-
infection and an agreement on whether the ‘∃’ over in- erties because either humans have not determined the
fects should really be a ‘some’ (or an ‘only’ or ‘at most boundaries or it is inherently difficult to measure. This
1’) or the converse. will make it practically difficult to determine when some
thing is a pandemic, especially because the fuzzy proper-
7. Contagiousness This refers to the transmission ties may generate multiple optima/minima under which
process, i.e., how it is being spread, and thus entails the a certain situation is classified as being a pandemic or not.
infectiousness property. Only a limited set of options of For SARS-CoV-2 and Covid-19, for instance, at least early
transmission are possible. For humans, it can be from in 2020, it easily ticked all those boxes and so a pandemic
person to person (i.e., contagious) or through some other ontology with a suitable automated reasoner would have
medium, such as an animal intermediary (e.g., fleas, rats) classified the situation we were in, as a pandemic. But
or the environment (e.g., water, as with cholera), and now, in early 2022 after the first omicron variants of con-
among human-human, there are, touch, droplets, and air- cern? Of those properties, numbers 4 and 8 much less
borne. While it is relevant to know from a scientific and so, and number 5, on whether there will be worse novel
health policy viewpoint which of the possible values it ‘variants of concern’ to come, is a key question to answer.
is, it is irrelevant for calling something a pandemic [1] or There are still out-of-season infections as well.
calling an end to a pandemic. That makes this an optional
property for classifying something as a pandemic.
5. Discussion
8. Severity While Morens et al. note that severity is Based on the analysis, the guiding questions posed in the
not always included, they also observed that, historically, Introduction can be answered at least partially. Regarding
the term ‘pandemic’ has been applied more often for dis- what a pandemic is and what properties it has, this has
eases that are severe or that have relatively high fatality been made specific to some extent, but for as long as some
rates, such as HIV/AIDS (a pandemic since 1981 [13]) of the key characteristics are imprecise due to incomplete
and the three recent influenza pandemics of the past cen- data and knowledge by the domain experts, it is not
tury, than for milder ones. As such, it would be only an going to be resolved with more ontological analysis. It
optional property of the pandemic as a whole, or, more may be possible still to capture some of it with fuzzy
precisely, of the disease, not be part of the set of necessary representation [30] and reasoning [31] if one were to be
and sufficient conditions. However, regarding assessing willing to use data properties in an ontology. An informal
and representing this property, first, what is deemed se- visualisation summarising pandemic, attendant entities,
vere and what not is subjective, and thus it will be either and vagueness is included in Fig. 1. There is a multitude
fuzzy or some thresholds can be set, alike mild, interme- of ways to formalise it, be it according to a particular
diate, severe, and very severe, or to WHO’s [28] set of modelling style [23] or ontology ecosystem like the OBO
values for influenza ({below seasonal threshold, Foundry [32], and choice of logic to not only capture the
low,moderate,high,Extraordinary}). crisp, declarative, static knowledge, but also the fuzzy
Second, while severity is a property of the disease and and temporal constraints. The temporal constraints in
whose value depends on, among others, number infec- Fig. 1 were taken from the TREND language that uses
tions, case fatality rates, and treatment options, it is also the 𝒟ℒℛ𝒰 𝒮 Description Logic as foundation [33].
a compound property of a pandemic. More precisely, e.g., Concerning alignment to a FO, it appeared that the
Figure 1: Informal sketch about pandemic in extended UML notation, where the knowledge is shown in very condensed
format, such as depicting derived attributes that are likely to be represented formally with a set of axioms for each one
(rather than as OWL data properties). Text in orange and italics: currently un- or underspecified by domain experts and their
values may change over time; text in grey: content suppressed from the figure to avoid clutter; ‘anyType’: a suitable entity
type; bold: mandatory (possibly essential) element; clock: temporal entity; DEX (+dashed): “An epidemic may also become a
pandemic.”; DEV (+solid): “Each pandemic must evolve to epidemic ceasing to be a pandemic.”.
two with guidance were at least as good as the many As future work, it would be useful to develop a so-
hours spent trying to understand the other FOs and their called application ontology that then can drive a simu-
documentation. The little tooling support [3, 4] reduced lator to model the interactions between the parameters
the time to categorise pandemic to 1-2 minutes. Assess- to gain more insight and therewith improve the specifi-
ing more FOs did not help gain more insight, other than cation of what a pandemic is. It also would be useful if
solidifying the divide between process vs. event. In ad- domain experts could precisiate the vague properties.
dition, the absence of guidance entails a lack of quality
control mechanisms to ascertain correctness of the align-
ment, which does not induce confidence in the process References
compared to answering questions in a decision tree. This
[1] J. Piret, G. Boivin, Pandemics throughout history,
is exacerbated by the observation that for some FOs, mul-
Frontiers in Microbiology 11 (2021) 631736.
tiple points of alignment were defensible. A ‘contact the
[2] D. Morens, G. Folkers, A. Fauci, What is a pan-
authors’ guideline is undesirable as a general strategy
demic?, J. of Infectious Diseases 200 (2009) 1018–
for domain entity alignment. As also noted in [34, 5],
1021.
FO tooling is needed for use and quality and, indeed,
[3] C. M. Keet, M. T. Khan, C. Ghidini, Ontology au-
should be considered as a service to potential and actual
thoring with FORZA, in: Proc. of CIKM’13, ACM
FO users.
proceedings, 2013, pp. 569–578.
[4] C. Emeruem, C. M. Keet, Z. C. Khan, S. Wang, BFO
6. Conclusions Classifier: Aligning domain ontologies to BFO, in:
FOUST-VI: 6th Workshop on Foundational Ontol-
The assessment of domain and foundational ontologies ogy, volume in print of CEUR-WS, 2022. 15-19 Au-
and literature revealed that pandemic is an event (likely gust 2022, Jönköping, Sweden.
also an accomplishment) that unfolds in time. To be clas- [5] B. Smith, Ontology as product-service system:
sified as a pandemic, there are a number of features from Lessons learned from GO, BFO and DOLCE, in:
mostly attendant universals, such as the infectious agent A. D. Diehl, et al. (Eds.), Proc. of ICBO 2019, volume
and the disease it causes, that have to be satisfied. They 2931 of CEUR-WS, 2019, pp. B.1–9.
are not all crisp properties and those imprecise bound- [6] H. Kelly, The classical definition of a pandemic is
aries have not all been defined. This hampers defining not elusive, Bulletin of the WHO 89 (2011) 540–541.
pandemic. Consequently, it suggests why it is difficult to [7] D. Copp, What collectives are: Agency, individual-
determine when exactly a pandemic starts and ends. ism and legal theory, Dialogue 23 (1984) 249–269.
[8] S. Babcock, J. Beverley, L. Cowell, et al., The infec- [22] R. Mizoguchi, YAMATO: Yet Another More Ad-
tious disease ontology in the age of COVID-19, J. vanced Top-level Ontology, in: Proceedings of
of Biomedidal Semantics 12 (2021) 13. the Sixth Australasian Ontology Workshop, Con-
[9] T. Vega, J. E. Lozano, T. Meerhoff, R. Snacken, ferences in Research and Practice in Information,
J. Mott, R. Ortiz de Lejarazu, B. Nunes, In- CRPIT, 2010, pp. 1–16. Sydney : ACS.
fluenza surveillance in Europe: establishing epi- [23] P. R. Fillottrani, C. M. Keet, Dimensions affecting
demic thresholds by the moving epidemic method, representation styles in ontologies, in: Proc. of
Influenza and Other Respiratory Viruses 7 (2013) KGSWC’19, volume 1029 of CCIS, Springer, 2019,
546–558. pp. 186–200.
[10] D. Fleming, M. Zambon, A. Bartelds, J. de Jong, The [24] M. E. Martinez, The calendar of epidemics: Seasonal
duration and magnitude of influenza epidemics: a cycles of infectious diseases, PLOS Pathogens 14
study of surveillance data from sentinel general (2018) e1007327.
practices in England, Wales and the Netherlands, [25] T. Mossakowski, M. Codescu, F. Neuhaus, O. Kutz,
European J. of Epidemiology 15 (199) 467–473. The Road to Universal Logic–Festschrift for 50th
[11] P. Doshi, The elusive definition of pandemic in- birthday of Jean-Yves Beziau, Volume II, Studies in
fluenza, Bulletin of the WHO 89 (2011) 532–538. Universal Logic, Birkhäuser, 2015.
[12] C. Masolo, S. Borgo, A. Gangemi, N. Guar- [26] D. Adam, A guide to R – the pandemic’s misunder-
ino, A. Oltramari, Ontology library, Wonder- stood metric, Nature 583 (2020) 346–348.
Web Deliverable D18 (ver. 1.0, 31-12-2003)., 2003. [27] P. Fine, K. Eames, D. L. Heymann, “herd immunity”:
Http://wonderweb.semanticweb.org. a rough guide, Clinical infectious diseases 52 (2011)
[13] C. Beyrer, A pandemic anniversary: 40 years of 911–916.
HIV/AIDS, The Lancet 397 (2021) 241/243. [28] WHO, Pandemic influenza severity
[14] R. Arp, B. Smith, A. D. Spear, Building Ontologies assessment (PISA), Technical Report
with Basic Formal Ontology, The MIT Press, USA, WHO/WHE/IHM/GIP/2017.2, World Health
2015. Organisations, 2017. URL: https://apps.who.int/iris/
[15] Z. C. Khan, C. M. Keet, Foundational ontology handle/10665/259392.
mediation in ROMULUS, in: A. Fred, et al. (Eds.), [29] L. Domegan, P. Garvey, M. McEnery, R. Fiegenbaum,
Knowledge Discovery, Knowledge Engineering and E. Brabazon, K. I. Quintyne, L. O’Connor, J. Cuddihy,
Knowledge Management: IC3K’13 Selected Papers, J. O’Donnell, Establishing a COVID-19 pandemic
volume 454 of CCIS, Springer, 2015, pp. 132–152. severity assessment surveillance system in Ireland,
[16] C. Partridge, A. Mitchell, A. Cook, D. Leal, J. Sulli- Influenza and Other Respiratory Viruses 16 (2022)
van, M. West, A Survey of Top-Level Ontologies - 172–177.
to inform the ontological choices for a Foundation [30] F. Bobillo, U. Straccia, Fuzzy ontology representa-
Data Model, Technical Report, The Construction tion using OWL 2, Int. J. of Approximate Reasoning
Innovation Hub, Centre for Digital Built Britain, 52 (2011) 1073–1094.
2020. [31] F. Bobillo, M. Delgado, J. Gómez-Romero, Delorean:
[17] S. de Cesare, C. Partridge, BORO as a foundation A reasoner for fuzzy OWL 2, Expert Systems with
to enterprise ontology, Journal of Information Sys- Applications 39 (2012) 258–272.
tems 30 (2016) 83–112. [32] B. Smith, M. Ashburner, C. Rosse, et al., The
[18] H. Herre, General Formal Ontology (GFO): A foun- OBO Foundry: Coordinated evolution of ontolo-
dational ontology for conceptual modelling, in: gies to support biomedical data integration, Nature
R. Poli, M. Healy, A. Kameas (Eds.), Theory and Biotechnology 25 (2007) 1251–1255.
Applications of Ontology: Computer Applications, [33] C. M. Keet, S. Berman, Determining the preferred
Springer, Heidelberg, 2010, pp. 297–345. representation of temporal constraints in concep-
[19] I. Niles, A. Pease, Towards a standard upper ontol- tual models., in: Proc. of ER’17, volume 10650 of
ogy, in: C. Welty, B. Smith (Eds.), Proc. of FOIS’01, LNCS, Springer, 2017, pp. 437–450.
IOS Press, 2001. [34] C. M. Keet, Z. C. Khan, Foundational ontologies:
[20] A. B. Benevides, J. Bourguet, G. Guizzardi, From theory to practice and back, Journal of Knowl-
R. Peñaloza, J. P. A. Almeida, Representing a ref- edge Structures & Systems 3 (2022) 67–71.
erence foundational ontology of events in SROIQ,
Applied Ontology 14 (2019) 293–334.
[21] G. Guizzardi, A. B. Benevides, C. M. Fonseca,
D. Porello, J. P. A. Almeida, T. P. Sales, UFO: unified
foundational ontology, Applied Ontology 17 (2022)
167–210.