When we can declare the covid-19 pandemic to be over? I mulled about that earlier in January this year when the omicron wave was fizzling out in South Africa, and wrote a blog post as a step toward trying to figure out and a short general public article was published by The Conversation (republished widely, including by The Next Web). That was not all and the end of it. In parallel – or, more precisely, behind the scenes – that ontological investigation did happen scientifically and in much more detail.
The conclusion is still the same, just with a more detailed analysis, which is now described in the paper entitled Exploring the ontology of pandemic , which was accepted at the International Conference on Biomedical Ontology 2022 recently.
First, it includes a proper discussion of how the 9 relevant domain ontologies have pandemic represented in the ontology – the same as epidemic, a sibling thereof, or as a subclass, and why – and what sort of generic top-level entity it is asserted to be, and a few more scientific references by domain experts.
Second, besides the two foundational ontologies that I discussed the alignment to (DOLCE and BFO) in the blog post, I tried with five more foundational ontologies that were selected meeting several criteria: BORO, GFO, SUMO, UFO, and YAMATO. That mainly took up a whole lot more time, but it didn’t add substantially to insights into what kind of entity pandemic is. It did, however, make clear that manually aligning is hard and difficult to get it as precise as it ought, and may need, to be, for several reasons (elaborated on in the paper).
Third, I dug deeper into the eight characteristics of pandemics according to the review by Morens, Folkers and Fauci (yes, him, from the CDC)  and disentangled what’s really going on with those, besides already having noted that several of them are fuzzy. Some of the characteristics aren’t really a property of pandemic itself, but of closely related entities, such as the disease (see table below). There are so many intertwined entities and relations, in fact, that one could very well develop an ontology of just pandemics, rather than have it only as a single class on an ontology as is now the case. For instance, there has to be a high attack rate, but ‘attack rate’ itself relies on the fact that there is an infectious agent that causes a disease and that R (reproduction) number that, in turn, is a complex thing that takes into account factors including susceptibility to infection, social dynamics of a population, and the ability to measure infections.
Finally, there are different ways to represent all the knowledge, or a relevant part thereof, as I also elaborated on in my Bio-Ontologies keynote last month. For instance, the attack rate could be squashed into a single data property if the calculation is done elsewhere and you don’t care how it is calculated, or it can be represented in all its glory details for the sake of it or for getting a clearer picture of what goes into computing the R number. For a scientific ontology, the latter is obviously the better choice, but there may be scenarios where the former is more practical.
The conclusion? The analysis cleared up a few things, but with some imprecise and highly complex properties as part of the mix to determine what is (and is not) a pandemic, there will be more than one optimum/finish line for a particular pandemic. To arrive at something more specific than in the paper, the domain experts may need to carry out a bit more research or come up with a consensus on how to precisiate those properties that are currently still vague.
Last, but not least, on attending ICBO’22, which will be held from 25-28 September in Ann Arbour, MI, USA: it runs in hybrid format. At the moment, I’m looking into the logistics of trying to attend in person now that we don’t have the highly anticipated ‘winter wave’ like the one we had last year and that thwarted my conference travel planning. While that takes extra time and resources to sort out, there’s that very thick silver lining that that also means we seem to be considerably closer to that real end of this pandemic (of the acute infections at least). According to the draft characterisation pandemic, one indeed might argue it’s over.
 Keet, C.M. Exploring the Ontology of Pandemic. 13th International Conference on Biomedical Ontology (ICBO’22). CEUR-WS. Michigan, USA, September 25-28, 2022.
 Morens, DM, Folkers, GK, Fauci, AS. What Is a Pandemic? The Journal of Infectious Diseases, 2009, 200(7): 1018-1021.