Functions in Basic Formal Ontology

Abstract

Abstract. The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO's account of function, provide some reasons for favoring it over competing views, and defend it against objections.

Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request

“…Because drug products are extensively designed and planned to have certain therapeutic indications, these indications are functions. We also note that this usage is consistent with the most recent exposition of functions as they are represented by BFO [ 17 ]. Figure 3 illustrates the relationship of drug products to therapeutic functions.…”

“…For example, consider a drug product that is a tablet with an indication (function) “to treat X.” Suppose that later researchers discover that the tablet also has the disposition “to treat Y.” Then all the tablets manufactured prior to the addition of this indication bear a function “to treat X” and a disposition “to treat Y”, whereas all the tablets manufactured after the change bear two functions: “to treat X” and “to treat Y.” It is possible that the exact same physical basis for the disposition exists for the function. This is analogous to the chopsticks example of Spear et al where there are two identical sticks of wood (in terms of structure and form) one with the function “to handle food” because it was designed and manufactured to handle food, and one with a disposition but not a function “to handle food” because it came to have its structure incidentally [ 17 ].…”

From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge

“…By the term canonical we refer to those biological dispositions that have been thoroughly mapped by the relevant sciences, making it possible to predict specific processes conditioned on said dispositions. Dispositions are potentialities we have in virtue of our physical constitution, and these dispositions are realized in specific processes if certain conditions prevail [e.g., ( 55 )]. For example, human beings are canonically disposed to develop 32 teeth (8 incisors, 4 canines, 8 premolars, 8 molars, and 4 wisdom teeth), and we can thereby assert that it is canonical for the human organism to have 32 teeth.…”

Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology

“…• Use a well-specified syntax • Share a common space of identifiers https://bioportal.bioontology.org/ontologies/BFO), which is an ISO/IEC approved standard 21838-2 (https://www.iso.org/standard/74572.html; https://standards.iso.org/iso-iec/21838/-2/ed-1/en/). BFO is a top-level ontology covering general classes such as material entity, quality, process, function, and role [1,23,24,25], and provides the architecture adverted in the last Foundry principle.…”