Biomedical ontologies: What part-of is and isn’t

Abstract

Mereological relations such as part-of and its inverse has-part are fundamental to the description of the structure of living organisms. Whereas classical mereology focuses on individual entities, mereological relations in biomedical ontologies are generally asserted between classes of individuals. In general, this practice leaves some basic issues unanswered: type constraints of mereological relations, e.g., concerning artifacts and biological entities, the relation between parthood and time, inferred parts and wholes as well as a delimitation of parthood against spatial inclusion. Furthermore, mereological relations can be asserted not only between physical objects but also between biological processes and medical procedures. We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies.

Extensional and intensional collectives and the de re/de dicto distinction

“…To express this, we need to relativise existence and membership to times, adding an additional temporal argument-place to each of the predicates Exists and M ember. Note that, membership being a specialised form of parthood, this is fully in keeping with the widespread practice of relativising parthood to time, as for example discussed in some detail in the context of biomedical ontologies by Schulz et al [26] and in a more general context by [5]. Our formula now becomes:…”

Continua in Biological Systems

“…10, [14][15][16][17][18][19][20][21][22][23][24][25][26] In this section, we will show that many of the terms used for this purpose designate biological repeatables whose instances have a partially fiat spatial or spatiotemporal boundary; otherwise, to mention this opportunity again, the terms remain vague.…”

“…Where in all these cases should the line be drawn between parthood and containment? The paper 25  TWENTYFIVE provides some heuristic rules for drawing these distinctions by introducing criteria for deciding where a locative relationship can be refined to a mereological one and where it cannot. The application of these criteria, however, remains in part a pragmatic matter.…”

Grains, components and mixtures in biomedical ontologies

“…Numerous subrelations of the foundational has_part relation, relevant for the biomedical domain, have been proposed in the context of biomedical ontologies such as GALEN [4] or the Foundational Model of Anatomy (FMA) [5]. In BioTop, a top-domain ontology for the biomedical domain ([3,6,8]), the number of relations has been restricted to a minimum, mostly following the precepts of the OBO relation ontology [7]. However, the need for two distinct mereological relations, has_grain and has_component , both subrelations of has_proper_part , has been advocated.…”