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Abstract The concept of biological function is fundamental not only for the philosophy of biology, but also for formal representations in biomedicine. Biologists describe the role of traits in certain organisms using functional language, and the notions of health and disease have been defined by means of functional terms. The purpose of this paper is to clarify the concepts biological function, constituent function, and functioning that are more or less explicit in recent work on formal ontology and its applications in the biomedical domain. I will review several articles by Johansson, Smith, et al. Those articles represent a “neo-Aristotelian” approach: they assume a neo-Aristotelian ontology and theory of definition. It is common to distinguish two major approaches to defining biological functions with several variants. The first major approach began with Robert Cummins’ theory and is called the ‘Causal-role’ analysis of function (CR-function). For Cummins, the function of a part of a system is its causal contribution to some activity of the system. The second approach, endorsed by authors such as L. Wright and Ruth G. Millikan, has been called the ‘etiological’ or ‘evolutionary’ analysis of function (E-function). Wright proposed that the function of an organ or artifact A are those of its effects which explain A’s presence by means of a causal history. According to more refined versions of the second approach, the (proper) function of a trait is tied to its evolutionary significance, or it is determined by natural selection. The neo-Aristotelian-function (NA-function) can be fully assimilated neither to CR-function nor to E-function. In general, the NA-function analysis attempts to capture the non-explanatory elements of functional language and is non-reductive in the sense that it admits universals. The NA-analysis provides a metaphysical account of BF, covering aspects that are not emphasized by the other approaches.
http://www.onto-med.de(this rabbit hole is expanding...holy smokes, they're using a wiki to get to the bottom of it too!)The design of a wiki-based curation system for the Ontology of Functions Robert Hoehndorf, Kay Prüfer, Michael Backhaus, Johann Visagie, Janet Kelso The Joint BioLINK and 9th Bio-Ontologies Meeting - 2006 Download the publication : Abstract Recently, studies argued that statistical and linguistic methods can be applied to extract information from biomedical ontologies, and represent the identified relations in the top-level ontology Ontology of Functions (OF). However, human intervention is required in order to clear noise from the generated data. A simple platform for collaborative work is needed. We propose here the use of a semantic wiki to represent relations between terms. We provide a relationship model for this semantic wiki, and add a core ontology as top-level type system to this wiki. We then discuss a design for the implementation of a platform for the curation of the OF, thereby enabling the community to curate the results of automatic extraction methods, and to add and correct ontology and annotation information. The aim of this collaborative effort is to provide a means to extend and correct the numerous ontologies which are used to describe biological functions in the OF.
