A. Patrice Seyed

BFO is built for ontologies of sciences. BFO and RO are used in the OBO Foundry. DOLCE was built by Guarino. BFO Continuant/Endurant is synonymous with DOLCE’s Endurant/Perdurant(/Quality/Abstract are also included). For specific dependence, a dependent continuant ‘inheres in’ an independent continuant (relationship between particular and type). Specialized dependence relations are ‘quality of’, ‘function of’, and ‘role of’. In DOLCE, a quality can be a ‘quality of’ another quality, endurant or perdurant. There are still some questions over when to use function or role, as identified by a number of talks at today’s SIG. And from a BFO perspective, qualities only inhere in independent continuants.

The constitutes relation. X constitutes Y when there are properties of X which are accidental to X but essential to Y. BFO does not include consititution, but it does have ‘role of’, which is the closest it has. They want to find a way to continue to merge, and figure out how to integrate a conceptualist-centric ULO with a realist-centric ULO.

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

Phillip Lord, Newcastle University

Will provide alternate definitions for BFO function and role. Function has been ontologized heavily already – but what really is it? He has some alternate definitions for both function and role: definitions which are simple, clear, and (critically) applicable.

Why do we need function? Why is it not enough to say “Phil participates in talking”? Because we want to say Phil is able to participate, meant to participate etc. In order to represent these, we need to have a disposition (function or role) that Phil is the bearer of, and which the function is realized in talking.

From now on, referring specifically to BFO. Yes, function is a big definition. In short: a hammer was made to hammer nails in a hammering process. This is good for a definition of Artifactual function and Artifact, but not good for biological function. So, last year a Biological Function definition was made, but there are some problems. A differentiated tumor would appear to have a function, but this would be counter to normal biological usage. Conversely, a male ant under this definition would not have a function, which doesn’t seem right.Further, by this older definition

A biological function is a RE where the homologous structures of individuals of closely related or the same species bear this same biological function.

What distinguishes a biological function from an artifactual function? It is the bearer that distinguishes it, not the process. How do the functions relate? Can a function be both biological and artifactual? Yes, example is a bacteria with some synthetically-added genes. It is the manner of bearing a relationship that distinguishes between BFO’s role and function.

He then used OBI as a test of the new definition. Take OBI function Perturb. I can perturb with both fingers (role) and instrument (function). For Measure, can measure with ruler (function) or arm (role). Most OBI functions are not purely functions. What about roles? With Label Role, S35 CTP was produced and manufactured specifically by people (therefore probably a function). Same with Reference role: the international kilogram prototype was manufactured for this purpose, so Reference would be its function and not its role. Function and Role should be defined subclasses.

How do we apply these definitions, though? He has some “assay” ideas. The definitions seek not to change the current usage but just formalise that usage.

What about gain of function mutations? He sides with Dumontier and says that at heart, genes and proteins only do what their structure allows.

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

…An application of non-monotonic reasoning,

Robert Hoehndorf et al.

Starts by describing the definition of BFO function. It’s rather lengthy, so I won’t reproduce it here – you can find it in the BFO file.  Fuctions may “typically” not be realized, e.g. sperm cells. Functions may be aquired through transformation. What is a realization? What makes a process a realization of a function? Participation of the function bearer is not sufficient. The mode of participation in a process necessary to understand realizations, and these modes are called roles or qua entities.

The ontology of function (OF) hopes to sort some of this out. What is the relation between function and disposition? Function and causality? Larry Wright says that the function of X is Z and this means: X is there because it does Z; Z is a consequence (or result) of X’s being there. The heart is there because it pumps blood, and pumping blood is a consequence of the heart being there. But this doesn’t work for “the heart makes pumping noises”, as the heart isn’t there to make pumping noises. Therefore you need some refinements.

John Searle says all functions are socially ascribed by an agent to an object; and functions are always observer-relative; function ascription is based on brute facts. Nicolai Hartmann says 3 steps: first, a goal in the future has to be set; second is planning the goal’s realization; third is realizing the goal (causally). 1 and 2 create functionality. The third one isn’t necessary for function. If we don’t need 3 to have a function, must that realization be possible at all? What happens if we set a goal and plan, but then something went wrong? No realization is then possible, and we have a missing disposition. The entity is malfunctioning with respect to its function. Functionality does not imply causality because things can malfunction. But when you look in BFO, what they use in their explanation, what they use is almost always some form of typicality or normality: normally, entities do not malfunction. They have created a formal framework for malfunctiongs.

In non-monotonic inference, it permits a sort of default reasoning that X is not malfunctioning as long as it is not proven otherwise. The use of default logics, circumscription or auto-epistemic logis. It can be implemented using answer-set programming. For the implementation, start with an Ear that has function Hearing. There is a disposition D to participate in the hearing process (realization) as a reciever (role). If an instance e of Ear is not malfunctioning, it has a disposition d (instance of D). Normally, instances of Ear are not malfunctioning. Deafness implies a malfunctioning.

BFO’s and other’s definitions of function needs refinement. There are a number of philosophical explanations of functions that can be divided into: reductions to causality, and social ascription. Each explanation relates functionality to causality, and most use normality/typicality. Non-monotonic reasoning is necessary to formalize normality. He proposes that we focus on the necessary conditions and inferences instead of definitions for function.

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!