Meetings & Conferences Semantics and Ontologies

An evolutionary approach to function (ISMB Bio-Ont SIG 2009)

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!

By Allyson Lister

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