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Formal Methods for Biologists

Half-day tutorial

July 20, 2009 (Morning)

This tutorial doubles as the introductory part of the class on Spatial Ontology and Qualitative Reasoning to be held on July 20-21, 2009.

Anybody who is interested in biomedical ontologies will find out rather quickly that people with a background in biology or medicine tend to have a very different perspective on biomedical ontologies than people with a background in computer science or logic. This might be natural and to some extend healthy, but often it makes communication difficult and leads to frustration. This tutorial is intended to help to ease the situation: it is an introduction into formal methods for domain experts. If you are a biologist and you ever wondered why some people seem to be obsessed with necessary and sufficient conditions or why the OBO Relations Ontology (RO) is so weird, this tutorial might be of interest to you.

In the first part of the course will consist in an introduction to basic logical concepts. We will discuss the relationship between ontology and logic, the role of definitions, logical entailment, and automatic reasoning.

In the second part of the course we will use the results of the first part in order to discuss the OBO Relations Ontology (RO). This includes the role of the RO as glue between the different ontologies in the OBO Foundry, the way type level relationship are defined on top of the instance level relationships and the role of axioms (which are missing from the RO).


Any introductory text on logic. There is a number of good textbooks available (e.g. Colin Allen and Michael Hand: 'Logic Primer', MIT Press). This website by Stefan Waner and Steven R. Costenoble contains an introduction to the basic concepts of formal logic.

Neuhaus, Smith: Relations in Anatomical Ontologies, 2008


Fabian Neuhaus is a researcher at the Manufacturing Systems Integration Division of the National Institute of Standards and Technology. His research is focused on logic, ontology and their applications.