Exceptions in OWL

Alan Rector

BioHealthInformaticsGroup

OpenGALEN

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The problem

• OWL translates to logic– OWL restrictions are about all individuals in

the given class• “Cell has_part some Nucleus”

– Means

• “All cells have part some nucleus”

• But few things in biology are absolute– How to deal with exceptions?

Two approaches

• Representing exceptions in OWL– Express the exceptions explicitly in OWL

• Defaults and exceptions managed by the classifier– The topic of this tutorial

• Representing exceptions around OWL– Use the inferred classification as a framework

• Express the exceptions using inheritance with defaults – Defaults & exceptions ignored by the classifier

» Requires more infrastructure that we haven’t built yet in OWL (Used extensively in GALEN and PEN&PAD

Some basics: Prototype schema

• “All cells except red blood cells”– Cell AND NOT Red_blood_cell

• “Cells”– Features that really are universal for cells

• “Typical_cells”– Features of most cells

Universals & Prototypes

• Molusc• has_body_type SOME Soft

– Typical_molusc– has_part SOME Shell

– Celphalopod• Typical_cephalopod

» NOT has_part SOME Shell

• Nautiloid» has_part SOME Shell

Universals & Prototypes

• All cephalopods are moluscs– All nautiloids are cephalopods

• Typical cephalopods are NOT typical moluscs– Typical nautiloids are not typical cephalopods

• But typical nautiloids are typical moluscs– (at least with respect to shells)

• “The chambred nautilus is a shelled shelless shellfish”

• Universals ‘inherit’– Prototypes do not

Graphically in OWLViz

Explicit Representation of Prototypes and Universals

• Works as long as there are only a few dimensions for typicality– For multidimensional prototypical

statements need true defaults and exceptions

Exercise

• Cells can be divided into Prokaryotic and Eukaryotic– Typical Eukaryotic cells have exactly 1 nucleus

• Typical vertebrate red blood cells have no nucleus• Mammalian skeletal muscle cells have multiple

nuclei• Avian red blood cells have one nucleus

• Only eukaryotic cells have nuclei