Primer on formalization
From Program on Ontologies of Neural Structures
Contents |
Primer on formalization
Expansions
'N1 is_synapsed_to some N2' expands to:
N1 has_part some (
'pre-synaptic membrane ; GO:0042734' that part_of some (
'synapse ; GO:0045202' that has_part some (
'post-synaptic membrane ; GO:0045211' that part_of some N2 ))))
Can be rendered in English as:
If every N1 is_synapsed_to some N2 then every N1 has a presynaptic membrane that is part of a synapse whose post synaptic membrane is part of N2.
Property restrictions
- Domain: Specification of the classification of the subject of the relation (in this case N1).
- Range: Specification of the classification of the object of the relation (in this case N2).
- Property hierarchy: If X rel2 Y and rel2 is a sub property of rel1 then X rel1 Y.
- Property chains: rel1 o rel2 -> rel3 is equivalent to the rule: If X rel1 Y and Y rel2 Z then X rel3 Z.
Limitations of class level expansion as a way of defining relations
Sometimes we want to say more than one thing about the relationship of X to Y. Say I want to say that a relationship (relA) between two single objects X and Y only applies if X overlaps with Y and X is aligned with Y. One might naively try to express this with an expansion to a class level expression in OWL:
'X relA some Y' expands to:
(X overlap some Y) AND (X aligned_with some Y)
But this would be wrong. For this to apply, the Y that X overlaps with need not be the same Y that X is aligned with. In such cases we need to resort to instance level definitions that are opaque to OWL reasoning. However, we can often get back useful reasoning using property hierarchies or property chains. In this case if we make relA a subproperty of both overlap and aligned_with, then, give an ontology that contains the relationship X rel A some Y, a reasoner can find Y in response to a query for classes of things that overlap some X.
Further reading
go back to Relations page
