In this talk we will go back to basics with ontologies and from that project forwards to their future. I’ll base most of what I talk about on my experience in bio-ontologies, but most experience will be applicable in many domains; most domains are not as special as they think. When it comes down to the basics, we need to know what our data represent or mean; that is where ontologies come into play; We need to know what we’re talking about. Once we have that clear we can proceed. There is much that one can do with data once we know what it means. We can exploit those data through knowing what it represents. We can exploit these data better if our ontologies are also better. In taking this simple point of view forwards, I will use this talk to establish a set of principles for ontologists.

1. What are we talking about?
Robert Stevens
School of Computer Science
University of Manchester
United Kingdom
Robert.Stevens@Manchester.ac.UK

2. 27
What are we talking about?

3. We know it’s a length, but
does the computer?
27mm
What are we talking about?

4. A tail of what and
what is a tail?27mm
What are we talking about?

5. What is a mouse,
what do we know
about mice?
27mm
What are we talking about?

6. mm
Unit of
measurement
MouseTail
Mouse
partOf
kindOf
Rodent
kindOf
Mammal
Length
subClassOf
subClassOf
kindOf
BodyPart
What are we talking about?

7. GO:1905426
positive regulation of Wnt-
mediated midbrain dopaminergic
neuron differentiation
rdfs:label
Any process that activates or increases the
frequency, rate or extent of Wnt signaling
pathway involved in midbrain dopaminergic
neuron differentiation.
Textual definition:
What is this thing and what is it called?

8. GO:1905426
positive regulation of Wnt-
mediated midbrain dopaminergic
neuron differentiation
rdfs:label
Any process that activates or increases the frequency,
rate or extent of Wnt signaling pathway involved in
midbrain dopaminergic neuron differentiation.
Textual definition:
positive regulation of Wingless
signaling pathway involved in DA
neurogenesis from midbrain floor plate
oboInOwl:hasExactSynonym
up regulation of Wg
signaling pathway
involved in midbrain
DA neurogenesis
up-regulation of Wingless signalling
pathway involved in mDA neuron
differentiation
upregulation of frizzled signaling
pathway involved in midbrain
dopaminergic neuron production
activation of Wnt-
mediated midbrain
DA neuron
differentiation
What is this thing and what is it called?

9. Neoplasm
Malignant
new growth
New growth
subClassOfsubClassOf
Worry about definitions not labels

10. • Over modelling makes finer and finer
distinctions
• If the distinction makes no difference then
don’t make it
• Angels on the head of a pin: How many?
No Distinction without a
Difference

11. I Apple
II Seed
III Cotyledon
IV Start
V Glucose
VI Carbon
VII proton
VIII quark
Don’t model the world

12. Be as complex as necessary, not as much as you want

13. Protein
EnzymeHolo protein
Holo enzyme
subClassOfsubClassOf
subClassOf
Prosthetic
group
hasPart
hasPart
Catalytic
activity
hasFunction
hasFunction
Let the reasoner do the work

14. Protein
EnzymeHolo protein
Holo enzyme
subClassOfsubClassOf
subClassOf
Prosthetic
group
hasPart
hasPart
Catalytic
activity
hasFunction
hasFunction
subClassOf
Let the reasoner do the work

15. • Using OWL semantics and a reasoner can
help maintain structure
• It won’t make the domain knowledge
correct
• It can reveal what we didn’t know we
knew…
Let the reasoner take the strain

16. Do what is necessary for the purpose
Application
Ontology
Reference
Ontology
“What is necessary
for the application”
“All we know about a
domain of interest”

17. Be wary of edge cases

18. • The purpose is to know what we’re talking
about
• Don’t be too beholden to a philosophical
stance
• Don’t model the whole world
• Beware of edge cases
• “Maximise the work not done” – re-use,
patterns and reason
• Worry about definitions not labels
• Be consistent
Some Principles