This document discusses the need for philosophy in ontology engineering. It summarizes a presentation given at the International Conference on Biomedical Ontology in Buffalo, NY in 2009. The presentation argues that ontology engineering needs guidance from philosophy to properly represent universals and avoid issues that arise from pragmatic or arbitrary modeling decisions. It provides examples from the Gene Ontology and Wine Ontology to illustrate terminological and classification problems that can result without philosophical oversight.

1. ICBO
International Conference on
Biomedical Ontology
Buffalo, NY. July 20-26, 2009
http://icbo.buffalo.edu
1

2. 2
Why Ontology
Engineering needs
Philosophy
Barry Smith
University at Buffalo
http://ontology.buffalo.edu/smith

3. 3
Why Biomedical Science
needs Ontological
Engineering
Barry Smith
University at Buffalo
http://ontology.buffalo.edu/smith

4. Multiple kinds of data in multiple
kinds of silos
Lab / pathology data
Electronic Health Record data
Clinical trial data
Patient histories
Medical imaging
Microarray data
Protein chip data
Flow cytometry
4

5. Example ontologies
Gene Ontology (GO)
Environment Ontology (EnvO)
Infectious Disease Ontology (IDO)
Cell Ontology (CL)
Sequence Ontology (SO)
Protein Ontology (PRO)
Common Anatomy Reference Ontology
(CARO)
5

6. Uses of ‘ontology’ in PubMed abstracts
6

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How to do biology across the genome?

8. 8
Gene Ontology
ca. 25,000 nodes
organized in a
logical hierarchy

9. 9

10. Why is the Gene Ontology so useful
in counteracts silos in biomedical
research where so many other
ontologies have failed?
1. it was built by biologists
2. philosophers play a role in its evolution
10

11. 11
Smith, et al., “Coordinated Evolution of
Ontologies to Support Biomedical Data
Integration”, Nature Biotechnology, 25, 2007
Why Ontology
Engineering needs
Philosophy

12. 12
male courtship behavior,
orientation prior to leg
tapping and wing vibration
Gene Ontology
ca. 25,000 nodes

13. What is an ontology?
universal vs. particular
class vs. instance
(catalog vs. inventory)
(science text vs. diary)
(human being vs. Arnold Schwarzenegger)13

14. The central distinction
universal vs. particular
class vs. instance
(catalog vs. inventory)
(science text vs. diary)
(human being vs. Arnold Schwarzenegger)14

15. are representations of universals
in reality
= representations of what is
general in reality
Science texts, theories

16. An ontology is a representation
of universals
aka kinds, types, categories,
species, genera, ...
in reality
16
What is an Ontology

17. siamese
mammal
cat
organism
substance
animal
instances
frog
universals
17

18. An ontology is a representation of
universals
We learn about universals from
examining the results of scientific
experiments
Experiments are performed always on
instances
18

19. Whether something is an instance or a
universal is not a matter of arbitrary choice
19

20. You can’t take a photograph of a
universal
20

21. 21
Why, oh Why, Ontology
Engineering needs
Philosophy

22. The standard engineering methodology
• Pragmatics (‘usefulness’) is
everything
• Usefulness = we get to write
software which runs on our
machines
• People will pay us for writing new
ontologies
22

23. • It is easier to write useful software if one
works with a simplified model
• (“…we can’t know what reality is like in
any case; we only have our concepts…”)
• This looks like a useful model to me
• (One week goes by:) This other thing
looks like a useful model to him
• Data in Pittsburgh does not interoperate
with data in Paderborn
The standard engineering methodology

24. The standard engineering methodology
Pragmatics (‘usefulness’) is everything
Ontology engineering undermines the
very promise of ontology to solve the
silo problem
24

25. ‘agent’
ontologies
from the
DAML/OIL
ontology
catalog

26. ontology
engineering
needs adult
supervision

27. Ontology Development 101: A Guide to
Creating Your First Ontology
Natalya Noy and Deborah McGuinness
Example: The Wine Ontology
27

28. 28
red = instances, black = classes, io = instance of

29. 29
Why the Wine Ontology
Engineering needs
Philosophy

30. Terminological problems
Classes describe concepts in the domain. For
example, a class of wines represents all
wines. Specific wines are instances of this
class. The Bordeaux wine in the glass in front
of you … is an instance of the class of
Bordeaux wines.
30

31. Creating Instances
… we can create an individual instance Chateau-
Morgon-Beaujolais to represent a specific type of
Beaujolais wine.
Chateau-Morgon-Beaujolais is an instance of the class
Beaujolais representing all Beaujolais wines. This
instance has the following slot values defined
• Body: light, Color: red, Flavor: delicate, Tannin level:
low
• Grape: Gamay (instance of the Wine grape class)
• Maker: Chateau-Morgon (instance of the Winery class)
• Region: Beaujolais (instance of the Wine-Region class)
31

32. The definition of an instance of the Beaujolais class
The instance is Chateaux Morgon Beaujolais from
the Beaujolais region, produced from the Gamay
grape by the Chateau Morgon winery.
32

33. instance of the class Wine grape
33

34. An instance or a class?
Deciding whether a particular
concept [e.g. the Bourgogne region]
is a class in an ontology or an
individual instance depends on what
the potential applications of the
ontology are.
34

35. Wines are instances
pairing wine with food  Sterling Vineyards
Merlot as instance in our knowledge base
inventory  individual bottles as instances
record different properties for each vintage
 Sterling Vineyards Merlot 1993 as
instance
35

36. What about wine regions
“we may define main wine regions, such as
France, United States, Germany, and so
on, as classes and specific wine regions
within these large regions as instances.
( Bourgogne is an instance of France).
36

37. However, we would also like to say that the
Cotes d’Or region is a Bourgogne region.
Therefore, Bourgogne region must be a
class … However, making Bourgogne
region a class and Cotes d’Or region an
instance of Bourgogne region seems
arbitrary: it is very hard to clearly distinguish
which regions are classes and which are
instances. Therefore, we define all wine
regions as classes. ( Cote d’Or is a class)
37

38. From the Protégé glossary:
Instance: Concrete occurrence of
information about a domain that is entered
into a knowledge base. For example, Fran
Smith might be an instance for a Name slot.
An instances is entered via a form
generated by Protégé-2000.
38

39. 39
Barry Smith
University at Buffalo
http://ontology.buffalo.edu/smith
Why Ontology
Engineering needs
Philosophy

40. Why build scientific ontologies?
“There are many ways to create
ontologies …”
Multiple ontologies simply make our data
silo problems worse
Q: What is to serve as constraint?
A: Reality as revealed by mature
experimentally-based science
40

41. Ontological (scientific) realism
• Ontology is ineluctably a multi-
disciplinary enterprise – it cannot be
left to knowledge engineers
• Find out what the world is like by
doing science
• Build representations adequate to this
world, not to some simplified model in
your laptop
41

42. International Conference on
Biomedical Ontology
Buffalo, NY. July 20-26, 2009
http://icbo.buffalo.edu
42