Screen shot of a news page from the bbc web site about polio outbreak in Namibia
Same BBC page, but showing terms highlighted from the ontology, each highlighted term is a new link
Same page with link box on top with targets to other pages, broader resources are also shown.
Link from BBC to Neli site, NeLI page on polio with some terms highlighted
Spectrum of what can be an ontology
1. Choosing and Building
Bio Health Informatics Group
School of Computer Science
University of Manchester
• Do you need an ontology?
• A case in point
• What is an ontology?
• What is an vocabulary?
• Top down, bottom up, middle out,
3. • BBC News page that shows an article about an
outbreak of Polio in Namibia
BBC news article
4. • COHSE highlights terms from the underlying
5. • COHSE provides links to NELI, Wikipedia and
New link targets
6. • COHSE highlights terms from underlying ontology
generating more link targets
Link to NeLI from BBC
Polio The DiseasePolio The Virus
Labels and Meaning
(The Thing e.g a
aliquot of vaccine)
(Treatment, the form of
9. So what is an ontology?
After Chris Welty et al
10. Define: Ontology• Specification of a conceptualisation of a knowledge domain. An ontology is a controlled vocabulary
that describes objects and the relations between them in a formal way, and has a grammar for
using the vocabulary terms to express something meaningful within a specified domain of interest.
The vocabulary is used to make queries and assertions. Ontological commitments are agreements
to use the vocabulary in a consistent way for knowledge sharing. ...
• A description (like a formal specification of a program) of the concepts and relationships that can
exist for an agent or a community of agents. In biomedicine, such ontologies typically specify the
meanings and hierarchical relationships among terms and concepts in a domain.
• The creation of a systematically ordered data structure that enhances exchange of information
between computers and scientists. Ontologies enable the definition and sharing of domain-specific
• The study of the broadest range of categories of existence, which also asks questions about the
existence of particular kinds of objects, such as numbers or moral facts.
• The study of the nature of being, reality, and substance. [www.carm.org/atheism/terms.htm]
• Branch of philosophy concerned with the study of being, of reality in its most fundamental and
• The collection of distinct entities that is considered to exist within a particular view of a portion of the
• Is derived from the two Greek words (ontos) meaning "to be" and (logos) meaning "word." Ontology
is the science or study of being. [www.theapologiaproject.org/glossary.htm]
11. Knowledge Artefacts
• A set of discriminations in style and
• They all capture knowledge in some form
• CS types call anything that does this an
• Philosophers very much do not
• Formal language and formal ontology
12. Back to Gruber
• “In the context of knowledge sharing, I use the term
ontology to mean a specification of a conceptualisation.
That is, an ontology is a description (like a formal
specification of a program) of the concepts and
relationships that can exist for an agent or a community of
agents. This definition is consistent with the usage of
ontology as set-of-concept-definitions, but more general.
And it is certainly a different sense of the word than its use
13. A Stronger Definition
• a set of logical axioms designed to account for the
intended meaning of a formal vocabulary used to describe
a certain (conceptualisation of) reality [Guarino 1998]
• “conceptualisation of” inserted by me
• “Logical axioms” means a formal definition of meaning of
terms in a formal language
• Formal language—something a computer an reason with
• Use symbols to make inferences
• Symbols represent things and their relationships
• Making inferences about things computationally
14. OWL represents
classes of instances
15. Hexokinase activity in GO
16. • A book of synonyms, often including related
and contrasting words and antonyms.
• A book of selected words or concepts, such
as a specialized vocabulary of a particular
field, as of medicine or music.
•Words are symbolic representations of concepts
• Often used in information retrieval - a key
aspect of which is navigation
What is a Thesaurus?
17. MeSH is a vocabulary of
terms used for indexing
medical documents on the
Medical Subject Headings (MeSH)
19. Things you can say about a concept
20. What can we Say?
• All ears are part of some head
• All head have part some ear?
• Head is a broader term than ear
• Ear is a narrower term than head
• Interesting conversion issues
21. Ontological Distinctions
• Upper level ontologies: Continuant, occurrants,
Independence and dependence, etc. etc.
• Guides to make common distinctions and choose
appropriate relationships (Top down)
• Describe and define a load of classes and use a reasoner
• Start with a load of terms and sort it out (Middle out)
• Move along the spectrum as you need features (Migratory)
• Ontology normalisation…