Choosing and Building Knowledge Artefacts

Robert Stevens

Bio Health Informatics Group

School of Computer Science

University of Manchester

Robert.stevens@manchester.ac.uk

Introduction

• Do you need an ontology?

• A case in point

• What is an ontology?

• What is an vocabulary?

• Top down, bottom up, middle out, migratory, …

• BBC News page that shows an article about an outbreak of Polio in Namibia

BBC news article

• COHSE highlights terms from the underlying background knowledge

Term identification

• COHSE provides links to NELI, Wikipedia and NaTHNac services.

New link targets

• COHSE highlights terms from underlying ontology generating more link targets

Link to NeLI from BBC

Polio

Polio The DiseasePolio The Virus

Labels and Meaning

Vaccine(The Thing e.g a aliquot of vaccine)

Vaccination(Treatment, the form of delivery)

Immunisation(The Process)

Both processes but mean different things

So what is an ontology?

Catalog/ID

Thesauri

Terms/glossary

Informal Is-a

FormalIs-a

Formalinstance

Frames(properties)

General Logicalconstraints

Valuerestrictions

Disjointness,Inverse, partof

Gene Ontology

Mouse AnatomyEcoCyc

PharmGKB

TAMBIS

Arom

After Chris Welty et al

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. ... [members.optusnet.com.au/~webindexing/Webbook2Ed/glossary.htm]

• 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. [www.cordis.lu/ist/ka1/administrations/publications/glossary.html]

• 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 vocabularies. [www.genpromag.com/Glossary~LETTER~O.html]

• 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.[www.filosofia.net/materiales/rec/glosaen.htm]

• 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 comprehensive forms.[www.atf.org.au/papers/glossary.asp]

• The collection of distinct entities that is considered to exist within a particular view of a portion of the universe.[www.geocities.com/CapitolHill/1284/glossdef.html]

• 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]

Knowledge Artefacts

• A set of discriminations in style and purpose

• They all capture knowledge in some form

• CS types call anything that does this an ontology

• Philosophers very much do not

• Formal language and formal ontology

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 in philosophy.”

• http://www-ksl.Stanford.edu/kst/what-is-an-ontology.html

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

OWL represents classes of instances

A

BC

Hexokinase activity in GO

• 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?

MeSH is a vocabulary of terms used for indexing medical documents on the web.

Medical Subject Headings (MeSH)

SKOS Idea

Annotation Concept Concept Scheme

Resource Concept ConceptScheme

Image Doc Page…

describedBy organisedIn

Things you can say about a concept

Concept

inScheme

isSubjectOf

broader

narrower

related

scopeNote

definition

historyNote

altLabel

prefLabel

altSymbol

prefSymbol

symbol

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

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 (Bottom up)

• Start with a load of terms and sort it out (Middle out)

• Move along the spectrum as you need features (Migratory)

• Ontology normalisation…