choosing and building knowledge artefacts
DESCRIPTION
a presentation at Edinburgh, 2006TRANSCRIPT
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Choosing and Building Knowledge Artefacts
Robert Stevens
Bio Health Informatics Group
School of Computer Science
University of Manchester
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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, …
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• BBC News page that shows an article about an outbreak of Polio in Namibia
BBC news article
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• COHSE highlights terms from the underlying background knowledge
Term identification
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• COHSE provides links to NELI, Wikipedia and NaTHNac services.
New link targets
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• COHSE highlights terms from underlying ontology generating more link targets
Link to NeLI from BBC
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Polio
Polio The DiseasePolio The Virus
Labels and Meaning
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Vaccine(The Thing e.g a aliquot of vaccine)
Vaccination(Treatment, the form of delivery)
Immunisation(The Process)
Both processes but mean different things
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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
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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]
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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
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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
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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
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OWL represents classes of instances
A
BC
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Hexokinase activity in GO
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• 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?
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MeSH is a vocabulary of terms used for indexing medical documents on the web.
Medical Subject Headings (MeSH)
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SKOS Idea
Annotation Concept Concept Scheme
Resource Concept ConceptScheme
Image Doc Page…
describedBy organisedIn
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Things you can say about a concept
Concept
inScheme
isSubjectOf
broader
narrower
related
scopeNote
definition
historyNote
altLabel
prefLabel
altSymbol
prefSymbol
symbol
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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
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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…