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Ontologies in Bioinformatics
Robert Stevens
Department of Computer Science
University of Manchester
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Introduction
What is knowledge?
What is an ontology?
Relationships between the two communities
The last decade of bio-ontologiesontologies
The future
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What is Knowledge?
Knowledge ± all information andan understanding to carry out
tasks and to infer new
information
Information -- data equipped withmeaning
Data -- un-interpreted signals
that reach our senses
Michael AshburnerProfessor
University of Cambridge
UK
ISM
B
NameJob
Institution
Country
Con
f
manacademic, senior
ancient university, 5 ratedEuropean
important figure in biology
BI
O
L
O
G
Y
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Things, Symbols & Concepts Humans require words (or at least symbols) to communicate
efficiently. The mapping of words to things is only indirectlypossible. We do it by creating symbols that stand for things.
The relation between symbols and things has been described in theform of the meaning triangle:
³Jaguar³
Concept
[Ogden, Richards, 1923]
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Representing Knowledge
Language uses symbols and rules (natural language) tocommunicate knowledge
Need human intelligence to deal with pragmatics
NLP notoriously difficult Need to capture knowledge in a computationally amenable
manner
Ontology: A conceptual model
Ontology plus lexicon is a terminology
Primary aim of creating a shared understanding of a domain andthe relationships within that domain
Common symbols for the things within a domain
Capturing domain knowledge with fidelity and precision
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Sh
aring info
Sharing meaning
Metadata
Data describing the content and
meaning of resources and
services.
But everyone must speak the same
language«
Terminologies
Shared and common vocabularies
For search engines, agents,
curators, authors and users
But everyone must mean the same
thing«
Serviceprovider
Serviceprovider Service
provider
Serviceprovider
Serviceprovider
Ontologies
Shared and commonunderstanding of a domain
Essential for search, exchange and
discovery
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What is an Ontology?
Concepts: Units of thought: Classes and individuals;
Protein, Gene, DNA, Hexokinase, glycolysis,«
Terms: Labels for concepts ³Protein´, ³Gene´,«
Relationships: Semantic links between concepts
Is-a-kind, is-a, part-of, name-of,«
Taxonomy backbone of ontology
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So what Counts as an ontology?[Deborah McGuinness, Stanford]
Catalog/ID
Thesauri
Terms/
glossary
InformalIs-a
FormalIs-a
Formalinstance
Frames(properties)
GeneralLogicalconstraints
Valuerestrictions
Disjointness,Inverse, partof
Gene Ontology
Mouse AnatomyEcoCyc
PharmGKB
TAMBIS Arom
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The art of ranking things in genera and species is of no small importanceand very much assists our judgment as well as our memory. You know
how much it matters in botany, not to mention animals and other
substances, or again moral and notional entities as some call them.
Order largely depends on it, and many good authors write in such a
way that their whole account could be divided and subdivided
according to a procedure related to genera and species. This helps onenot merely to retain things, but also to find them. And those who have
laid out all sorts of notions under certain headings or categories have
done something very useful.
Gottfried Wilhelm Leibniz, New Essays on Human Understanding
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The Gene Ontology
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Bio-Ontologies in the Past Decade
Explicit use of ontologies fairly recent
EcoCyc and RiboWeb using Frame Based Systems to createknowledge bases
An area in which the CS community can test their technology Large, complex and dynamic
³A knowledge based discipline´
The post-genomic era encourages the need for sharedunderstanding
Cross-genome comparisons need structured, controlledvocabularies
Moved from small nich to a much bigger niche
Biologists are building ontologies
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Uses of Bio-Ontologies
Controlled vocabularies for annotation
Describing schema dn the content of schema
Domain maps
Query mechanisms
Resolution of semantic heterogeneiety
Text analysis«.
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The Gene Ontology
Tutorial and the first Bio-Ontologies meeting at ISMB 1998 in
Montreal
Fly, mouse and yeast get together to develop GO
First release some 3,500 terms covering Molecular Function,
biological Process and Cellular Component
Now some 15,000 terms and growing
Gene Ontology Consortium covers some 15 organism
databases plus SWISS-PROT and others
Synonyms, abbreviations and associations to gene products:
Access to names, genes etc.
A common understanding across a community
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GO
DAG for heparin biosynthesis
GO:0003673 : Gene_Ontology (46199)
GO:0008150 : biological_process (30188)GO:0008151 : cell growth and/or maintenance (20547)
GO:0008152 : metabolism (14693)
GO:0016051 : carbohydrate metabolism (267)GO:0006023 : aminoglycan metabolism (18)
GO:0030203 :glycosaminoglycan metabolism
GO:0030202 : heparin metabolism (3)
GO:0030210 : heparin biosynthesis (3)
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Open bio-Ontologies (OBO) Go, though large, is narrow
Sequence Ontology
Chemical Ontology
Promotes a common ontology format, tools and house-style
Micro-array community a further boost ± avoiding mistakes of
previous bioinformatics resources
Need ontolgoies for phenotype, tissues, anatomies, etc.
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Two CommunitiesComputer ScientistsBuilding ontologies KR Reasoning
Better Ontologies
BiologistsOntology content
Domain Knowledge
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What are
We Saying?
Person
WomanMan
is-ais-a
Are all instances of Man instances of Person?Can an instance of Person be both a Manand an instance of Woman?Can there be any more kinds of Person?
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This Year¶s Meeting
A theme of text analysis and ontology
First time talks have matched theme
Ontologies and indexing
Integrating ontologies into NLP systems
Ontologies in information retrieval
Developing terminologies
GO in NLP
New Ontologies Semantic Similarity
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Opportunities Ontologies to help text analysis
Text analysis to help build ontologies
Biology community steadily building a large number of large
domain ontologies
CS community can help build computationally amenable
ontologies
Vast quantities of domain knowledge in natural language forms
in literature and databanks
Opportunities for language and ontology communities
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