Ontologies in tics

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Ontologies in Bioinformatics

Robert Stevens

Department of Computer Science

University of Manchester

[email protected]




Introduction

What is knowledge?

What is an ontology?

Relationships between the two communities

The last decade of bio-ontologiesontologies

The future




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




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]




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




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




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




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




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




The Gene Ontology




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




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«.




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




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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http://img.cs.man.ac.uk/stevens

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




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

Ontologies in tics

Documents

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