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Introduction to (Geo)Ontology

Barry Smith

http://ontology.buffalo.edu/smith

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natural language labels

to make the data cognitively accessible to human beings

and algorithmically tractable to computers

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compare: legends for mapscompare: legends for maps

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compare: legends for mapscommon legends allow (cross-border) integration

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ontologies are legends for data

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compare: legends for diagrams

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legends

help human beings use and understand complex representations of reality

help human beings create useful complex representations of reality

help computers process complex representations of reality

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computationally tractable legends

help human beings find things in very large complex representations of reality

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maps may be correct by reflecting topology, rather than geometry

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two kinds of annotations

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names of types

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names of instances

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First basic distinction

type vs. instance

(science text vs. diary)

(human being vs. Tom Cruise)

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Ontology types Instances

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Ontology = A Representation of Types

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An ontology is a representation of types

We learn about types in reality from looking at the results of scientific experiments in the form of scientific theories

experiments relate to what is particular science describes what is general

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where in the body ? where in the cell ?

what kind of organism ?

what kind of disease process ?

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to yield: distributed accessibility of the data to humansreasoning with the datacumulation for purposes of researchincrementality and evolvabilityintegration with clinical data

Creating broad-coverage semantic annotation systems for biomedicine

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The Gene Ontology

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The Idea of Common Controlled Vocabularies

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity

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The Idea of Common Controlled Vocabularies

MouseEcotope GlyProt

DiabetInGene

GluChem

Holliday junction helicase complex

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what cellular component?

what molecular function?

what biological process?

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Michael Ashburner

GEO.OBO• biological samples

• populations, epidemics

• speciation, evolutionary processes in space and time

• museum artifacts

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