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Ontologie als konkretisierte Darstellung der Wirklichkeit

Barry Smith

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MeSH

Medical Subject Headings

National Library of Medicine

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What MeSH is for

Indexing (Tagging) Medical Literature

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MeSH Descriptors

Index Medicus Descriptor

Anthropology, Education, Sociology and Social Phenomena (MeSH Category)

Social Sciences

Political Systems

National Socialism

What (bio-)ontologies are for

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what molecular function ?

what disease process ?

need for semantic annotation of data

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need for semantic annotation of data

through labels (nouns, noun phrases)which are algorithmically processable

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warum ist die Gene Ontologie so erfolgreich?

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natural language tags

to make the data cognitively accessible to human beings

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compare: legends for mapscompare: legends for maps

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or legends for cartoons

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ontologies are legends for data

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ontologies are legends for images

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what brain region ?

what brain function ?

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xi = vector of measurements of gene i k = the state of the gene ( as “on” or “off”)θi = set of parameters of the Gaussian model......

ontologies are legends for mathematical equations

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The Gene Ontology as Integrator

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity

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annotation using common ontologies yields integration of databases

MouseEcotope GlyProt

DiabetInGene

GluChem

Holliday junction helicase complex

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annotation using common ontologies can yield integration of image data

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annotation using common ontologies can support comparison of image data

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truth

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simple representations can be true

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there are true cartoons

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a cartoon can be a veridical representation of reality

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Cartographic Projection

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maps may be correct by reflecting topology, rather than geometry

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a fully labeled image can be aneven more veridical representation of reality

an image can be a veridical representation of reality

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cartoons, like maps, always have a certain threshold of granularity

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grain resolution

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grain resolution serves cognitive accessibility

we transform true imagesinto true cartoons

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instances vs. types

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two kinds of annotations

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names of instances

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names of types

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pathway maps are representations of complexes of types

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molecular images and radiographic images are

representations of instances

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MIAKT system

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Patient #47920

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Mammography #31667

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Mammography #31667

Medical-Image #44922

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MRI-Exam #32388

Medical-Image #44922

Mammography #31667

Patient #47920

Breast #1388

Abnormality #86023

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There is only one realitybut many different representations thereof, including many different ontologies

different ontologies can be simultaneously veridical, e.g. because of non-overlapping domains, or because of differential selection

(“multi-perspectivalism”)

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Reality exists before any representation

R

And also most structures in reality are there a priori

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The ontologist becomes with a mental representation (‘Bild’)

R

B1

Some portions of reality escape his attention.

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R

a part of which he concretizes in an ontology

O1

B1

#1

both mental representation and ontology refer to the same reality

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R

A second ontologist makes a different selection

O1

B2B1

O2

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R

Veridical ontologies can always be mapped by taking reality as

benchmark

O1

B2B1

O2

Om

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but ontologies can be non-veridical, because of different

kinds of errors

errors of mismatch with reality

errors of understanding

errors of coding

RR

O1O1

B2B2B1B1

O2O2

OmOm

RR

O1O1

B2B2B1B1

O2O2

OmOm

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Typology of errors (Werner Ceusters)

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http://org.buffalo.edu

RR

O1O1

B2B2B1B1

O2O2

OmOm