1 Doing Ontology Over Images Barry Smith. What ontologies are for

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Doing Ontology Over Images

Barry Smith

What 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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natural language labels

to make the data cognitively accessible to human beings

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compare: legends for mapscompare: legends for maps

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compare: 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 lesion ?

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 OBO Foundry Idea

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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there are also true cartoon sequences

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Pathway diagrams are annotated dynamic cartoons

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pathways can be represented at different levels of granularity

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the jaw

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Joint capsule

Netter

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Mandible and condyle movement

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Condyle position in fossa wrt location of disc

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TMJ in jaw open and closed positions

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Parts• 1 head of condyle F• 2 neck of condyle F• 3 disc B• 4 retrodiscal tissue B• 7 articular eminence F• 8 zygomatic arch F• 10 upper head of lateral pterygoid muscle F• 11 lower head of lateral pterygoid muscle F

Holes• 5 lower joint compartment B• 6 upper joint compartment B

Holes and Parts

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ANTERIOR

Temporomandibular Joint (TMJ)

from Thomas Bittner and Louis Goldberg, KR-MED 2006

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adjacency relations

No connectednessOnly (temporary) adjacency

Connectednessadjacencygraph

Adjacency relations

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Frames of reference

Rigid = do notchange shape(bones)

A

BC

DE

F

The extension of the axis of the condyleintersects the fossa in region D

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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