Doing Ontology Over Images
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Doing Ontology Over Images
Barry Smith
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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