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 maps
compare 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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ontologies are legends for mathematical equations
xi vector of measurements of gene i k the
state of the gene ( as on or off) ?i set of
parameters of the Gaussian model ... ...
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The OBO Foundry Idea
GlyProt
MouseEcotope
sphingolipid transporter activity
DiabetInGene
GluChem
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annotation using common ontologies yields
integration of databases
GlyProt
MouseEcotope
Holliday junction helicase complex
DiabetInGene
GluChem
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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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an image can be a veridical representation of
reality
a fully labeled image can be an even more
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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Holes and Parts

• 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

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Temporomandibular Joint (TMJ)
ANTERIOR
from Thomas Bittner and Louis Goldberg, KR-MED
2006
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adjacency relations
Connectedness adjacency graph
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Frames of reference
F
C
E
Rigid do not change shape (bones)
B
D
A
The extension of the axis of the
condyle intersects 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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Medical-Image 44922
Mammography 31667
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Patient 47920
Medical-Image 44922
Breast 1388
MRI-Exam 32388
Mammography 31667
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SNAP and SPAN in brain imaging

• SNAP CT Computer TomographyPET Positron
  emission tomographySPECT Single Photon Emission
  CTMRTfMRTMRSSPANEKP event correlate
  potentialquantitative electroencephalographyqEEG
  

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• canonicity !
• fiatness !
• granularity !

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• digital representations of analogue reality