Doing Ontology Over Images

1. Doing Ontology Over Images • Barry Smith

2. What ontologies are for

3. what molecular function ? what disease process ? need for semantic annotation of data

4. need for semantic annotation of data through labels (nouns, noun phrases) which are algorithmically processable

5. natural language labels to make the data cognitively accessible to human beings

6. compare: legends for maps compare: legends for maps

7. compare: legends for cartoons

8. ontologies are legends for data

9. ontologies are legends for images

10. what lesion ? what brain function ?

11. ontologies are legends for mathematical equations 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 ... ...

12. The OBO Foundry Idea GlyProt MouseEcotope sphingolipid transporter activity DiabetInGene GluChem

13. annotation using common ontologies yields integration of databases GlyProt MouseEcotope Holliday junction helicase complex DiabetInGene GluChem

14. annotation using common ontologies can yield integration of image data

15. annotation using common ontologies can support comparison of image data

16. truth

17. simple representations can be true

18. there are true cartoons

19. a cartoon can be a veridical representation of reality

20. Cartographic Projection

21. maps may be correct by reflecting topology, rather than geometry

22. an image can be a veridical representation of reality a fully labeled image can be an even more veridical representation of reality

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

26. grain resolution

27. grain resolution serves cognitive accessibility we transform true imagesinto true cartoons

28. there are also true cartoon sequences

30. Pathway diagrams are annotated dynamic cartoons

31. pathways can be represented at different levels of granularity

32. the jaw

34. Joint capsule Netter

35. Mandible and condyle movement

36. Condyle position in fossa wrt location of disc

37. TMJ in jaw open and closed positions

38. 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

39. Temporomandibular Joint (TMJ) ANTERIOR from Thomas Bittner and Louis Goldberg, KR-MED 2006

40. No connectedness Only (temporary) adjacency Adjacency relations adjacency relations Connectedness adjacency graph

41. 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

42. instances vs. types

43. two kinds of annotations

44. names of instances

45. names of types

46. pathway maps are representations of complexes of types

47. molecular images and radiographic images are representations of instances

48. MIAKT system