Interest in "ontologies": Neuroinfromatics Working Group February 2001 meetings HBP PIs

2. Human Brain Project • Interest in "ontologies": • Neuroinfromatics Working Group • February 2001 meetings • HBP PIs • Neuroanatomy Ontology Workshop

3. Human Brain Project Expectations: Neuroanatomy Ontology should • "Index and retrieve neuroscience information • by species for mouse, rat, macaque, human; • Define several hierarchical schemes • for grouping primary structures • to support accessing information in bigger chunks; • Specify the relation of several thousand synonyms • to allow the retrieval of information • in terms of different nomenclatures; • Provide atlases of segmented coronal brain sections • for warping of MRI and PET scans." Neuroanatomy Ontology Workshop Summary

4. Explaining the Brain to a Computer Cornelius Rosse M.D., D.Sc., Structural Informatics Group University of Washington Mark S. Tuttle Ph.D., Apelon Federal Services, Inc.

5. Explaining the Brain to a Computer • Goals: • Why we need to explain the brain to a computer? • What to explain about the brain to a computer? • How to do it? • What uses will it have?

6. Why to explain the Brain to a Computer? • "Few researchers use existing ontologies; • why do another one that no one will use?" • Neuroanatomy Ontology Workshop Summary • ”Why do we need a standard taxonomy? • May disenfranchise a substantial user community." • "Neuro-ontology development is an ill-posed problem.” • HBP PIs' question/comment

7. Why to explain the Brain to a Computer? • Prototype problem: • Cortical language mapping • Human Brain Project grant: • Structural Information Framework for Brain Mapping • J.F. Brinkley PI.

8. Cortical language mapping Superior temporal gyrus

9. Intra-operative language sites Locations tested Active language site

10. Variant gyri Supramarginal gyrus Variant gyral pattern

11. Intra-operative language sites Cortical language sites

12. Functional MRI language sites

13. Superimposed FMRI and cortical language maps

14. Incidence of cortical language sites recorded with surface coordinate system of Caviness et al

15. Montreal Average Brain All Male Patients N=15

16. Why to explain the Brain to a Computer? • Graphical models: • Document existence of probabilistic • structure /function correlations • Cannot reveal • nature of relationships • meaning of relationships • Requirement: • Add meaning to graphical data • Symbolic Model

17. Why to explain the Brain to a Computer? • Symbolic model • toempower the computer to make inferences about the brain; • to support knowledge-based applications for addressing neuroscience problems.

18. Explaining the Brain to a Computer • Goals: • Why we need to explain the brain to a computer? • What to explain about the brain to a computer? • How to do it? • What uses will it have?

19. What • to explain about the brain to a computer? • "What is the knowledge we need to classify?" • "What levels of knowledge are to be included?" • "Explicit definition of domain of neuroscience is a daunting task." • HBP PIs' question/comments

20. What • to explain about the brain to a computer? • Two key strategic issues: • 1. Constraints • 2. Priorities

21. What • Constraints? Subdomains in language mapping problem at UW: Neuroanatomy Richard Martin Kate Mulligan Neuroradiology Ken Maravilla Neurosurgery George Ojemann Psychology David Corina Karen Kinbar

22. What • Constraints? • Subdomains in language mapping problem at UW: • Neuroanatomy Structural Informatics Richard Martin Graphical modeling • Kate Mulligan Andrew Poliakov, Jeff Prothero, Kevin Hinshaw • Neuroradiology Symbolicmodeling • Ken Maravilla Cornelius Rosse, Richard Martin, • Jose Mejino, Linda Shapiro • NeurosurgeryDatabase • George Ojemann Rex Jakobovits • PsychologyInformation System design • David Corina Jim Brinkley • Karen Kinbar

23. What • Priorities? • Motivation for Structural Informatics: • Manifestations of health and disease • may be regarded as • attributes of anatomical structures; • Logical and consistent representation of anatomical structure • can provide the foundation for organizing • other biomedical information.

24. What • Priorities? • "Any integrative approach by necessity will require a neuroanatomical basis" • "Neuroanatomical ontology should provide the logical framework for • organizing and locating information about the brain." • Neuroanatomy Ontology Workshop Summary

25. What is anatomy? • "Anatomy" …….. a homonym for anatomy (structure) • e.g., anatomy of the frog, hand, brain anatomy (science) • systematized branch of knowledge accumulated about anatomy (structure).

26. What is structure? • "Structure" ……. a homonym for something composed of parts; • (e.g., a building, a cell, a plant, brain) • i.e., a material object the arrangement or interrelation of all the parts of a whole. • (e.g., of a sentence, a symphony, • or of society, government, • or of the atom, the hand) • i.e., relationships

27. What is structure? • Structure of a material object • Structure of Structure = • Subobjects (parts) + Structural Relationships • The components of an object • and their manner of arrangement in constituting a whole.

28. What is anatomical structure? • ”Anatomical Structure" … a homonym for • a material object generated by the coordinated expression of an organism's • own structural genes; • the arrangement (physical interrelation) of • all the parts of an anatomical structure • in constituting the whole. • Synonym: 'biological structure'

29. What • Priorities? • Question: • What to explain first about the brain to a computer? • Answer: • The structure of anatomical structures • that constitute the brain. • StructureBrain= ({SubobjectBrain}, {Structural relationship Brain})

30. What • Priorities? • Question: • What to enter in the computer to explain (model) • the structure of the brain? • Answer: • Symbols for anatomical structures • of the brain. • Symbols for structural relationships • within the brain.

32. Referent What kind of symbols? Triangle of Meaning Symbol “Term” Thought “Concept”

33. What is a symbolic model? • Symbolic model, • a conceptualization of a domain of discourse • represented with non-graphical symbols; • in computer-processible (“understandable”) form; • supports inference (reasoning).

34. What is a foundational model? • Foundational Model • is a symbolic model; • declares the principles • for including concepts and relationships • that are implicitly assumed • when knowledge of the domain • is applied in different contexts; • explicitly defines • concepts and relationships • necessary and sufficient for consistently • modeling the structure of the • coherent knowledge domain.

35. What is the Foundational Model of Anatomy (FM)? • Foundational Model of Anatomy • is a symbolic model of the physical organization of the human body; • declares the principles • for including concepts and relationships • that are implicitly assumed • when knowledge of anatomy • is applied in different contexts; • explicitly defines • concepts and relationships • necessary and sufficient for consistently • modeling the structure of the • human body.

36. What is the Foundational Model of Anatomy (FM)? • A symbolic model of anatomy (science) • represents the physical organization (structure) • of biological organisms; • currently limited to the human body. • "Foundational" because • anatomy is fundamental to all • biomedical sciences; • anatomical concepts encompassed by FM • generalize to all biomedical domains.

37. Foundational Model of Anatomy Fm = (Ao, ASA, ATA, Mk) where: Ao = Anatomy ontology ASA = Anatomical Structural Abstraction ATA = Anatomical Transformation Abstraction Mk = Metaknowledge (principles, rules, axioms)

38. Foundational Model of Anatomy Anatomical Structural Abstraction Fm = (Ao, ASA, ATA, Mk) (1) ASA = (Do, Bn, Pn, SAn) (2) where: Do = Dimensional ontology Bn = Boundary network Pn = Part-of network SAn = Spatial Association network

39. Foundational Model of Anatomy Spatial Association Network Fm = (Ao, ASA, ATA, Mk) (1) ASA = (Do, Bn, Pn, SAn) (2) SAn = (Ln, On, Cn) (3) where: Ln = Location On = Orientation Cn = Connectivity

40. Anatomy Ontology Anatomical Structure Organ Part Organ Subdivision Cardiac Chamber -is a- Right Ventricle

41. Dimensional Ontology Anatomy Ontology Anatomical Structure Volume (3-D) Organ Part Organ Subdivision Polyhedron Cardiac Chamber -is a- Right Ventricle

42. Spatial Ontology Anatomy Ontology Boundary Network Anatomical Structure Line (1-D) Surface (2-D) Volume (3-D) Organ Part Anterior Interventricular Sulcus Anatomical Feature Organ Subdivision Polyhedron -is a- Right Coronary Sulcus Cardiac Chamber Sternocostal Surface bounded by -is a- bounded by Inferior margin of heart boundary of Diaphragmatic Surface Coronary Sulcus bounded by Posterior IV Sulcus Anatomical Landmark -is a- Apex Crux of heart Point (1-D) Right Ventricle

43. Spatial Ontology Anatomy Ontology Boundary Network Anatomical Structure Line (1-D) Surface (2-D) Volume (3-D) Organ Part Anterior Interventricular Sulcus Anatomical Feature Organ Subdivision Polyhedron -is a- -is a- Heart Right Coronary Sulcus Cardiac Chamber Sternocostal Surface bounded by Part-of Network has -is a- super- object bounded by Infundibulum Inferior margin of heart Inflow part of RV has boundary of subobject Diaphragmatic Surface Coronary Sulcus Wall of RV Cavity of RV bounded by Posterior IV Sulcus Anatomical Landmark Cavity of infund. Cavity of infl.part -is a- Apex Crux of heart Point (1-D) Right Ventricle

44. Spatial Ontology Anatomy Ontology Boundary Network Anatomical Structure Line (1-D) Surface (2-D) Volume (3-D) Organ Part Anterior Interventricular Sulcus Anatomical Feature Organ Subdivision Polyhedron -is a- -is a- Heart Right Coronary Sulcus Cardiac Chamber Sternocostal Surface bounded by Part-of Network has -is a- super- object bounded by Infundibulum Inferior margin of heart Inflow part of RV has boundary of subobject Diaphragmatic Surface Coronary Sulcus Wall of RV has adjacency Cavity of RV bounded by has adjacency Posterior IV Sulcus Anatomical Landmark Cavity of infund. Cavity of infl.part to left anterior inferior inferior Left ventricle -is a- Pericardial sac Diaphragm Apex Crux of heart Point (1-D) Spatial Association Network Right Ventricle

45. Foundational Model of Anatomy Fm = (Ao, ASA, ATA, Mk) FmBODY = {FmANATOMICAL_ENTITY}

46. Explaining the Brain to a Computer • Goals: • Why we need to explain the brain to a computer? • What to explain about the brain to a computer? • How to do it? • What uses will it have?

47. Explaining the Brain to a Computer • What about non-anatomical information? • Is it an attribute of an anatomical structure? • Does it need its own symbolic model? • Adopt from existing sources? • Integrate with anatomy model?

48. What • to explain about the brain to a computer? • "What is the knowledge we need to classify?" • "What levels of knowledge are to be included?" • "Explicit definition of domain of neuroscience is a daunting task." • HBP PIs' question/comments

49. What • to explain about the brain to a computer? • Summary of strategy • Constrain concept domain • "Divide and conquer”; • Priority: Symbolic Model of anatomical structure • non-ambiguity • comprehensiveness • highest level of granularity • Use anatomy model as the logical foundation for • other concept domains.