Earth to Major Tom Barry Smith

http://ontologist.com1 Earth to Major Tom Barry Smith http://ontologist.com

2 Earth = GIS Human Body = AIS

http://ontologist.com3 Two sides to SDTS Quantitative: Spatial Object Definitions (Raster/Vector...) Qualitative: Standard Entities

4 SDTS Spatial Object Definitions – 0-, 1-, 2-dimensions – elemental and aggregates – some examples from SDTS Node: topological junction of two or more links or chains, or is at an end point of link or chain Chain: nonbranching sequence on non-intersecting line segments or arcs, bounded by nodes at each end http://campus.fct.unl.pt/ama/tsig/slides/overview.ppt

5 Conceptual Level Standard Entities –Watercourse: a way or course through which water may or does flow (includes stream, river, anabranch, barranca, branch, brook, canal, channel, creek, culvert, ditch, drain, flume, fork, lode, narrows,... wash) Standard Attributes –Intermittent/Perennial: occurring in interrupted sequence vs. present at all seasons of the year

http://ontologist.com6 GIS strong on quantitative side, weak on qualitative side No robust geospatial ontology = no theoretically grounded taxonomy of the types of entities and relations in the geospatial world

http://ontologist.com7 http://www.sedris.org/stc/2004/tu/edcs/sld02 4.htm

http://ontologist.com8 Layers of the epidermis kidshealth.org/kid/ body/skin_noSW.html

http://ontologist.com9 Digital Anatomist Foundational Model of Anatomy (Department of Biological Structure, University of Washington, Seattle)

http://ontologist.com10 Goal in Biomedical Informatics use the methodology of formally defined relations and a common top-level ontology to bridge the granularity gap between genomics and proteomics data and phenotype (clinical, pharmacological, patient centered) data From molecules to diseases

http://ontologist.com11 Examples of simple formal- ontological structures is_a hierarchies part_of hierarchies

http://ontologist.com12 Pleural Cavity Pleural Cavity Interlobar recess Interlobar recess Mesothelium of Pleura Mesothelium of Pleura Pleura(Wall of Sac) Pleura(Wall of Sac) Visceral Pleura Visceral Pleura Pleural Sac Parietal Pleura Parietal Pleura Anatomical Space Organ Cavity Organ Cavity Serous Sac Cavity Serous Sac Cavity Anatomical Structure Anatomical Structure Organ Serous Sac Mediastinal Pleura Mediastinal Pleura Tissue Organ Part Organ Subdivision Organ Subdivision Organ Component Organ Component Organ Cavity Subdivision Organ Cavity Subdivision Serous Sac Cavity Subdivision Serous Sac Cavity Subdivision part_of is_a

http://ontologist.com13 A Window on Reality

http://ontologist.com14 Dependence Relations OrganismsDiseases

http://ontologist.com15 A Window on Reality OrganismsDiseases

http://ontologist.com16 Pleural Cavity Pleural Cavity Interlobar recess Interlobar recess Mesothelium of Pleura Mesothelium of Pleura Pleura(Wall of Sac) Pleura(Wall of Sac) Visceral Pleura Visceral Pleura Pleural Sac Parietal Pleura Parietal Pleura Anatomical Space Organ Cavity Organ Cavity Serous Sac Cavity Serous Sac Cavity Anatomical Structure Anatomical Structure Organ Serous Sac Mediastinal Pleura Mediastinal Pleura Tissue Organ Part Organ Subdivision Organ Subdivision Organ Component Organ Component Organ Cavity Subdivision Organ Cavity Subdivision Serous Sac Cavity Subdivision Serous Sac Cavity Subdivision part_of is_a

http://ontologist.com17 A Window on Reality

http://ontologist.com18 We can reason across such hierarchies and combinations but only if the top-level categories and associated formal-ontological relations are well-defined and used consistently

http://ontologist.com19 Formal-Ontological Categories object process site layer fragment quality function relation boundary region

http://ontologist.com20 Formal-Ontological Relations is_identical_to is_a part_of develops_ from derives_ from located_at depends_on is_boundary_of has_participant has_agent adjacent_to contained_in precedes is_functioning_of has_function intends

http://ontologist.com21 To support integration of ontologies relational expressions such as is_a part_of... should be used in the same way by all the ontologies to be integrated

http://ontologist.com22 to define these relations properly we need to take account of both universals and instances in reality

http://ontologist.com23 A is_a B = def. ‘A’ is more specific in meaning than ‘B’

http://ontologist.com24 unicorn is_a one-horned mammal alien implant removal is_a surgical process Chios energy healing is_a therapeutic process

http://ontologist.com25 This linguistic reading yields a more or less coherent reading of relations like: ‘is_a’ ‘synonymous_with’ ‘associated_to’

http://ontologist.com26 but it fails miserably when it comes to relations of other types part_of = def. composes, with one or more other physical units, some larger whole contains =def. is the receptacle for fluids or other substances.

http://ontologist.com27 for how can concepts, on the linguistic reading, figure as relata of relations like: part_of adjacent_to connected_to

http://ontologist.com28 connected_to =def. Directly attached to another physical unit as tendons are connected to muscles. How can a meaning or concept be directly attached to another physical unit as tendons are connected to muscles ?

http://ontologist.com29 is_a human is_a mammal all instances of the universal human are as a matter of necessity instances of the universal mammal

http://ontologist.com30 Evaluation Good ontologies are those whose general terms correspond to universals in reality, and thereby also to corresponding instances in reality.

http://ontologist.com31 Kinds of relations : is_a, part_of,... : this explosion instance_of the universal explosion : Mary’s heart part_of Mary

http://ontologist.com32 Instance-level relations part_of is_located_at has_participant has_agent earlier...

http://ontologist.com33 part_of For instances: part_of = instance-level parthood (for example between Mary and her heart) For universals: A part_of B =def. given any instance a of A there is some instance b of B such that a part_of b

http://ontologist.com34 Different scientific cultures/terminologies immunology genetics cell biology

http://ontologist.com35 But: each (clinical, pathological, genetic, proteomic, pharmacological …) information system uses its own classification system How can we overcome the incompatibilities which become apparent when data from distinct sources is combined?

http://ontologist.com36 Answer: “Ontology”

http://ontologist.com37 Virtual Soldier Project Major Tom

http://ontologist.com38 Virtual Soldier Project Anatomy Reference Ontology = theoretical framework surrounding the Digital Anatomist Foundational Model of Anatomy

http://ontologist.com39 Virtual Soldier Project: Reference Ontology of Anatomy Reference Ontology of Physiology Reference Ontology of Disease Pathways

http://ontologist.com40

http://ontologist.com41 The Anatomy Reference Ontology is organized in a graph-theoretical structure involving two sorts of links or edges: is-a (= is a subtype of ) (pleural sac is-a serous sac) part-of (cervical vertebra part-of vertebral column)

http://ontologist.com42 Parthood vs. Location a part_of b = a located_in b OR a contained_in b

http://ontologist.com43 Pleural Cavity Pleural Cavity Interlobar recess Interlobar recess Mesothelium of Pleura Mesothelium of Pleura Pleura(Wall of Sac) Pleura(Wall of Sac) Visceral Pleura Visceral Pleura Pleural Sac Parietal Pleura Parietal Pleura Anatomical Space Organ Cavity Organ Cavity Serous Sac Cavity Serous Sac Cavity Anatomical Structure Anatomical Structure Organ Serous Sac Mediastinal Pleura Mediastinal Pleura Tissue Organ Part Organ Subdivision Organ Subdivision Organ Component Organ Component Organ Cavity Subdivision Organ Cavity Subdivision Serous Sac Cavity Subdivision Serous Sac Cavity Subdivision

http://ontologist.com44 at every level of granularity

http://ontologist.com45 Top-Level Categories in the FMA anatomical entity non-physical anatomical entity physical anatomical entity anatomical relationship body substance material physical anatomical entity anatomical structure non-material physical anatomical entity body space boundaryanatomical attribute

http://ontologist.com46 anatomical structure body substance anatomical space boundary anatomical attribute anatomical relationship

http://ontologist.com47 anatomical structure (cell, lung, nerve, tooth) result from the coordinated expression of structural genes have their own 3-D shape

http://ontologist.com48 portion of body substance inherits its shape from contained urine menstrual flood blood...

http://ontologist.com49 anatomical space cavities, conduits

http://ontologist.com50 boundary bona fide fiat www.enel.ucalgary.ca/ People/Mintchev/stomach.htm

http://ontologist.com51 anatomical attribute mass weight temperature your temperature its value now

http://ontologist.com52 anatomical relationship located_in contained_in adjacent_to connected_to surrounds lateral_to (West_of) anterior_to

http://ontologist.com53 DNA Protein Organelle Cell Tissue Organ Organism 10 -5 m 10 -1 m Scales of anatomy 10 -9 m

http://ontologist.com54 Complexity of biological structures 30,000 genes in human 200,000 proteins 100s of cell types 100,000s of disease types 1,000,000s of biochemical pathways (including disease pathways)

http://ontologist.com55 Quantities in AIS – raster/vector, no fixed coordinates (flexible earth), 3-Dimensional views

http://ontologist.com56 Normativity/Canonicity Instances Statistics Pathology

http://ontologist.com57 Development and growth

http://ontologist.com58 single-cell zygote multi-cell zygote morula early blastocyst gastrula new born infant adolescent young adult

http://ontologist.com59 together with SPAN ontologies for processes/transformations physiological processes development processes aging processes growth processes SNAP

http://ontologist.com60 time canonical vs. non-canonical

http://ontologist.com61 time undeformed  deformed

http://ontologist.com62 time undeformed  deformed these are not instances

http://ontologist.com63 time undeformed  deformed WINDOWS ON REALITY

http://ontologist.com64 time undeformed  deformed SYMBIOSIS OF KNOWLEDGE ABOUT UNIVERSALS AND INSTANCES

http://ontologist.com65 time undeformed  deformed

http://ontologist.com66 Homology Comparative interplanetary GIS

http://ontologist.com67 time undeformed  deformed human chimpanzee mouse fly yeast bacteria

http://ontologist.com68 time undeformed  deformed human chimpanzee mouse fly yeast bacteria

http://ontologist.com69 What do the kidneys do? Modularity

http://ontologist.com70 How does a kidney work? NEPHRON

http://ontologist.com71 Nephron Functions FUNCTIONAL SEGMENTS

http://ontologist.com72 Bodily Systems respiratory digestive skeletal circulatory musculatory immune

http://ontologist.com73 ENDOCRINE SYSTEM

http://ontologist.com74 Taking parts out tissue samples

http://ontologist.com75 Functions Genetic programming

http://ontologist.com76 Time, pathology

http://ontologist.com77 To define bio-ontological relations we need to take into account both components and processes (= continuants and occurrents) Components are that which changes; they are the bearers of processes. cell participates_in cell division

http://ontologist.com78 C c at t c at t 1 C 1 transformation_of

http://ontologist.com79 C c at t c at t 1 C 1 embryological development

http://ontologist.com80 C c at t c at t 1 C 1 tumor development

http://ontologist.com81 transformation_of fetus transformation_of embryo larva transformation_of pupa adult transformation_of child C 2 transformation_of C 1 =def. any instance of C 2 was at some earlier time an instance of C 1

http://ontologist.com82 derives_from c derives_from c 1 =def c and c 1 are non-identical and exist in continuous succession

http://ontologist.com83 the new component detaches itself from the initial component, which itself continues to exist C c at t C c at t C 1 c 1 at t 1 c at t 1 C 1 c 1 at t the initial component ceases to exist with the formation of the new component

http://ontologist.com84 two initial components fuse to form a new component C c at t C 1 c 1 at t 1 C' c' at t

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