Earth to Major Tom Barry Smith

2 Earth = GIS Human Body = AIS

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

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

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

4.htm

Layers of the epidermis kidshealth.org/kid/ body/skin_noSW.html

Digital Anatomist Foundational Model of Anatomy (Department of Biological Structure, University of Washington, Seattle)

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

Examples of simple formal- ontological structures is_a hierarchies part_of hierarchies

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

A Window on Reality

Dependence Relations OrganismsDiseases

A Window on Reality OrganismsDiseases

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

A Window on Reality

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

Formal-Ontological Categories object process site layer fragment quality function relation boundary region

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

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

to define these relations properly we need to take account of both universals and instances in reality

A is_a B = def. ‘A’ is more specific in meaning than ‘B’

unicorn is_a one-horned mammal alien implant removal is_a surgical process Chios energy healing is_a therapeutic process

This linguistic reading yields a more or less coherent reading of relations like: ‘is_a’ ‘synonymous_with’ ‘associated_to’

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.

for how can concepts, on the linguistic reading, figure as relata of relations like: part_of adjacent_to connected_to

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 ?

is_a human is_a mammal all instances of the universal human are as a matter of necessity instances of the universal mammal

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

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

Instance-level relations part_of is_located_at has_participant has_agent earlier...

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

Different scientific cultures/terminologies immunology genetics cell biology

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?

Answer: “Ontology”

Virtual Soldier Project Major Tom

Virtual Soldier Project Anatomy Reference Ontology = theoretical framework surrounding the Digital Anatomist Foundational Model of Anatomy

Virtual Soldier Project: Reference Ontology of Anatomy Reference Ontology of Physiology Reference Ontology of Disease Pathways

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)

Parthood vs. Location a part_of b = a located_in b OR a contained_in b

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

at every level of granularity

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

anatomical structure body substance anatomical space boundary anatomical attribute anatomical relationship

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

portion of body substance inherits its shape from contained urine menstrual flood blood...

anatomical space cavities, conduits

boundary bona fide fiat People/Mintchev/stomach.htm

anatomical attribute mass weight temperature your temperature its value now

anatomical relationship located_in contained_in adjacent_to connected_to surrounds lateral_to (West_of) anterior_to

DNA Protein Organelle Cell Tissue Organ Organism m m Scales of anatomy m

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)

Quantities in AIS – raster/vector, no fixed coordinates (flexible earth), 3-Dimensional views

Normativity/Canonicity Instances Statistics Pathology

Development and growth

single-cell zygote multi-cell zygote morula early blastocyst gastrula new born infant adolescent young adult

together with SPAN ontologies for processes/transformations physiological processes development processes aging processes growth processes SNAP

time canonical vs. non-canonical

time undeformed  deformed

time undeformed  deformed these are not instances

time undeformed  deformed WINDOWS ON REALITY

time undeformed  deformed SYMBIOSIS OF KNOWLEDGE ABOUT UNIVERSALS AND INSTANCES

time undeformed  deformed

Homology Comparative interplanetary GIS

time undeformed  deformed human chimpanzee mouse fly yeast bacteria

time undeformed  deformed human chimpanzee mouse fly yeast bacteria

What do the kidneys do? Modularity

How does a kidney work? NEPHRON

Nephron Functions FUNCTIONAL SEGMENTS

Bodily Systems respiratory digestive skeletal circulatory musculatory immune

ENDOCRINE SYSTEM

Taking parts out tissue samples

Functions Genetic programming

Time, pathology

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

C c at t c at t 1 C 1 transformation_of

C c at t c at t 1 C 1 embryological development

C c at t c at t 1 C 1 tumor development

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

derives_from c derives_from c 1 =def c and c 1 are non-identical and exist in continuous succession

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

two initial components fuse to form a new component C c at t C 1 c 1 at t 1 C' c' at t