Http://ontologist.com1 Earth to Major Tom Barry Smith .

http://ontologist.com 1

Earth to Major Tom

Barry Smith

http://ontologist.com


Earth = GISHuman 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

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


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://www.sedris.org/stc/2004/tu/edcs/sld024.htm

http://www.sedris.org/stc/2004/tu/edcs/sld024.htm


Layers of the epidermis

kidshealth.org/kid/ body/skin_noSW.html

http://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


Pleura(Wall of Sac)

Pleura(Wall of Sac)

VisceralPleura

VisceralPleura

Pleural SacPleural Sac

Parietal Pleura

Parietal Pleura

Anatomical SpaceAnatomical Space

OrganCavityOrganCavity

Serous SacCavity

Serous SacCavity

AnatomicalStructure

AnatomicalStructure

OrganOrgan

Serous SacSerous Sac

MediastinalPleura

MediastinalPleura

TissueTissue

Organ PartOrgan Part

Organ Subdivision

Organ Subdivision

Organ Component

Organ Component

Organ CavitySubdivision


Serous SacCavity

Subdivision

Serous SacCavity

Subdivision

part

_of

is_a


A Window on Reality


Dependence Relations

Organisms Diseases


A Window on Reality

Organisms Diseases


Pleural Cavity

Pleural Cavity

Interlobar recess

Interlobar recess



Pleura(Wall of Sac)

Pleura(Wall of Sac)

VisceralPleura

VisceralPleura


Parietal Pleura

Parietal Pleura



Serous SacCavity

Serous SacCavity

AnatomicalStructure

AnatomicalStructure

OrganOrgan


MediastinalPleura

MediastinalPleura

TissueTissue


Organ Subdivision

Organ Subdivision

Organ Component

Organ Component



Serous SacCavity

Subdivision

Serous SacCavity

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 Relationsis_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

<universal, universal>: is_a, part_of, ...

<instance, universal>: this explosion instance_of the universal explosion

<instance, instance>: 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


Anatomical Entity

Physical Anatomical Entity

Material Physical Anatomical Entity

-is a-

Non-material Physical Anatomical Entity

ConceptualAnatomical Entity

AnatomicalStructure

BodySubstance

BodyPart

HumanBody

OrganSystem

OrganCell

OrganPart

AnatomicalSpace

Anatomical Relationship

CellPart

Biological Macromolecule

Tissue


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



Pleura(Wall of Sac)

Pleura(Wall of Sac)

VisceralPleura

VisceralPleura


Parietal Pleura

Parietal Pleura



Serous SacCavity

Serous SacCavity

AnatomicalStructure

AnatomicalStructure

OrganOrgan


MediastinalPleura

MediastinalPleura

TissueTissue


Organ Subdivision

Organ Subdivision

Organ Component

Organ Component



Serous SacCavity

Subdivision

Serous SacCavity

Subdivision


at every level of granularity


Top-Level Categories in the FMAanatomical

entity

non-physicalanatomical entity

physicalanatomical entity

anatomical relationship

body substance

material physical anatomical entity

anatomical structure

non-material physical anatomical entity

body space

boundary anatomical attribute


anatomical structure

body substance

anatomical space

boundary

anatomical attribute



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

www.enel.ucalgary.ca/ People/Mintchev/stomach.htm

http://www.enel.ucalgary.ca/People/Mintchev/stomach.htm




anatomical attribute

mass

weight

temperature

your temperature

its value now



located_in

contained_in

adjacent_to

connected_to

surrounds

lateral_to (West_of)

anterior_to


DNA

Protein

Organelle

Cell

Tissue

Organ

Organism

10-5 m

10-1 m

Scales of anatomy

10-9 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

t i m et i m ephysiological processes

t i m

e

t i m

e

development processest i m

e

t i m

e

aging processest i m et i m egrowth processes

SNAP


time

canonical vs. non-canonical


timeunde

form

ed

d

efor

med


timeunde

form

ed

d

efor

med

these are not instances


timeunde

form

ed

d

efor

med

WINDOWS ON REALITY


timeunde

form

ed

d

efor

med

SYMBIOSIS OF KNOWLEDGE ABOUT UNIVERSALS AND INSTANCES


timeunde

form

ed

d

efor

med


Homology

Comparative interplanetary GIS


timeunde

form

ed

d

efor

med

hum

an c

him

panz

ee m

ouse

fly

ye

ast

bact

eria


What do the kidneys do?Modularity


How does a kidney work?NEPHRON


Nephron FunctionsFUNCTIONAL SEGMENTS


Bodily Systems

respiratorydigestive skeletal circulatorymusculatory 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 t1

C1

transformation_of


C

c at t c at t1

C1

embryological development


C

c at t c at t1

C1

tumor development


transformation_of

fetus transformation_of embryo

larva transformation_of pupa

adult transformation_of child

C2 transformation_of C1 =def. any instance

of C2 was at some earlier time an instance

of C1


derives_from

c derives_from c1

=def c and c1 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

C1

c1 at t1

c at t1

C1

c1 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

C1

c1 at t1

C'

c' at t

Http://ontologist.com1 Earth to Major Tom Barry Smith .

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