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http://ontologist.com 3
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
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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.com 6
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.com 7
http://www.sedris.org/stc/2004/tu/edcs/sld024.htm
http://www.sedris.org/stc/2004/tu/edcs/sld024.htm
http://ontologist.com 8
Layers of the epidermis
kidshealth.org/kid/ body/skin_noSW.html
http://ontologist.com 9
Digital Anatomist Foundational Model of Anatomy
(Department of Biological Structure, University of Washington, Seattle)
http://ontologist.com 10
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.com 11
Examples of simple formal-ontological structures
is_a hierarchies
part_of hierarchies
http://ontologist.com 12
Pleural Cavity
Pleural Cavity
Interlobar recess
Interlobar recess
Mesothelium of Pleura
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
Organ CavitySubdivision
Serous SacCavity
Subdivision
Serous SacCavity
Subdivision
part
_of
is_a
http://ontologist.com 16
Pleural Cavity
Pleural Cavity
Interlobar recess
Interlobar recess
Mesothelium of Pleura
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
Organ CavitySubdivision
Serous SacCavity
Subdivision
Serous SacCavity
Subdivision
part
_of
is_a
http://ontologist.com 18
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.com 19
Formal-Ontological Categories
object
process
site
layer
fragment
quality
function
relation
boundary
region
http://ontologist.com 20
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
http://ontologist.com 21
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.com 22
to define these relations properly
we need to take account of both universals and instances in reality
http://ontologist.com 24
unicorn is_a one-horned mammal
alien implant removal is_a surgical process
Chios energy healing is_a therapeutic process
http://ontologist.com 25
This linguistic reading
yields a more or less coherent reading of relations like:
‘is_a’
‘synonymous_with’
‘associated_to’
http://ontologist.com 26
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.com 27
for how can concepts, on the linguistic reading, figure as relata of
relations like: part_of
adjacent_to
connected_to
http://ontologist.com 28
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.com 29
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.com 30
Evaluation
Good ontologies are those whose general terms correspond to universals in reality, and thereby also to corresponding instances in reality.
http://ontologist.com 31
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
http://ontologist.com 32
Instance-level relations
part_of
is_located_at
has_participant
has_agent
earlier
. . .
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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.com 34
Different scientific cultures/terminologies
immunology
genetics
cell biology
http://ontologist.com 35
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.com 38
Virtual Soldier Project
Anatomy Reference Ontology =
theoretical framework surrounding the Digital Anatomist Foundational Model of Anatomy
http://ontologist.com 39
Virtual Soldier Project:
Reference Ontology of Anatomy
Reference Ontology of Physiology
Reference Ontology of Disease Pathways
http://ontologist.com 40
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
http://ontologist.com 41
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.com 43
Pleural Cavity
Pleural Cavity
Interlobar recess
Interlobar recess
Mesothelium of Pleura
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
Organ CavitySubdivision
Serous SacCavity
Subdivision
Serous SacCavity
Subdivision
http://ontologist.com 45
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
http://ontologist.com 46
anatomical structure
body substance
anatomical space
boundary
anatomical attribute
anatomical relationship
http://ontologist.com 47
anatomical structure (cell, lung, nerve, tooth)
result from the coordinated expression of structural genes
have their own 3-D shape
http://ontologist.com 48
portion of body substance
inherits its shape from contained
urine
menstrual flood
blood ...
http://ontologist.com 50
boundary
bona fide
fiat
www.enel.ucalgary.ca/ People/Mintchev/stomach.htm
http://ontologist.com 51
anatomical attribute
mass
weight
temperature
your temperature
its value now
http://ontologist.com 52
anatomical relationship
located_in
contained_in
adjacent_to
connected_to
surrounds
lateral_to (West_of)
anterior_to
http://ontologist.com 53
DNA
Protein
Organelle
Cell
Tissue
Organ
Organism
10-5 m
10-1 m
Scales of anatomy
10-9 m
http://ontologist.com 54
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.com 55
Quantities in AIS
– raster/vector, no fixed coordinates (flexible earth), 3-Dimensional views
http://ontologist.com 58
single-cell zygote
multi-cell zygote
morula
early blastocyst
gastrula
new born
infant
adolescent
young adult
http://ontologist.com 59
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
http://ontologist.com 64
timeunde
form
ed
d
efor
med
SYMBIOSIS OF KNOWLEDGE ABOUT UNIVERSALS AND INSTANCES
http://ontologist.com 67
timeunde
form
ed
d
efor
med
hum
an c
him
panz
ee m
ouse
fly
ye
ast
bact
eria
http://ontologist.com 68
timeunde
form
ed
d
efor
med
hum
an c
him
panz
ee m
ouse
fly
ye
ast
bact
eria
http://ontologist.com 77
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.com 81
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
http://ontologist.com 82
derives_from
c derives_from c1
=def c and c1 are non-identical
and exist in continuous succession
http://ontologist.com 83
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