http://ontologist.com1 from knowledge representation to reality representation barry smith
Post on 22-Dec-2015
217 views
TRANSCRIPT
http://ontologist.com 2
2002
Institute for Formal Ontology and Medical Information Science (Germany)
initially: work on formal ontology
and on ontology-based quality control in medical terminologies
(UMLS, SNOMED, NCI Thesaurus, etc.)
http://ontologist.com 3
Fruit
Orange
VegetableSimilarTo
ApfelsineSynonymWith
NarrowerThan
Goble & Shadbolt
Problem: Associative approach to word meanings
http://ontologist.com 4
both testes is_a testis
plant leaves is_a plant
menopause part_of death
bacterium causes experimental model of disease
not normal cell is_a cell
not abnormal cell is_a cell
http://ontologist.com 5
move from associative relations between meanings to ontological
relations between the entities themselves
supplementing data mining approaches with1) better data2) better annotations3) better integration4) the possibility of strong logical reasoning
http://ontologist.com 6
First crack in the wall
Digital Anatomist Foundational Model of Anatomy(Department of Biological Structure, University of Washington, Seattle)
Virtual Soldier Project: Reference Ontology of AnatomyReference Ontology of PhysiologyReference Ontology of Disease Pathways
http://ontologist.com 7
Second Crack in the Wall
Gene Ontology Consortium
Open Biological Ontologies
http://ontologist.com 8
NCOR: National Center for Ontological Research
Buffalo Center of Excellence in Bioinformatics)
Stanford Medical Informatics (Protégé 2000)
Berkeley Drosophila Genome Project (Model Organism Phenotype Ontology
Project)
http://ontologist.com 9
NCOR: National Center for Ontological Research
plus industrial parners
Ontology Works...
http://ontologist.com 10
NCOR Methodology
work with content developers to ensure rigorous conformity with good principles of classification and definition
use formally defined categories and relations to ensure interoperability and support automatic reasoning
and to move beyond mere statistical / associative techniques
http://ontologist.com 11
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 12
Examples of simple formal-ontological structures
is_a hierarchies
part_of hierarchies
dependence relations
http://ontologist.com 17
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 19
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 20
Formal-Ontological Categories
object
process
site
layer
fragment
quality
function
relation
boundary
region
http://ontologist.com 21
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 22
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
NCOR goal
http://ontologist.com 23
to define these relations properly
we need to take account of reality
If we remain in the realm of concepts we will forever face problems of interoperability
http://ontologist.com 24
to define these relations properly
we need to take account not of concepts,
but of universals and instances in reality
http://ontologist.com 26
The Concept Orientation
Work on biomedical ontologies grew out of work on medical dictionaries and thesauri
led to the assumption that all that need be said about concepts can be said without appeal to time or instances.
& fostered an impoverished regime of definitions
http://ontologist.com 27
‘Concept’ in ontology runs together:
a) the meaning that is shared in common by a collection of synonymous terms
b) an idea shared in common in the minds of those who use synonymous terms (psycho-linguistic view)
c) a universal, feature or property shared by entities in the world which fall under the concept
http://ontologist.com 28
Problem of evaluation
if an ontology is a mere “specification of a conceptualization,” then the distinction between good and bad ontologies loses its foothold in reality
http://ontologist.com 29
There are more word meanings than there are types of entities in
reality
unicorn
devil
cancelled performance
avoided meeting
prevented pregnancy
imagined mammal ...
http://ontologist.com 31
unicorn is_a one-horned mammal
alien implant removal is_a surgical process
Chios energy healing is_a therapeutic process
http://ontologist.com 32
This linguistic reading
yields a more or less coherent reading of relations like:
‘is_a’
‘synonymous_with’
‘associated_to’
http://ontologist.com 33
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 34
for how can concepts, on the linguistic reading, figure as relata of
relations like: part_of
adjacent_to
connected_to
http://ontologist.com 35
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 36
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 37
Evaluation
Good ontologies are those whose general terms correspond to universals in reality, and thereby also to corresponding instances.
http://ontologist.com 38
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 39
Instance-level relations
part_of
is_located_at
has_participant
has_agent
earlier
. . .
http://ontologist.com 40
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 42
transformation_of
fetus transformation_of embryo
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 43
derives_from
c derives_from c1
=def c and c1 are non-identical
and exist in continuous succession
http://ontologist.com 44
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
http://ontologist.com 45
two initial components fuse to form a new component
C
c at t
C1
c1 at t1
C'
c' at t
http://ontologist.com 46
Functions
your heart has the function: to pump blood
= your heart is predisposed (has the potential or casual power) to realize a process of the type pumping blood.
has_agent (instance-level relation)
p is_functioning_of c p has_agent c
http://ontologist.com 48
Two entities coincide (partially) when they overlap (share parts)
my hand coincides with my body
the European Union coincides with the British Commonwealth
(United Kingdom … Malta, Cyprus)
http://ontologist.com 49
Some entities coincide even though they share no parts
any material object coincides with its spatial region
a portion of food coincides with my stomach cavity
http://ontologist.com 50
Holes may coincide with material objects
The hole in the chunk of amber coincides completely with, but does not overlap, the encapsulated insect which fills it
Sometimes holes and objects are moving independently (a bullet flying through a railway carriage moving through a tunnel)
http://ontologist.com 52
Layered Ontology of Lakes
L1. a region layer
L2. a lake layer, consisting of a certain concave portion of the earth’s surface together with a body of water
L3. a fish layer
L4. a chemical contaminant layer
http://ontologist.com 53
Layered Epidemiology Ontology
L1. a two-dimensional region layer in some undisclosed location
L2. a topographical layer, consisting of mountains, valleys, deserts, gullies
L3. a storm-system occupying sub-regions of L2
L4: an airborne cloud of smallpox virus particles.
http://ontologist.com 55
Parthood (P)
Parthood is a partial ordering:
(P1) Pxx (reflexive)(P2) Pxy & Pyx x = y (antisymmetric)(P3) Pxy & Pyz Pxz (transitive)(P4) ~Pxy z(Pzx & ~Ozy) (the remainder principle: if x is not part of y,
then x has a part that does not overlap y)
http://ontologist.com 57
The Region Function
r(x) = the region at which x is exactly located.
r is a new primitive
r maps (collapses) entities on all higher layers onto the region layer
http://ontologist.com 59
Some Theorems
Ry r(y) = y
(every region is located at itself)
(x & x( Rx) &
y (Oyz x ( & Oyx))) Rz
(every sum of regions is a region)
http://ontologist.com 60
Defined Relations
ECxy =: Cxy & ~ Oxy
(x and y are externally connected)
Axy =: EC(r(x), r(y))
(x and y abut)
http://ontologist.com 61
Towards Dynamic Spatial Ontology
From spatial coincidence to spatio-temporal coincidence
http://ontologist.com 62
Objects move through space
An adequate ontology of motion requires at least two independent sorts of spatial entities:
1. locations, which remain fixed,
2. objects, which move relative to them.
http://ontologist.com 63
Standard (RCC) approaches
sparrow 152 moves from one location (region A) to another (region B)
Becomes:
each member of this continuous sequence of sparrow-shaped regions, starting with A and ending with B, has at successive times, rufous-winged (etc.) attributes.
Instead of talking about sparrows flying through the sky, we talk of mappings of the form:
Sparrow152: time regular closed subsets of R3.
http://ontologist.com 64
Region-based approaches (RCC, etc.)
have no means of distinguishing true overlap (i.e. the sharing of parts) from mere spatial co-location.
They identify the relation of a fish to the lake it inhabits with the relation of a genuine part of a lake (a bay, an inlet) to the lake as a whole.
They identify the genuine parts of the human body, such as the heart or lungs, with foreign occupants such as parasites or shrapnel.
http://ontologist.com 65
The solution
is to recognize both objects and locations, on separate layers
and then we need a theory of coincidence and of layered mereotopology to do justice to the entities in these two categories
http://ontologist.com 66
Some entities coincide spatially even though they share no parts
a portion of food coincides with my stomach cavity at a certain time
http://ontologist.com 67
Some entities coincide spatio-temporally even though they
share no parts
the course of a disease coincides with the treatment of the disease
http://ontologist.com 68
Processes may coincide with each other
The manouvres of the coalition troops coincide, but do not share parts in common, with the activities of the terrorists
http://ontologist.com 69
Spatiotemporal Coincidence without Sharing of Parts
The Great Plague of 1664 coincides with, but does not overlap, the history of Holland in the 17th century
A process of deforestation coincides with, but does not overlap, the history of the forest
http://ontologist.com 70
Objects and processes do not coincide
For they are of different dimension:
Objects are 3-dimensional
Processes are 4-dimensional
Object-layers are always 3-dimensional
Process-layers are always 4-dimensional
http://ontologist.com 71
Two ontologies of motion and change
series of samples, or snapshots
object x1 is at region r1 at time t1
object x2 is at region r2 at time t2
object x3 is at region r3 at time t3
SNAP ontologies (ontologies indexed by times)
http://ontologist.com 77
SPAN ontology
is an ontology which recognizes processes, changes, themselves
= four-dimensional (spatio-temporal) entities
not via a sequence of instantaneous samplings but via extended observations
http://ontologist.com 78
Many different interconnections traverse the SNAP-SPAN divide But SNAP and SPAN entities are never related by part_of, connected_to or coincidence (layer) relations
http://ontologist.com 80
SPAN
SPANEntity extended in time
Portion of Spacetime
Fiat part of process *First phase of a clinical trial
Spacetime worm of 3 + Tdimensions
occupied by life of organism
Temporal interval *projection of organism’s life
onto temporal dimension
Aggregate of processes *Clinical trial
Process[±Relational]
Circulation of blood,secretion of hormones,course of disease, life
Processual Entity[Exists in space and time, unfolds
in time phase by phase]
Temporal boundary ofprocess *
onset of disease, death
http://ontologist.com 81
There are layers in both the SNAP (object) ontology and the
SPAN (process) ontology
In SNAP the region layer = space
In SPAN the region layer = spacetime
http://ontologist.com 82
But
distinguishing layers in the process realm of SPAN is a matter of gerrymandering (of fiat carvings) to a much greater degree than in the realm of SNAP
http://ontologist.com 83
One big difference between SNAP and SPAN
In SNAP, higher layers are categorially well-distinguished nicely separated (physical objects, holes, administrative entities …)
In SPAN
everything is flux