Transcript John Searle`s Ontology of Social Reality Its Glory and Its Misery

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The First IndustrialStrength
Philosophy
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IFOMIS
Institute for Formal Ontology
and Medical Information Science
http://ifomis.de
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Medicine
needs to find a way to enable the huge
amounts of data resulting from formal
trials and from informal clinical
practice
to be (f)used together
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The problem
Different communities of medical
researchers use different and often
incompatible category systems in
expressing the results of their work
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Example: Medical Nomenclature
MeSH (Medical Subject Headings):
blood is a tissue
SNoMed (Systematized Nomenclature
of Medicine):
blood is a fluid
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The solution
“ONTOLOGY”
Remover “Ontology Impedance”
But what does “ontology” mean?
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Two alternative readings
Ontologies are oriented around terms or
concepts = currently popular IT conception
Ontologies are oriented around the entities
in reality = traditional philosophical
conception, embraced also by IFOMIS
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Ontology as a branch of
philosophy
seeks to establish
the science of the kinds and structures of
objects, properties, events, processes and
relations in every domain of reality
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Ontology a kind of generalized
chemistry or zoology
(Aristotle’s ontology grew out of
biological classification)
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Aristotle
world’s first ontologist
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World‘s first ontology
(from Porphyry’s Commentary on Aristotle’s Categories)
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Linnaean Ontology
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Medical Diagnostic Ontology
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Ontology is distinguished
from the special sciences
it seeks to study all of the various
types of entities existing at all
levels of granularity
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and to establish how they
hang together to form a
single whole (‘reality’ or
‘being’)
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Sources for ontological
theorizing:
the study of ancient texts
thought experiments (we are philosophers,
after all)
the development of formal theories
the results of natural science
now also:
working with computers
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The existence of computers
and of large databases
allows us to express old philosophical
problems in a new light
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Example: The Gene Ontology (GO)
hormone ; GO:0005179
%digestive hormone ; GO:0046659
%peptide hormone ; GO:0005180
%adrenocorticotropin ; GO:0017043
%glycopeptide hormone ; GO:0005181
%follicle-stimulating hormone ; GO:0016913
% = subsumption (lower term is_a higher term)
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as tree
hormone
digestive hormone
adrenocorticotropin
peptide hormone
glycopeptide hormone
follicle-stimulating hormone20
GO
is very useful for purposes of
standardization in the reporting of
genetic information
but it is not much more than a telephone
directory of standardized designations
organized into hierarchies
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GO deals with such basic
ontological notions very
haphazardly
GO’s three main term-hierarchies are:
component, function and process
But GO confuses functions with
structures, and also with executions of
functions
and has no clear account of the relation
between functions and processes
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Moreover,
GO can in practice be used only by
trained biologists
whether a GO-term stands in the
subsumption relationship
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A still more important problem
There exist multiple databases:
GDB
Genome Database of Human Genome
Project
GenBank
National Center for Biotechnology
Information, Washington DC
etc.
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What is a gene?
GDB: a gene is a DNA fragment that can
be transcribed and translated into a
protein
GenBank: a gene is a DNA region of
biological interest with a name and that
carries a genetic trait or phenotype
GO uses ‘gene’ in its term hierarchy,
but it does not tell us which of these
definitions is correct
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How resolve such incompatibilities?
The Semantic Web Initiative
(Tim Berners-Lee, the inventor of the
internet):
enforce terminological compatibility via
standardized term hierarchies, with
standardized definitions of terms
applied as meta-tags to websites
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The Semantic Web
The Web is a vast edifice of
heterogeneous data sources
Needs the ability to query and integrate
across different conceptual systems
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Metadata: the new Silver Bullet
We agree on a metadata standard for
washing machines as concerns: size,
capacity, energy consumption, water
consumption, price
We create machine-readable databases of
our inventories and put them on the net
A consumer can then query multiple sites
simultaneously
and thereby search the Internet for highly
specific, reliable, context-sensitive results
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Cary Doctorow:
A world of exhaustive,
reliable metadata would be a
utopia.
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Problem 1: People lie
Meta-utopia is a world of reliable
metadata.
But poisoning the well can confer
benefits to the poisoners
Metadata exists in a competitive world.
Some people are crooks. Some people
are cranks.
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Problem 2: People are lazy
Half the pages on Geocities are called
“Please title this page”
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Problem 3: People are stupid
The vast majority of the Internet's users
(even those who are native speakers of
English)
cannot spell or punctuate
Will internet users suddenly and en masse
learn to accurately categorize their
information according to whatever DLhierarchy they're supposed to be using?
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Problem 4: Metrics influence
results
raw MHz scores privilege Intel's CISC
chips over Motorola's RISC chips.
Every player in a metadata standards
body will want to emphasize their highscoring axes
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Problem 5: Multiple descriptions
We impart information
He chatters
They gossip
Requiring everyone to use the same
vocabulary to describe their material
denudes the cognitive landscape,
enforces homogeneity in ideas.
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Problem 6: Ontology Impedance
= semantic mismatch between ontologies
being merged
This problem recognized in Semantic Web
literature:
http://ontoweb.aifb.unikarlsruhe.de/About/Deliverables/ontoweb-del7.6-swws1.pdf
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Solution 1: treat it as (inevitable)
‘impedance’
and learn to find ways to cope with the
disturbance which it brings
Suggested here:
http://ontoweb.aifb.uni-karls-ruhe.de/About/Deliverables/ontoweb-del-7.6-swws1.pdf
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Solution 2: resolve the impedance
problem on a case-by-case basis
Suppose two databases are put on the
web.
Someone notices that "where" in the
friends table and "zip" in a places table
mean the same thing.
http://www.w3.org/DesignIssues/Semantic.html
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Both solutions fail
1. treating mismatches as ‘impedance’
inappropriate in an area like medicine
and ignores the problem of error
propagation
2. resolving impedance on a case-bycase basis defeats the very purpose
of the Semantic Web
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Problem 5: Multiple descriptions
Requiring everyone to use the
same vocabulary to describe
their material not always
practicable especially in the
medical domain
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Clinicians
often do not use category systems at all
– they use unstructured text
from which useable data has to be
extracted in a further step
Reasons for this: every case is different,
much patient data is context-dependent
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Proposed IFOMIS solution
distinguish two separate tasks:
- the task of developing computer
applications capable of running in real
time
- the task of developing an expressively
rich framework of a sort which will
allow us to resolve incompatibilities
between definitions
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different terminology systems
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need not interconnect at all
for example they may relate to
entities of different granularity
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we cannot make incompatible
terminology-systems interconnect
just by looking at concepts,
or knowledge or language
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we cannot make incompatible
terminology-systems interconnect
or by staring at the terminology
systems themselves
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to decide which of a plurality of
competing definitions to accept
we need some tertium quid
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we need, in other words,
to take the world itself into account
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BFO
= basic formal ontology
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BFO
ontology is defined not as the
‘standardization’ or ‘specification’ of
conceptualizations
(not as a branch of knowledge or
concept engineering)
but as an inventory of the entities
existing in reality
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The BFO framework
will solve the problem of ontological
impedance and provide tools for
quality-control on the output of
computer applications
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BFO not a computer application
but a Reference Ontology
(something like old-fashioned
metaphysics)
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Reference Ontology
a theory of a domain of entities in the
world
based on realizing the goals of maximal
expressiveness and adequacy to reality
sacrificing computational tractability for
the sake of representational adequacy
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Reference Ontology
a theory of the tertium quid
– called reality –
needed to hand-callibrate
database/terminology systems
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Methodology
Get ontology right first
(realism; descriptive adequacy; rather
powerful logic);
solve tractability problems later
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A reference ontology
is a theory of reality
But how is this possible?
How can we get beyond our concepts?
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Answer:
draw on 2 millennia of philosophical research
• pertaining to realism, scepticism, error,
theory change, and the
language/concept/world relation
• pertaining to the structure of reality itself at
different levels of granularity
APPLY THE RESULTS TO THE DOMAIN OF
MEDICAL REALITY
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try to find ways to look at the
same objects at different levels
of granularity:
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and also:
look not at concepts, representations, of a
passive observer
but rather at agents (clinicians) acting in the
world
taking account of the tacit knowledge of
reality which the domain experts possess
GO useable only by biologists, because only
they know how given terms function in given
contexts
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The Reference Ontology
Community
IFOMIS (Leipzig)
Laboratories for Applied Ontology
(Trento/Rome, Turin)
Foundational Ontology Project (Leeds)
Ontology Works (Baltimore)
Ontek Corporation (Buffalo/Leeds)
Language and Computing (L&C)
(Belgium/Philadelphia)
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Domains of Current Work
IFOMIS Leipzig: Medicine, Bioinformatics
Laboratories for Applied Ontology
Trento/Rome: Ontology of Cognition/Language
Turin: Law
Foundational Ontology Project: Space, Physics
Ontology Works: Genetics, Molecular Biology
Ontek Corporation: Biological Systematics
Language and Computing: Natural Language
Understanding
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Recall:
GDB: a gene is a DNA fragment that can
be transcribed and translated into a
protein
Genbank: a gene is a DNA region of
biological interest with a name and that
carries a genetic trait or phenotype
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Ontology
‘fragment’, ‘region’, ‘name’, ‘carry’, ‘trait’,
‘type’
... ‘part’, ‘whole’, ‘function’, ‘inhere’,
‘substance’ …
are ontological terms in the sense of
traditional (philosophical) ontology
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BFO
not just a system of categories
but a formal theory
with definitions, axioms, theorems
designed to provide the resources for
reference ontologies for specific
domains
of sufficient richness that
terminological incompatibilities can be
resolved intelligently rather than by
brute force
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Two basic oppositions
Granularity (of molecules, genes, cells,
organs, organisms ...)
SNAP vs. SPAN
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SNAP vs. SPAN
Two different ways of existing in time:
continuing to exist (of organisms, their
qualities, roles, functions, conditions)
occurring (of processes)
SNAP vs. SPAN = Anatomy vs. Physiology
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SNAP: Entities existing in toto at a time
MedO Draft 0.0004
Enduring Entity
[Exists in space and time,
has no temporal parts]
Dependent Entity
[±Relational]
Spatial Entity
Occupied
Spatial region of 3
dimensions
occupied by organism
Spatial region of 2
dimensions *
occupied by burn, bruise
SNAP
Unoccupied
Quality
[Sometimes form qualityregions or scales]
Tunnel
Alimentary Canal
Hollow
Nostril
Cavity
Interior of Lung
Requisite
[Have determinable/
determinate structure]
Temperature. height
Optional
Diabetes
State
Being pregnant, being thirsty
Independent Entity
Role, Function, Power, Disposition
[Have realizations, called processes]
To circulate blood, to secrete hormones
Substance
Organism, organ
Fiat part of substance *
Extremity, upper body
Boundary of substance *
Surface of skin or hide
Aggregate of substances *
Family, mother and fetus
Three kinds of SNAP entities
1. Independent: Substances,
Objects, Things
2. Dependent: Qualities,
Functions, Conditions, Roles
3. Spatial regions
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SNAP: Dependent
.0004
Enduring Entity
[Exists in space and time,
has no temporal parts]
SNAP
Dependent Entity
[±Relational]
Quality
[Sometimes form qualityregions or scales]
Requisite
[Have determinable/
determinate structure]
Temperature. height
Optional
Diabetes
State
Being pregnant, being thirsty
Role, Function, Power, Disposition
[Have realizations, called processes]
To circulate blood, to secrete hormones
SNAP-Spatial Region
Spatial Entity
Occupied
Unoccupied
[Somet
regi
Spatial region of 3
dimensions
occupied by organism
Spatial region of 2
dimensions *
occupied by burn, bruise
Tunnel
Alimentary Canal
Hollow
Nostril
Cavity
Interior of Lung
Requisite
[Have determinable/
determinate structure]
Temperature. height
SNAP SNAP-Independent
Independent Entity
Role, Function, Power, Disposition
[Have realizations, called processes]
To circulate blood, to secrete hormones
Substance
Organism, organ
Fiat part of substance *
Extremity, upper body
Boundary of substance *
Surface of skin or hide
Aggregate of substances *
Family, mother and fetus
SPAN: Entities occurring in
time
Entity extended in time
Processual Entity
[Exists in space and time, unfolds
in time phase by phase]
Portion of Spacetime
Spacetime worm of 3 + T
dimensions
occupied by life of organism
Temporal interval *
projection of organism’s life
onto temporal dimension
SPAN
Process
[±Relational]
Circulation of blood,
secretion of hormones,
course of disease, life
Fiat part of process *
First phase of a clinical trial
Aggregate of processes *
Clinical trial
Temporal boundary of
process *
onset of disease, death
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SPAN: Dependent (Processes)
Entity extended in time
SPAN
Processual Entity
[Exists in space and time, unfolds
in time phase by phase]
Process
[±Relational]
Circulation of blood,
secretion of hormones,
course of disease, life
Fiat part of process *
First phase of a clinical trial
Aggregate of processes *
Clinical trial
Temporal boundary of
process *
onset of disease, death
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SPAN: Spatiotemporal
Regions
Entity extende
Portion of Spacetime
Proce
Spacetime worm of 3 + T
dimensions
occupied by life of organism
Temporal interval *
projection of organism’s life
onto temporal dimension
[±Relatio
Circulation o
secretion of h
course of dis
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Realization (SNAP-SPAN)
the execution of a plan
the expression of a function
the exercise of a role
the realization of a disposition
the course of a disease
the application of a therapy
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SNAP dependent entities and
their SPAN realizations
plan
function
role
disposition
disease
therapy
SNAP
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SNAP dependent entities and
their SPAN realizations
execution
expression
exercise
realization
course
application
SPAN
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More examples:
performance of a symphony
projection of a film
expression of an emotion
utterance of a sentence
increase of body temperature
spreading of an epidemic
extinguishing of a forest fire
movement of a tornado
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BFO = SNAP/SPAN + Theory of
Granular Partitions +
theory of universals and instances
theory of part and whole
theory of boundaries
theory of functions, powers, qualities, roles
theory of environments, contexts
theory of spatial and spatiotemporal regions
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MedO: medical domain ontology
universals and instances and normativity
theory of part and whole and absence
theory of boundaries/membranes
theory of functions, powers, qualities, roles,
(mal)functions, bodily systems
theory of environments: inside and outside
the organism
theory of spatial and spatiotemporal
regions: anatomical mereotopology
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MedO: medical domain ontology
theory of granularity: relations between
molecule ontology
gene ontology
cell ontology
anatomical ontology
etc.
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IFOMIS project
collaborate with L&C to show how an
ontology constructed on the basis of
philosophical principles can help in
overhauling and validating L&C’s large
terminology-based medical ontology
LinkBase®
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Testing the BFO/MedO approach
within a software environment for NLP of
unstructured patient records
collaborating with
Language and Computing nv
(www.landcglobal.be)
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L&C
LinKBase®: world’s largest
terminology-based ontology
with mappings to UMLS, SNOMED, etc.
+ LinKFactory®: suite for developing and
managing large terminology-based
ontologies
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LinKBase
LinKBase still lacking a formal theory
• BFO and MedO designed to add better
reasoning capacity
• by tagging LinKBase domain-entities with
corresponding BFO/MedO categories
• by constraining links within LinKBase
according to the theory of granular partitions
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L&C’s long-term goal
Transform the mass of unstructured
patient records into a gigantic medical
experiment
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IFOMIS’s long-term goal
Build a robust high-level BFO-MedO
framework
THE WORLD’S FIRST INDUSTRIALSTRENGTH PHILOSOPHY
which can serve as the basis for an
ontologically coherent unification of
medical knowledge and terminology
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END
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