1 formal ontology and information systems barry smith

Formal Ontology and Information Systems

Barry Smith

http://ifomis.de

Institute for Formal Ontology and Medical Information Science

(IFOMIS)

Faculty of Medicine

University of Leipzig

http://ifomis.de

The Idea

Computational medical research

will transform the discipline of medicine

… but only if communication problems can be solved

Database standardization

is desperately needed in medicine

to enable the huge amounts of data

resulting from trials by different groups

to be fused together

How resolve incompatibilities?

“ONTOLOGY” = the solution of first resort

(compare: kicking a television set)

But what does ‘ontology’ mean?

Current most popular answer: a collection of terms and definitions satisfying constraints of description logic

Enterprise Ontology

A Sale is an agreement between two Legal-Entities for the exchange of a Product for a Sale-Price.

A Strategy is a Plan to Achieve a high-level Purpose.

A Market is all Sales and Potential Sales within a scope of interest.

Wall Street Journal 11 July 2002

… that the original high hopes of B2B automation were not realized turns on the fact that there are many highly nuanced features of business transactions, known only tacitly to those involved, the failure to take account of which has had disastrous consequences for those involved

Gene Ontology

Molecular Function Ontology: tasks performed by individual gene products; examples: transcription factor, DNA helicase

Biological Process Ontology: broad biological goals accomplished by ordered assemblies of molecular functions; examples: mitosis, purine metabolism

Cellular Component Ontology: subcellular structures, locations, and macromolecular complexes;examples: nucleus, telomere

Example from Molecular Function Ontology

hormone ; GO:0005179

%digestive hormone ; GO:0046659 %peptide hormone ; GO:0005180 %adrenocorticotropin ; GO:0017043 %glycopeptide hormone ; GO:0005181 %follicle-stimulating hormone ; GO:0016913

as tree

hormone

digestive hormone peptide hormone

adrenocorticotropin glycopeptide hormone

follicle-stimulating hormone

Problem: There exist multiple databases

genomic cellular

structural phenotypic

… and even for each specific type of information, e.g. DNA sequence data, there exist several databases of different scope and organisation

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

(from Schulze-Kremer)

What is blood?

Unified Medical Language System (UMLS):

blood is a tissueSystematized Nomenclature of Medicine (SNOMED):

blood is a fluid

Statements of Accounts

Company Financial statements may be prepared under either the (US) GAAP or the (European) IASC standards

These allocate cost items to different categories depending on the laws of the countries involved.

Ontology’s job

is to develop an algorithm for the automatic conversion of income statements and balance sheets between the two systems.

Not even this relatively simple problem has been satisfactorily resolved

… why not?

Applications ontology:

grew out of work in knowledge representation

Applications ontology:

Ontologies are applications running in real timeontologies are inside the computer thus subject to severe constraints on expressive power (effectively the expressive power of description logic, a logic for manipulating hierarchies of concepts/general terms)

Applications ontology cannot solve the data-fusion problem

because of its roots in knowledge mining

different conceptual systems

need not interconnect at all

because of the limits of knowledge mining

we cannot make incompatible concept-systems interconnect

just by looking at concepts, or knowledge – we need some tertium quid

Applications ontology

has its philosophical roots in Quine’s doctrine of ontological commitment and in the ‘internal metaphysics’ of Carnap/Putnam Roughly, for an applications ontology the world and the semantic model are one and the sameWhat exists = what the system says exists

again: semantic models need not interconnect at all

What is needed

in some sort of wider common framework which is sufficiently rich and nuanced to allow concept systems deriving from different sources to be hand-callibrated

What is needed

is not an applications ontology

a reference ontology

Reference Ontology

… grew out of logic and analytic metaphysics

An ontology is a theory of the relevant domain of entities

Ontology is outside the computer

seeks maximal expressiveness and adequacy to reality

willing to sacrifice computational tractability for the sake of representational adequacy

Belnap

“it is a good thing logicians were around before computer scientists;

“if computer scientists had got there first, then we wouldn’t have numbers

because arithmetic is undecidable”

It is a good thing

Aristotelian metaphysics was around before description logic,

because otherwise we would have only hierarchies of

concepts/universals/classes and no individual instances …

Reference Ontology

a theory of the tertium quid

– called

reality –needed to hand-callibrate

database/terminology systems

Methodology

Get ontology right first

(realism; descriptive adequacy; rather powerful logic);

solve tractability problems later

The Reference Ontology Community

IFOMIS (Leipzig) Laboratories for Applied Ontology

(Trento, Rome, Turin)Foundational Ontology Project (Leeds)Ontology Works (Baltimore)Ontek Corporation (Buffalo/Leeds)LandC (Belgium/Philadelphia)

Domains of Current Work in Reference Ontology

IFOMIS Leipzig: MedicineLaboratories for Applied Ontology

Trento/Rome: Ontology of Cognition/LanguageTurin: Law

Foundational Ontology Project (Leeds): Space, Physics

Ontology Works (Baltimore): Genetics, Molecular Biology

Ontek Corporation (Buffalo/Leeds): Biological Systematics

LandC (Belgium/Philadelphia): Medical NLP

Some Historical Background on Reference Ontology

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

(from Schulze-Kremer)

Ontology

Note that terms like ‘fragment’, ‘region’, ‘name’, ‘carry’, ‘trait’, ‘type’

… along with terms like ‘part’, ‘whole’, ‘function’, ‘substance’, ‘inhere’ …

are ontological terms in the sense of traditional (philosophical) ontology

Aristotle

First ontologist

First ontology

(from Porphyry’s Commentary on Aristotle’s Categories)

Linnaean Ontology

Formal Ontology

term coined by Edmund Husserl

= the theory of those ontological structures

such as part-whole, universal-particular

which apply to all domains whatsoever

Edmund Husserl

Husserl outlines a new methodof constituent ontology

to study a domain ontologically

is to establish the parts of the domain

and the interrelations between them

especially the dependence relations

Logical Investigations¸1900/01

Aristotelian theory of universals and particulars

theory of part and whole

theory of ontological dependence

the theory of boundaries and fusion

Formal Ontology

contrasted with material or regional ontologies

(compare relation between pure and applied mathematics)

Husserl’s idea:

If we can build a good formal ontology, this should save time and effort in building reference ontologies for each successive domain

Basic Formal Ontology

BFOThe Vampire Slayer

Basic Formal Ontology

Aristotelian theory of universals and instances

theory of boundary, continuity and contact

theory of states, powers, qualities, roles (SPQR-entities)

theory of processes

theory of environments/niches/contexts and spatial and spatio-temporal regions

BFOnot just a system of categories

but a formal theory

with definitions, axioms, theorems

designed to provide the resources for reference ontologies for specific domains

the latter should be of sufficient richness that terminological incompatibilities can be resolves intelligently rather than by brute force

Three types of reference ontology

1) formal ontology = framework for rigorous definition of the highly general concepts – such as object, event, whole, part – employed in every domain

2) domain ontology, a top-level system with a few highly general concepts, applies formal ontology to a particular domain, such as genetics or medicine

3) terminology-based ontology, a very large system embracing many concepts and inter-concept relations

MedO = medical domain ontology

including sub-ontologies:

cell ontology

drug ontology

protein ontology

gene ontology

other sub-ontologiesanatomical ontology

epidemiological ontology

disease ontology

therapy ontology

pathology ontology

the whole designed to give structure to the medical domain

(currently medical education comparable to stamp-collecting)

and its various sub-ontologies will inherit the definitions and axioms of BFO but will add new definitions and axioms of their own

Granularity

cell ontology

drug ontology

protein ontology

gene ontology

imply that we need also a theory of granularity

Ontology

like cartography

must work with maps at different scales

How fit these maps (conceptual grids) together into a single system?

IFOMIS is developing a theory of granular partitions designed to provide a framework within which different maps/views of the same reality can be combined together

Testing the BFO/MedO approach

within a software environment for NLP of unstructured patient records

collaborating with

Language and Computing nv (www.landc.be)

LinKBase®: world’s largest terminology-based ontology

incorporating UMLS, SNOMED, etc.

+ LinKFactory®: suite for developing and managing large terminology-based ontologies

LinKBase

LinKBase close to being a flat list

BFO and MedO designed to add depth, and so also reasoning capacity

by tagging LinKBase terms with corresponding BFO/MedO categories

Part Two

Reference Ontology

and Agent-Based/Situated Computing

Agents: encapsulated computer systems that are situated in some environment and are capable of flexible, autonomous action in that environment in order to meet their design objectives.

Interactions: Such agents invariably need to interact with one another in order to manage their inter-dependencies. These interactions involve agents cooperating, negotiating and coordinating with one another.

Organisations: The agents' interactions take place within some organisational context (eg a marketplace or some other form of electronic institution).

Particular prominence is given to automated cooperation, coordination and negotiation using techniques such as game theory, argumentation, computational economics, and belief-desire-intention models.

From Southampton IAM

Shimon Edelman’s Riddle of Representation

two humans, a monkey, and a robot are looking at a piece of cheese;

what is common to the representational processes in their visual systems?

Answer:

The cheese, of course

Rodney Brooks

opposition between the Engineering view and the SMPA View

SMPA modelSense Model Plan Act

the agent first senses its environment through sensors

then uses this data to build a model of the world

then produces a plan to achieve goals

then acts on this plan

Proposal

SMPA belongs to the same methodological universe as Applications Ontology

If we want to build an intelligent agent within this framework, there need to be representations of the domain within which the agent acts which are inside the computer

Engineering Approach

The system embodies a number of distinct layers of activity (compare: faculties of the mind)

These layers operate independently and connect directly to the environment outside the system

Each layer operates as a complete system that copes in real time with a changing environment

Layers evolve through interaction with the environment (artificial insects/vehicles …)

Brooks’ Engineering Approach

lends very little weight to the role of representations or models

At the same time it insists that AI should use the world in all its complexity in producing systems that react directly to the world

An ontology appropriate for this approach would have to include within its purview both the world and the system,

thus be essentially richer than the system alone

An intelligent system

must be situatedit is situatedness which gives the

processes within each layer meaningmeaning exists precisely in the relation

to the world,the world serves also as to unify the

different layers together and to make them compatible

I know where the book is= I know how to find it

I know what the square root of 2489 is= I know how to calculate it

I know how to recognize the presence of a tiger

= by smell, noise … (in real-world context)

A. Clark, Being There

humans can accomplish much without building detailed, internal models; we rely on

Epistemic action =

writing one large number above another to multiply them with pen on paper

A. Clark, Being Therewe can rely also on

External scaffolding = maps, models, tools, landmarks, buildings, language, culture

we act so as to simplify cognitive tasks by "leaning on" the structures in our environment.

Cf. Brooks:

Organisms, especially humans, find their dispositions in their muscle-tone and in the balance of hormones coursing through their blood streams, not just in their brains. They fix their beliefs not only in their heads but in their worlds, as they attune themselves differently to different parts of the world as a result of their experience. And they pull the same trick with their memories, not only by rearranging their parsing of the world (their understanding of what they see), but by marking it. They place traces out there which changes what they will be confronted with the next time it comes around. Thus they don't have to carry their memories with them.

Brooks, “Intelligence without Representation”

Not all calculations are done inside the head

Not all thinking is done inside the head

Gibsonian Ecological Psychology

To understand human cognition we should study the moving, acting human person as it exists in its real-world environment

and taking account how it has evolved into this real-world environment

We are like tuning forks – tuned to the environment which surrounds us, and this is a social environment which includes records and representations

Gibsonian Ecological View of Information Systems

To understand information systems we should study the hardware as it exists embedded in its real-world environment

and taking account of the environment for which it was designed and built

Information systems are like tuning forks – they resonate in tune to their surrounding environments e.g. through their biological and chemical sensors

The World Wide Web

Vast amount of heterogeneous data sources

Needs: dramatically better support for richly structured ontologies in databases

+ ability to query and integrate across different ontologies (e.g. Semantic Web)

Quineanism:

They took ontology as the study of the ontological commitments or presuppositions embodied in the beliefs of experts

Can we do better with the Gibsonian approach?

Test Domain:

Medical Terminology

So what is the ontology of blood?

We cannot solve this problem just by looking at concepts in Fodorian fashion

concept systems may be simply incommensurable

the problem can only be solved

by taking the world itself into account

and by recognizing

that the same object can be apprehended at different levels of granularity:

at the perceptual level blood is a liquid

at the cellular level blood is a tissue

This implies a view of ontology

not as a theory of concepts

but as a theory of reality

But how is this possible?

How can we get beyond our concepts?

answer: ontology must be maximally opportunistic

it must relate not to beliefs, concepts, syntactic strings but to the world itself

“Maximally opportunistic”

means:

look at concepts and beliefs critically

and always in the context of a wider view which includes independent ways to access the objects themselves

at different levels of granularity

and taking account of tacit knowledge of those features of reality of which the domain experts are not consciously aware

“Maximally opportunistic”

means:

look not at what the expert says

but at what the expert does

Experts have expertise = knowing how

Ontologists can have windows on reality, by focusing on categories, and can extract some form of knowing that

Gibsonianism: experts don’t know what the ontologist knows

Ontology must be maximally opportunistic

This means:

don’t just look at beliefs

look at the objects themselves

from every possible direction,

formal and informal

scientific and non-scientific …

Maximally opportunistic

means:look at the same objects at different levels of granularity:

Second step: select out the good conceptualizations

these have a reasonable chance of being integrated together into a single ontological system

• based on tested principles• robust• conform to natural science

Partitions should be cuts through reality

a good medical ontology should NOT be compatible with a conceptualization of disease as caused by evil spirits

A Theory of Contexts, Settings, Environments for Social Acts

X counts as Y in context C

What kinds of entities are social contexts?

Reinach

a priori ontological structures in the

social realm are transcategorial:involving experiences, intentions,

language, action, deontic powers, background collective habits, mental competences, records,

PLUS: social environments

The bonds

established by Reinach’s proto-structures of promise, claim and obligation …

can normally arise only within miniature civil societies,

within which special sorts of environmental conditions are satisfied

The Idea: Contexts can be Nested One Inside Another

Many settings occur in assemblies:

A unit in the middle range of a nesting structure is simultaneously both circumjacent and interjacent,

both whole and part, both entity and environment. (Roger Barker)

Compare the hierarchical organization of the human body into organs, cells, …

Human body

Rigidly hierachical, modular organization – with many things which can go wrong

Held together by physico-chemical bonds

Large-scale social organizations

are held together by micro-social bonds as described by Reinach

The whole organized as a rigidly hierarchical, modular nesting structure, with many things which can go wrong

Ecological Psychology

Gibson: Perception

:: Roger Barker: Society

Barker’s

Ecological Ontology of Social Reality

Barker on Unity of Social Reality

On Reinach’s transcategoriality:

“The conceptual incommensurability of phenomena which is such an obstacle to the unification of the sciences does not appear to trouble nature’s units.

Within the larger units, things and events from conceptually more and more alien sciences are incorporated and regulated.”

Barker on Unity of Social Reality

“As far as our behaviour is concerned, … even the most radical diversity of kinds and categories need not prevent integration”

we must be tuned, automatically, to social reality

J. J. Gibson’s ecological psychology: we are tuned automatically to perceptual reality

How to solve this problem

(and why are buildings important?)

Compare the way in which the physical properties of ROADS help people to obey the

traffic laws when driving

Deal with obligations, norms not via deontic logic but via the comparison with roads?

First step: A Theory of Environments

Biological environments

Niches

Places

Environments a Neglected Major Category in the History of Ontology

Substances

States, Qualities, Powers, Roles …

Processes

Environments

-- environments missing from Aristotle, from DOLCE, from entity-relationship models

Ecological Niche Concepts

niche as particular place or subdivision of an environment that an organism or population occupies (TOKEN)

niche as function of an organism or population within an ecological community (TYPE)

Human beings live in complex environments

Recall Reinach’s notion of transcategorial relations

Merlin Donald,The Origins of the Modern Mind:

notion of external memory

The Ecological Psychology of J. J. Gibson and Roger Barker

Affordances

“The affordances of the environment are what it offers the animal, what it provides or furnishes, either for good or evil.”

James J. Gibson, The Ecological Approach to Visual Perception

Organisms are tuning forks

They have evolved to resonate automatically and directly to those quality regions in their niche which are relevant for survival

-- perception is a form of automatic resonation-- cognitive beings resonate to speech acts and

to linguistic records-- cognitive beings resonate deontically

affordances: positive and negative features of the

environment:

permissions and prohibitions

Roger Barker: Niche as Behavioral SettingNiches are recurrent settings which serve as the environments for our everyday activities:

my swimming pool,

your table in the cafeteria,

the 5pm train to Long Island.

Behavior Settings

Each behavior setting is associated with certain standing patterns of behavior.

Settings, for Barker,

are natural units in no way imposed by an investigator.

To laymen they are as objective as rivers and forests

— they are parts of the objective environment that are experienced as directly as rain and sandy beaches are experienced. (Barker 1968, p. 11)

SettingsEach setting has a boundary which separates an organized internal (foreground) pattern from a differing external (background) pattern.

ORGANIZATIONS ARE BUILDINGSORGANIZATIONS ARE NESTED SYSTEMS OF SETTINGS SETTINGS ARE LIKE THE INTERIORS OF BUILDINGS

The Ontology of Niches

Niches are in some ways like the interiors of substances

Two concepts of spaceship:John is in the spaceshipThe embryo is in the uterusThe yoghurt is in the refrigerator

Niches and quasi-nichesSubstances and quasi-substances

Two concepts of spaceship

John is in LondonJohn saw London from the air London London

IBM IBM

John admired her carJohn was sitting in her car

A is part of B vs. A is in the interior of B as a tenant is in its niche

The Ontology of Niches

Niches as endurants

Niches as four-dimensional spatiotemporally extended volumes

Marks of (bodily) substance

i. Rounded-offness

ii. Occupies space

iii. Complete boundary

iv. May have substantial parts (nesting)

v. May be included in larger substances

vi. Has a life (manifests contrary accidents at different times)

Corresponding Marks of Niches

(i) A niche enjoys a certain natural completeness or rounded-offness,

being neither too small nor too large

—in contrast to the arbitrary undetached parts of environmental settings and to arbitrary heaps or aggregates of environmental settings.

(ii) A niche takes up space,

it occupies a physical-temporal locale,

and is such as to have spatial parts.

Within this physical-temporal locale is a privileged locus—a hole—

into which the tenant or occupant of the setting fits exactly.

(iii) A niche

has an outer boundary:

there are objects which fall clearly within it,

and other objects which fall clearly outside it.

(The boundary itself need not be crisp.)

(iv) A niche

may have actual parts which are also environmental settings(hierarchical nesting)

(v) A niche

may be a proper part of larger, circumcluding niche.

(vi) A niche has a life

is now warm, now cold

now at peace, now at war ….

now expanding, now contracting

Marks of (bodily) substance

i. Rounded-offness

ii. Occupies space

iii. Complete boundary

iv. May have substantial parts (nesting)

v. May be included in larger substances

vi. Has a life; is now warm, now cold

Niche Construction

Lewontin: niches normally arise in symbiosis with the activities of organisms or groups of organisms;

they are not already there, like vacant rooms in a gigantic evolutionary hotel, awaiting organisms who would evolve into them.

“ecosystem engineering”

Applications of the niche concept

in biology, ecology

in medicine (embryology …)

in anthropology

in economics

in the ontology of artifacts

in law

in politics

Where are Niches?Concrete Entity

[Exists in Space and Time]Concrete Entity

[Exists in Space and Time]

Entity in 3-D Ontology[Endure. No Temporal Parts]

Entity in 4-D Ontology[Perdure. Unfold in Time]Entity in 4-D Ontology

[Perdure. Unfold in Time]

Processual EntityProcessual EntitySpatio-Temporal Region

Dim = T, T+0, T+1, T+2, T+3Spatio-Temporal Region

Dim = T, T+0, T+1, T+2, T+3

Spatial Regionof Dimension 0,1,2,3

Spatial Regionof Dimension 0,1,2,3 Dependent EntityDependent Entity

Independent EntityIndependent Entity

Quality (Your Redness, My Tallness)[Form Quality Regions/Scales]

Role, Function, PowerHave realizations (called: Processes)

Substance[maximally connected causal unity]

Boundary of Substance *Fiat or Bona Fide or MixedBoundary of Substance *

Fiat or Bona Fide or Mixed

Aggregate of Substances * (includes masses of stuff? liquids?)

Fiat Part of Substance * Nose, Ear, Mountain

Process [Has Unity]Clinical trial; exercise of role

Fiat Part of Process*Fiat Part of Process*

Aggregate of Processes*Aggregate of Processes*

Instantaneous Temporal Boundary of Process (= Ingarden’s 'Event’)*

Quasi-ProcessJohn’s Youth. John’s Life

Quasi-Quality Prices, Values, Obligations

Quasi-SubstanceChurch, College, Corporation

Quasi-Role/Function/PowerThe Functions of the PresidentQuasi-Role/Function/Power

The Functions of the President

Where are Places?Concrete Entity

[Exists in Space and Time]Concrete Entity

[Exists in Space and Time]

Entity in 3-D Ontology[Endure. No Temporal Parts]

Entity in 4-D Ontology[Perdure. Unfold in Time]Entity in 4-D Ontology

[Perdure. Unfold in Time]

Processual EntityProcessual EntitySpatio-Temporal Region

Dim = T, T+0, T+1, T+2, T+3Spatio-Temporal Region

Dim = T, T+0, T+1, T+2, T+3

Spatial Regionof Dimension

0,1,2,3

Spatial Regionof Dimension

0,1,2,3

Dependent EntityDependent Entity

Independent EntityIndependent Entity

Gibson’s theory of surface layout

Niches = systems of barriers, openings, pathways to which organisms are specifically attuned,

Include: temperature gradients, patterns of movement of air or water molecules, electro-chemical signals guiding the movements of micro-organisms

But also: traffic signs, instructions posted on notice boards or displayed on the computer screen

Nesting

Many settings occur in assemblies:

A unit in the middle range of a nesting structure is simultaneously both circumjacent and interjacent,

both whole and part,

both entity and environment.

Unity of Behaviour and Ecological Setting

A physical-behavioural unit is a unit: its parts are unified together, but not through any similarity or community of substance.

The Systematic Mutual Fittingness of Behaviour and

Ecological SettingThe behaviour and the physical objects … are intertwined in such a way as to form a pattern that is by no means random: there is a relation of harmonious fit between the standard patterns of behaviour occurring within the unit and the pattern of its physical components.

Compare the way in which the processes in the body are constrained by the hierarchical organization of body, organs, cells …

The Systematic Mutual Fittingness of Behaviour and

Ecological Setting(The seats in the lecture hall face the speaker. The speaker addresses his remarks out towards the audience. The boundary of the football field is, leaving aside certain predetermined exceptions, the boundary of the game. The beginning and end of the school music period mark the limits of the pattern of music behaviour.)

Non-transposability

This mutual fittingness of behaviour and physical environment extends to the fine, interior structure of behaviour in a way which will imply a radical nontransposability of standing patterns of behaviour from one environment to another.

The physical or historical or ceremonial conditions obtaining in particular settings are in addition as essential for some kinds of behaviour as are persons with the requisite authority, motives and skills.

Power and Authority

There are various forces which help to bring about and to sustain this mutual fittingness and thus to constitute the unity of the physical-behavioural unit through time. Forces which flow in the direction from setting to behaviour include physical constraints exercised by hedges, walls or corridors or by persons with sticks; they include social forces manifested in the authority of the teacher, in threats, promises, warnings;

The Unifying Effects of the Physical Environment

they include the physiological effects of climate, the need for food and water; and they include the effects of perceived physiognomic features of the environment

(open spaces seduce children, a businesslike atmosphere encourages businesslike behaviour).

Mutual Fittingness

can be reinforced by learning, and also by a process of selection of the persons involved, whether this be one of self-selection (of children who remain in Sunday school class in light of their ability to conform to the corresponding standing patterns of behaviour), or of externally imposed mental or physical entrance tests.

Behaviour shapes Setting

Influences which flow from behaviour to setting, include all those ways in which a succession of separate and uncoordinated actions can have unintended consequences in the form of new types of actions and new, modified types of settings in the future (as the passage of many feet causes pathways to form in the hillside).

Settings shape Persons

Each person has many strengths, many intelligences, many social maturities, many speeds, many degrees of liberality and conservativeness, and many moralities, depending in large part on the particular contexts of the persons behavior. For example, the same person who displays marked obtusiveness when confronted with a mechanical problem may show impressive skill and adroitness in dealing with social situations.

Aurel Kolnai

a human society

… comprehends the same individual over and over again in line with his various social affiliations …

Daily life

= passage through a succession of physical-behavioural units which are as much a part of the furniture of reality as are garden-variety continuants and occurrents (such as you and me). Physical-behavioural units have parts.And they have consequences:contracts signed, orders issued, judgments passed, medals awarded.

The bonds

established by Reinach’s protostructures of promise, claim and obligation …can normally arise only within miniature civil societies,within which special sorts of environmental conditions are satisfiedAustin: a promise is a sort of ritualHolds of commands in large-scale organizations too.

Theory of roles/functions/powers

of greater and lesser generality

How are roles/functions/powers within a hierarchical organization themselves nested together hierarchically?

Orders not issued in a vacuum:

systems of external memory:

records and representations

procedures for authentication

A niche may have actual parts which are also environmental settings(hierarchical nesting)

Theory of the organization of organizations:

the roles you take on as inhabitant of the niche called IBMthe roles you take on as inhabitant of the niche called US-Division 4B/661 of IBM (YOU ARE

THE BOSS)the roles you take on as inhabitant of the niche called your local office (YOU ISSUE

COMMANDS)

SPAN: Entities extended in time

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

spatio-temporal volumes

4-dimensional environments

Lobsters have evolved into environments marked by cyclical patterns of temperature change

Tudor EnglandThe Afghan winterThe window of opportunity for an invasion of Iraq

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

spatio-temporal volumes

standardizedpatterns of

behavior

147but also at the reality beyond

Logical Investigations¸1900/01

Aristotelian theory of universals and particulars

the theory of boundaries and fusion

Husserl outlines a new methodof constituent ontology

to study a domain ontologically

is to establish the parts of the domain

and the interrelations between them

especially the dependence relations

Ontological Dependence

a wife is dependent on a husband

a king is dependent on his subjects

a color is dependent on an extension

a charge is dependent on a conductor

a speech act is dependent on a speaker

Husserl’s theory of part, whole and dependence

applied by him to the ontological structure of language

invention of categorial grammar,

later formalized by Ajdukiewicz, Lambek …

Husserl’s theory of part, whole and dependence

applied by his student Adolf Reinach to the ontological structure of law

invention of speech act theory in Reinach’s A Priori Foundations of the Civil Law in 1913

Speech Acts

Examples: requesting, questioning, answering, ordering, imparting information, promising, commanding, baptising

‘acts of the mind’ which do not have in words and the like their accidental additional expression

Social acts = acts which “are performed in the very act of speaking”

Reinach’s theory of social acts

part of a complete ‘a priori ontology of social interaction’

a theory of actions, agents, ogligations,

Communication between agents

Luc’s MSc thesis and Reinach…

Agents are in the world, they have to achieve their goals in relation to a particular environment, and adapt to this environment

Agents are with other agents: they have to cooperate with each other = not merely to communicate but also form agreement (form miniature civil societies)

Communication

can be with human beings or agents inside computers

therefore the ontology of communication cannot itself be inside the computer

it has to be much, much bigger

Reinach:

Commanding

does not involve an experience which is expressed but which could have remained unexpressed,

…there is nothing about commanding which could rightly be taken as the pure announcing of an internal experience.

Reinach:

Commanding is rather an experience all its own, a doing of the subject to which in addition to its spontaneity, its intentionality and its other-directedness, the need to be grasped is also essential.

Some events depend on underlying states

An assertion depends upon an underying state of conviction/belief

A command depends upon an underlying relational state of authority

Some events give rise to states

Perception gives rise to conviction/belief as its successor state: John sees that Mary is swimming

Promising gives rise to claim and obligation as its successor states

The Structure of the Promise

promiser

promiseethe promise

relations of one-sideddependence

promiser

promisee

act of speaking

act of registering

content

three-sided mutualdependence

oblig-ation

promiser

promisee

act of speaking

act of registering

content

two-sided mutual dependence

promiser

promisee

act of speaking

act of registering

content F

oblig-ation

action: do F

tendency towards realization

promiser

promisee

act of speaking

act of registering

content F

oblig-ation

action: do F

The Background (Environment)

sincere intention

Modifications of Social Acts

Sham promisesLies as sham assertions (cf. a forged

signature); rhetorical questionsSocial acts performed in someone else’s

name (representation, delegation)Social acts with multiple addressesConditional social acts

Collective social acts

Singing in a choir

Conversation

Dancing

Arguing

Religious rituals

promiser

promisee

act of speaking

act of registering

content F

oblig-ation

action: do F

sincere intention

How modific-ations occur

promiser

promisee

act of speaking

act of registering

content F

oblig-ation

action: do F

sincere intention

promiser

promisee

act of speaking

act of registering

content F

oblig-ation

action: do F

sincere intention

promiser

promisee

act of speaking

act of registering

content F

oblig-ation

action: do F

sincere intention

Contrast E-commerce application ontologies

billdeliverest-custidentify-product-priceorderoffer-productpurchasepay

Humans, Machines, and the Structure of Knowledge

Harry M. CollinsSEHR, 4: 2 (1995)

Knowledge-down-a-wireImagine a 5-stone weakling having his brain loaded with the knowledge of a champion tennis player.

He goes to serve in his first match

-- Wham! –

his arm falls off.

He just doesn't have the bone structure or muscular development to serve that hard.

Types of knowledge/ability/skill

1. those that can be transferred simply by passing signals from one brain/computer to another.

2. those that can’t:

Sometimes it is the body (the hardware) which knows

and sometimes it is the world outside which knows

Types of knowledge/ability/skill

1. those that can be transferred simply by passing signals from one brain/computer to another.

2. those that can’t: -- here the "hardware" is important;abilities/skills contained (a) in the body(b) in the world

The Methodological Solipsist Approach to Information Processing

ToThe Ecological Approach to Information

Processing

Fodorian Psychology

To understand human cognition we should study the mind/brain in abstraction from its real-world environment

(as if it were a hermetically sealed Cartesian ego)

1 formal ontology and information systems barry smith

Documents

the gene ontology barry smith march 2004

1 pax terminologica barry smith institute for formal...

1 basic formal ontology barry smith march 2004

a formal foundation for ontology-alignment interaction...

1 vt. 2 medical ontology barry smith

formal ontology meets industry: best practices

1 barry smith department of philosophy (buffalo) institute...

function, role, and disposition in basic formal ontology...

1 quantum mechanics: no comfort for kantians barry smith...

basic formal ontology: a common standard

conceptual realism as formal ontology

1 vt. 2 barry smith department of philosophy (buffalo)...

formal ontology and conceptual realism

1 semantic network (sn) and biomedical ontology barry smith...

the environment ontology barry smith ontology.buffalo/smith

formal ontology in information systems

1 introduction to (geo)ontology barry smith

framework for formal ontology barry smith and kevin...

1 the ontology of experiments barry smith

1 formal ontology 2 schedule sep. 4: introduction:...