1 BFO and GOL Ontological theory vs. ontology language GOL as an ontology representation language...

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BFO and GOL

Ontological theory vs. ontology languageGOL as an ontology representation

language analogous to KIF (thus maximally eclectic)BFO as an ontological theory of reality

designed as a real constraint on domain ontologies

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A Network of Domain Ontologies

Material (Regional) Ontologies

Basic Formal Ontology

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BFO

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ChemO

BFO

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MedO

ChemO

BFO

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Nouns and verbs

Substances and processesContinuants and occurrents

In preparing an inventory of realitywe keep track of these two different categories of entities in two different ways

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Natural languageglues them together indiscriminately

substance

t i m

e

process

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Snapshot vs. Video

substance

t i m

e

process

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Substances

Mesoscopic reality is divided at its natural joints into substances: animals, bones, rocks, potatoes

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The Ontology of Substances

Substances form natural kinds (universals, species + genera)

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Not only substances exist in toto at any time at which they exist at

allthe same holds of qualities, and of roles, functions, powers,

dispositions – each of these has executions (processes)

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Processes

t i m e

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ProcessesProcesses merge into one anotherProcess kinds merge into one another

… few clean joints either between instances or between types

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Some clean jointsderive from the fact that processes are dependent on substances(my headache is cleanly demarcated from your headache)

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Some clean jointsin realms of artefactual processes:

weddingschess gamesdog showsontology tutorialssharp divisions imputed via clocks, calendars

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Clean jointsalso through language= fiat demarcations

Quinean gerrymandering ontologies are attractive for processesnot for substancesQuine: there are no substances

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Substances and processes

t i m

e

process

demand different sorts of inventories

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Substances demand 3-D partonomies

space

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Processes demand 4D-partonomies

t i m e

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Processes have temporal partsThe first 5 minutes of my headache is a temporal part of my headacheThe first game of the match is a temporal part of the whole match

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Substances do not have temporal parts

The first 5-minute phase of my existence is not a temporal part of me It is a temporal part of that complex process which is my life

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Qualities, Roles, Functions, Powers, Dispositions

Do not have temporal parts

They belong to the SNAP ontology

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How do we glue these two different sorts of entities together mereologically?How do we include them both in a single inventory of reality

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How do we fit these two entities together within a single system of representations?within a directly depicting language?

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You are a substanceYour life is a process

You are 3-dimensionalYour life is 4-dimensional

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Substances and processes form two distinct orders of being

Substances exist as a whole at every point in time at which they exist at allProcesses unfold through time, and are never present in full at any given instant during which they exist.

When do both exist to be inventoried together?

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1. Four-dimensionalism

All entities are spatio-temporally extended portions of an atemporal four-dimensional whole called reality

Problems:substances (e.g. people) do not existchange does not exist

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2. Presentism

Both substances and processes exist, but only what exists now exists at all.

Problem:‘Napoleon ruled before Clinton’

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Neither of these solutions is completely adequate

Hencea good formal ontology must somehow contain them both

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A good formal ontologymust divide into two sub-ontologies:1. a four-dimensionalist ontology (of

processes) SPANcf. Quine2. a modified presentist ontology cf. Brentano, Aristotle, Chisholm(takes tense seriously) SNAP

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These represent two viewsof the same rich and messy reality, the reality captured promiscuously by TEE

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The SPAN Ontology

t i m e

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boundaries are mostly fiat

t i m e

everything is flux

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mereology works without restriction everywhere here

t i m e

clinical trial

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here time exists as part of the domain of the ontology

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The SNAP Ontologies

t1

t3

t2

here time exists outside the ontology, as an index or time-stamp

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mereology works without restriction in every instantaneous 3-D section through

reality

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Three views/partitions of the same reality

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all contain huge amounts of knowledge of this reality

against Kant

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The Time-Stamped (3-D) Ontology

t1

t3

t2

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each section through reality is to be conceived in presentist terms

each section includes everything which existsat the corresponding now

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Not in a SubjectSubstantial

In a SubjectAccidental

Said of a SubjectUniversal, General,Type

Second Substances

man, horse, mammal

Non-substantial Universals

whiteness, knowledge

Not said of a Subject Particular, Individual,Token

First Substances

this individual man, this horse this mind, this body

Individual Accidents

this individual whiteness, knowledge of grammar

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Aristotle’s Ontological SquareSubstantial Accidental

Second substance man cat ox

Second accident headache sun-tan dread

First substance this man this cat this ox

First accident this headache this sun-tan this dread

Uni

vers

alP

artic

ular

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Uni

vers

alP

artic

ular

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Uni

vers

alP

artic

ular

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Uni

vers

alP

artic

ular

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Uni

vers

alP

artic

ular

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Refining the Ontological SquareSubstantial Accidental





Uni

vers

alP

artic

ular

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Refining the Ontological SquareSubstantial Dependent Entities

Exercise of power Exercise of functionMovementAction

SubstancesCollectivesUndetached partsSubstantial boundaries

PowersFunctionsQualitiesShapes

Occ

urre

nts

Con

tinua

nts

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Refining the Ontological SquareSubstantial Dependent

Exercise of power Exercise of functionMovementAction



Occ

urre

nts

Con

tinua

nts

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The big bang???? Exercise of power Exercise of functionMovementAction Processes



Occ

urre

nts

Con

tinua

nts

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John‘s reddeningJohn‘s blushingJohn‘s bruising

SPANSubstancesCollectivesUndetached partsSubstantial boundaries

John‘s rednessJohn‘s blushJohn‘s bruise

SNAP

Occ

urre

nts

Con

tinua

nts

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John‘s reddeningJohn‘s blushingJohn‘s bruising

SPAN (perduring)

Stuff(Blood, Snow, Tissue)MixturesHoles


SNAP (enduring)

Occ

urre

nts

Con

tinua

nts

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A Refined Ontological SquareSubstantial Dependent Entities

John‘s reddeningJohn‘s professorshipMy knowledge of French

SPAN (perduring)Stuff(Blood, Snow, Tissue)MixturesHoles


SNAP (enduring)

Occ

urre

nts

Con

tinua

nts

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Species-genusgenus trees can be represented also as map-like partitions

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From Species to Genera

canary

animal

bird

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From Species to Genera

animal

bird

canarycanary

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Species Genera as Tree

canary

animal

bird fish

ostrich

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Species-Genera as Map/Partition

animal

bird

canary

ostrich

fish

canary

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Tree and Map-Partitions Together

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‘Granularity’ in two senses:depth of a tree hierarchy

resolution of a map-like partition

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There are many different species-genus hierarchies

many different ways to cut through the complex thicket of invariant patterns in reality

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Recall the distinct temporal partitions of reality as a whole

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Coarse-grained Partition

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Fine-Grained Partition

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Basic Formal Ontology

??

?

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Ontological Zooming

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Universe/Periodic Tableanimal

bird

canaryostrich

fishfolk biology

partition of DNA space

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Universe/Periodic Tableanimal

bird

canaryostrich

fish

both are transparent partitions of one and the same reality

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France

RegionsDepartments

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Perspectivalism

Perspectivalism

Different partitions may represent cuts through the same reality which are skew to each other

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An organism is a totality of molecules

An organism is a totality of cells

An organism is a single unitary substance

... all of these express veridical partitions

An organism is a totality of atoms

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all express partitions which are transparent,

at different levels of granularity, to the same reality beyond

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Ontologylike cartographymust work with maps at different scales

and with maps picking out different dimensions of invariants

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If Aristotelian realism is rightthen there are very many map-like partitions, at different scales,which are all transparent

to the reality beyond

the mistake arises when one supposesthat only one of these partitions is veridical

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There are not only map-like partitions of reality into spatial chunks

but also distinct partitions of reality into universals

-- mutually compatible ways of providing inventories of universals(among proteins, among cells, among organisms …)

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Varieties of granular partitionsPartonomies: inventories of the parts of

individual entitiesMaps: partonomies of spaceTaxonomies: inventories of the

universals covering a given domain of reality

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Periodic TablePeriodic Table of Chemical Elements

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Many partitions are transparent to reality

TEE is a ragbag of skew partitions, some of them transparentOne job of the ontological realist is to understand how different partitions of the same reality interrelate-- notion of projection

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Contrast this with ‘knowledge representation’

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problem of ‘knowledge representation’

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problem of ‘knowledge representation’ solved

by looking at the world

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How solve the problem?Ontology as maximally opportunistictheory of reality(not of ‘knowledge’)-- address the same reality at

different granularities

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Maximally opportunisticmeans:don’t just look at beliefslook at the objects themselvesfrom every possible direction, formal and

informal, scientific and non-scientific…

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BFO/MedO:

Basic Formal Ontology and Medical Ontology

Draft 0.0005 (25.6.02)

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Basic Formal Ontologyconsists in a series of sub-ontologies (most properly conceived as a series of perspectives on reality), the most important of which are:

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Basic Formal OntologySnapBFO, a series of snapshot ontologies (Oti ), indexed by timesSpanBFO a single videoscopic ontology (Ov).

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SNAP and SPANEach Oti is an inventory of all entities existing at a time. Ov is an inventory (processory) of all processes unfolding through time. (Each Oti is thus analogous to anatomy; Ov is analogous to physiology.)

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SNAP and SPAN

Each snapshot ontology represents a presentistic assay of the entities existing at some given present instant. Ov is a (God’s eye) partition of the totality of processes.

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Both SnapBFO and SpanBFO will serve as basis for a series of sub-ontologies at different levels of granularity.

The same portion of reality may appear at a plurality of levels of granularity. Thus masses at one level may be aggregates at another level.

What counts as a unitary process at one level may be part of a process-continuum at another level.

Granularity

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BFO applied to Medicine

What follows is a preliminary taxonomic tree (inspired in part by LADSEB work)examples of medical entities are indicated in green as a first step towards expanding BFO to MedO

http://ontology.buffalo.edu/bfo/MedO.htm

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SNAP: Entities existing in toto at a time

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SNAP

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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

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Each ontology above represents some partition of reality into categories or universals. Individual instances (tokens) are to be conceived as being located in cells of the diagrams.

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The ontologies here indicated are partial only (they are windows on just that portion of reality which is visible through the given ontology).

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Double-Counting

A cell labeled * within a given ontology represents a category division which involves some double-counting in relation to the categories within the same ontology represented by cells not so labeled.

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For example here

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Spatial RegionsThe spatial regions acknowledged by SnapBFO are, on the mesoscopic level of granularity, the sorts of domesticated spatial regions referred to by expressions such as:‘in the room’, ‘in the lung’, ‘on the table’, ‘in Poland’ etc. (Thus they are not the abstract spatial regions investigated by physics.)

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Free and bound portions of space

Free portions of space are spatial regions of the same (domesticated) kind but with no physical boundaries or retainers (such as walls, floor, ceiling). Bound portions of space can be bound either completely, as in the case of a closed room or an air-bubble inside your body, or partially, as in the case of a birdcage or nostril.

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Free and bound portions of space

Both free and bound portions of space retain their identity from one instant to the next even though they are projected in succession onto distinct abstract spatial regions in the physicist’s sense (just as substances retain their identity from one instant to the next even though they are projected in succession on distinct aggregates of molecules).

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Behavior SettingsThe spatiotemporal regions acknowledged by SpanBFO are similarly regions determined by domesticated portions of space over (for example) clock or calendar time. They are the spatiotemporal regions occupied by behavior settings in Roger Barker’s sense (the 5pm train to Long Island, the early morning swim, your meeting with the Dean).

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Relational Dependent Entities

Dependent entities, both within the SNAP and within the SPAN ontologies, are divided into:relational (for entities dependent on a plurality of entities) and non-relational (for entities dependent on a single entity).

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ProblemsHow are entities visible in the SPAN ontology

related to entities visible in the SNAP ontologies (e.g. via dependence, participation, initiation, sustaining in being,etc.)

How are entities visible in ontologies at different levels of granularity related to each other (most importantly: as part to whole)

1 BFO and GOL Ontological theory vs. ontology language GOL as an ontology representation language...

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